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|
||
data-ga-action="user_guide">
|
||
User Guide
|
||
</a>
|
||
</span>
|
||
|
||
</div>
|
||
</div>
|
||
|
||
|
||
</form>
|
||
|
||
|
||
<div id="article-page-header">
|
||
<div id="article-top-actions-bar" class="article-top-actions-bar">
|
||
<div class="inner-wrap">
|
||
<div class="actions-container">
|
||
<div class="return-to-search">
|
||
|
||
|
||
</div>
|
||
|
||
<div class="multiple-results-actions " role="region" aria-label="save, email, send to">
|
||
<button id="save-results-panel-trigger"
|
||
type="button"
|
||
class="save-results save-results-panel-trigger"
|
||
aria-expanded="false"
|
||
aria-controls="save-action-panel"
|
||
data-ga-category="save_share"
|
||
data-ga-action="save"
|
||
data-ga-label="open">
|
||
Save
|
||
</button><button id="email-results-panel-trigger"
|
||
type="button"
|
||
class="email-results email-results-panel-trigger"
|
||
aria-expanded="false"
|
||
aria-controls="email-action-panel"
|
||
data-ga-category="save_share"
|
||
data-ga-action="email"
|
||
data-ga-label="open">
|
||
Email
|
||
</button><div class="more-actions dropdown-block"><button id="more-actions-trigger"
|
||
type="button"
|
||
class="trigger more-actions-trigger"
|
||
ref="linksrc=show_moreactions_btn"
|
||
aria-label="Send to"
|
||
aria-controls="more-actions-dropdown">Send to</button><div id="more-actions-dropdown" class="dropdown dropdown-container" hidden><div class="content"><ul class="more-actions-links"><li><a class="clipboard-panel-trigger dropdown-block-link "
|
||
href="#"
|
||
role="button"
|
||
data-ga-category="save_share"
|
||
data-ga-action="clipboard"
|
||
data-ga-label="send">
|
||
Clipboard
|
||
</a></li><li><a role="button" class="dropdown-block-link bibliography-trigger-target" href="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39548374%2F%23open-bibliography-panel">My Bibliography</a></li><li><a role="button" class="dropdown-block-link collections-trigger-target" href="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39548374%2F%23open-collections-panel">Collections</a></li><li><a role="button" class="citation-manager-panel-trigger dropdown-block-link citation-manager-trigger-target" href="#">Citation manager</a></li></ul></div></div></div>
|
||
</div>
|
||
|
||
|
||
|
||
<div class="display-options" data-format-key="format"
|
||
data-default-format-value="abstract"
|
||
data-current-format-value="abstract" role="region">
|
||
<button
|
||
class="trigger usa-button"
|
||
title="Change format"
|
||
data-ga-category="display_options"
|
||
data-ga-action="display_options_dialog">
|
||
<span class="button-label">Display options</span>
|
||
</button>
|
||
|
||
<div class="dropdown" hidden>
|
||
<div class="title">
|
||
Display options
|
||
</div>
|
||
|
||
<div class="content">
|
||
|
||
<div class="format-container">
|
||
<span class="option-label">
|
||
Format
|
||
</span>
|
||
<select name="format" data-initial-value="abstract" aria-label="Display format" id="article-display-format">
|
||
<option value="abstract">Abstract</option>
|
||
|
||
<option value="pubmed">PubMed</option>
|
||
|
||
<option value="pmid">PMID</option>
|
||
|
||
</select>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S">
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div id="article-panels-container" class="article-panels-container">
|
||
<div id="save-action-panel" class="save-action-panel action-panel" aria-hidden="true">
|
||
<div class="inner-wrap">
|
||
<h2 class="action-panel-heading">
|
||
Save citation to file
|
||
</h2>
|
||
<form id="save-action-panel-form"
|
||
class="action-panel-content action-form"
|
||
action="/results-export-ids/"
|
||
data-by-search-action="/results-export-search-data/"
|
||
data-by-ids-action="/results-export-ids/"
|
||
method="post"
|
||
data-by-search-method="post"
|
||
data-by-ids-method="post">
|
||
|
||
<input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S">
|
||
|
||
|
||
|
||
<div class="action-panel-control-wrap">
|
||
<label for="save-action-format" class="action-panel-label">
|
||
Format:
|
||
</label>
|
||
<select id="save-action-format" name="results-format" class="action-panel-selector">
|
||
<option value="summary-text">Summary (text)</option>
|
||
<option value="pubmed-text">PubMed</option>
|
||
<option value="pmid">PMID</option>
|
||
<option value="abstract">Abstract (text)</option>
|
||
<option value="csv">CSV</option>
|
||
</select>
|
||
</div>
|
||
|
||
<div class="action-panel-actions">
|
||
<button class="action-panel-submit"
|
||
type="submit"
|
||
data-loading-label="Saving..."
|
||
data-ga-category="save_share"
|
||
data-ga-action="save"
|
||
data-ga-label="save">
|
||
Create file
|
||
</button>
|
||
<button class="action-panel-cancel"
|
||
aria-label="Close 'Save citations to file' panel"
|
||
ref="linksrc=close_save_panel"
|
||
aria-controls="save-action-panel"
|
||
aria-expanded="false"
|
||
data-ga-category="save_share"
|
||
data-ga-action="save"
|
||
data-ga-label="cancel">
|
||
Cancel
|
||
</button>
|
||
</div>
|
||
</form>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
<div id="email-action-panel"
|
||
class="email-action-panel action-panel"
|
||
aria-hidden="true"
|
||
data-recaptcha-script-url="https://www.recaptcha.net/recaptcha/enterprise.js?render=explicit&onload=onloadCaptchaCallback"
|
||
data-recaptcha-enabled="true">
|
||
<div class="inner-wrap">
|
||
<h2 class="action-panel-heading">
|
||
Email citation
|
||
</h2>
|
||
<form id="email-action-panel-form"
|
||
class="action-panel-content action-form"
|
||
action="/send-email/"
|
||
data-by-search-action="/results-export-email-by-search-data/"
|
||
data-by-ids-action="/send-email/"
|
||
data-by-search-method="post"
|
||
data-by-ids-method="post"
|
||
method="post"
|
||
>
|
||
<input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S">
|
||
|
||
<div class="action-panel-control-wrap">
|
||
<span class="action-panel-label">
|
||
Subject:
|
||
</span>
|
||
<span class="email-subject" id="email-subject" aria-label="Email subject">1 selected item: 39548374 - PubMed</span>
|
||
<input type="hidden" name="email-subject" value="1 selected item: 39548374"/>
|
||
<input type="hidden" name="email-subject-hash" value="75c72ecbe2fcbd4fc3f81a7bf70874aa2a09ed86246eca312efdbbff8e46b1a8"/>
|
||
</div>
|
||
|
||
<div class="action-panel-control-wrap">
|
||
<label for="email-to" class="action-panel-label required-field-asterisk">
|
||
To:
|
||
</label>
|
||
<input type="email" aria-label="Recipient Email Address" placeholder="email@example.com" id="email-to" class="email-to" pattern="^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$" maxlength="100" required>
|
||
</div>
|
||
|
||
<div class="action-panel-control-wrap">
|
||
<label for="email-from" class="action-panel-label">
|
||
From:
|
||
</label>
|
||
<input type="email" aria-label="Sender Email Address" placeholder="email@example.com" id="email-from" class="email-from" pattern="^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$" maxlength="256">
|
||
</div>
|
||
|
||
|
||
|
||
<div class="action-panel-control-wrap">
|
||
<label for="email-citation-format" class="action-panel-label">
|
||
Format:
|
||
</label>
|
||
<select id="email-citation-format" name="citation-format" class="action-panel-selector email-citation-format">
|
||
<option selected="selected" value="summary">Summary</option>
|
||
<option value="summary-text">Summary (text)</option>
|
||
<option value="abstract">Abstract</option>
|
||
<option value="abstract-text">Abstract (text)</option>
|
||
|
||
</select>
|
||
</div>
|
||
<div class="include-supplemental-container">
|
||
<input type="checkbox" aria-label="Include MeSH and other data" name="include-supplemental" id="email-include-supplemental" class="email-include-supplemental">
|
||
<label for="email-include-supplemental" class="email-include-supplemental-label">MeSH and other data</label>
|
||
</div>
|
||
|
||
|
||
|
||
<div class="form-field recaptcha ">
|
||
|
||
|
||
|
||
<div class="g-recaptcha" id="id-recaptcha" data-sitekey="6LfsWHMdAAAAAClKbtOpjQ2pMjgsGxvv7NdZW9uI"></div>
|
||
|
||
|
||
|
||
|
||
|
||
</div>
|
||
<div id="captcha-error-message" class="usa-input-error-message captcha-validation-message" role="alert"></div>
|
||
|
||
|
||
|
||
<div class="action-panel-actions">
|
||
<button class="action-panel-submit"
|
||
type="submit"
|
||
data-loading-label="Sending..."
|
||
data-ga-category="save_share"
|
||
data-ga-action="email"
|
||
data-ga-label="send">
|
||
Send email
|
||
</button>
|
||
<button class="action-panel-cancel"
|
||
aria-label="Close 'Email citations' panel"
|
||
ref="linksrc=close_email_panel"
|
||
aria-controls="email-action-panel"
|
||
aria-expanded="false"
|
||
data-ga-category="save_share"
|
||
data-ga-action="email"
|
||
data-ga-label="cancel">
|
||
Cancel
|
||
</button>
|
||
</div>
|
||
<input type="hidden" name="email-search-details" value="" />
|
||
<input type="hidden" name="email-search-details-hash" value="0e42663a6c3bd85498fcb88798998fed7bfdc45d457db35281e41afe13cc0524" />
|
||
</form>
|
||
</div>
|
||
</div>
|
||
|
||
<div id="collections-action-panel"
|
||
class="collections-action-panel action-panel in-progress-dots-panel"
|
||
aria-hidden="true"
|
||
data-collections-open-panel-enabled="false"
|
||
data-collections-open-panel-url-hash="#open-collections-panel">
|
||
<div class="inner-wrap">
|
||
<h3 class="action-panel-heading">
|
||
Add to Collections
|
||
</h3>
|
||
|
||
|
||
<form id="collections-action-panel-form"
|
||
class="collections-action-panel-form action-panel-content action-form action-panel-smaller-selectors"
|
||
data-existing-collections-url="/list-existing-collections/"
|
||
data-add-to-existing-collection-url="/add-to-existing-collection/"
|
||
data-create-and-add-to-new-collection-url="/create-and-add-to-new-collection/"
|
||
data-get-article-ids-by-search-url="/get-article-ids-by-search/"
|
||
data-myncbi-max-collection-name-length="100"
|
||
data-add-to-collection-max-amount="1000"
|
||
data-collections-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/">
|
||
|
||
<input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S">
|
||
|
||
|
||
|
||
<div class="choice-group" role="radiogroup">
|
||
<ul class="radio-group-items">
|
||
<li>
|
||
<input type="radio"
|
||
id="collections-action-panel-new"
|
||
class="collections-new"
|
||
name="collections"
|
||
value="new"
|
||
data-ga-category="save_share"
|
||
data-ga-action="collections"
|
||
data-ga-label="collections_radio_new">
|
||
<label for="collections-action-panel-new">Create a new collection</label>
|
||
</li>
|
||
<li>
|
||
<input type="radio"
|
||
id="collections-action-panel-existing"
|
||
class="collections-existing"
|
||
name="collections"
|
||
value="existing"
|
||
checked="true"
|
||
data-ga-category="save_share"
|
||
data-ga-action="collections"
|
||
data-ga-label="collections_radio_existing">
|
||
<label for="collections-action-panel-existing">Add to an existing collection</label>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
|
||
<div class="controls-wrapper">
|
||
<div class="action-panel-control-wrap new-collections-controls">
|
||
<label for="collections-action-panel-add-to-new" class="action-panel-label required-field-asterisk">
|
||
Name your collection:
|
||
</label>
|
||
<input
|
||
type="text"
|
||
name="add-to-new-collection"
|
||
id="collections-action-panel-add-to-new"
|
||
class="collections-action-add-to-new"
|
||
pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/"
|
||
maxlength="100"
|
||
data-ga-category="save_share"
|
||
data-ga-action="create_collection"
|
||
data-ga-label="non_favorties_collection">
|
||
<div class="collections-new-name-too-long usa-input-error-message selection-validation-message">
|
||
Name must be less than 100 characters
|
||
</div>
|
||
</div>
|
||
<div class="action-panel-control-wrap existing-collections-controls">
|
||
<label for="collections-action-panel-add-to-existing" class="action-panel-label">
|
||
Choose a collection:
|
||
</label>
|
||
<select id="collections-action-panel-add-to-existing"
|
||
class="action-panel-selector collections-action-add-to-existing"
|
||
data-ga-category="save_share"
|
||
data-ga-action="select_collection"
|
||
data-ga-label="($('#collections-action-add-to-existing').val() === 'Favorites') ? 'Favorites' : 'non_favorites_collection'">
|
||
</select>
|
||
<div class="collections-retry-load-on-error usa-input-error-message selection-validation-message">
|
||
Unable to load your collection due to an error<br>
|
||
<a href="#">Please try again</a>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="action-panel-actions">
|
||
<button class="action-panel-submit"
|
||
type="submit"
|
||
data-loading-label="Adding..."
|
||
data-pinger-ignore
|
||
data-ga-category="save_share"
|
||
data-ga-action="collections"
|
||
data-ga-label="add">
|
||
Add
|
||
</button>
|
||
<button class="action-panel-cancel"
|
||
aria-label="Close 'Add to Collections' panel"
|
||
ref="linksrc=close_collections_panel"
|
||
aria-controls="collections-action-panel"
|
||
aria-expanded="false"
|
||
data-ga-category="save_share"
|
||
data-ga-action="collections"
|
||
data-ga-label="cancel">
|
||
Cancel
|
||
</button>
|
||
</div>
|
||
</form>
|
||
</div>
|
||
</div>
|
||
|
||
<div id="bibliography-action-panel"
|
||
class="bibliography-action-panel action-panel in-progress-dots-panel"
|
||
aria-hidden="true"
|
||
data-bibliography-open-panel-enabled="false"
|
||
data-bibliography-open-panel-url-hash="#open-bibliography-panel">
|
||
<div class="inner-wrap">
|
||
<h3 class="action-panel-heading">
|
||
Add to My Bibliography
|
||
</h3>
|
||
<form id="bibliography-action-panel-form"
|
||
class="bibliography-action-panel-form action-panel-content action-form action-panel-smaller-selectors"
|
||
data-add-to-bibliography-max-amount="100"
|
||
data-add-to-bibliography-batch-size="10"
|
||
data-bibliography-delegates-url="/list-bibliography-delegates/"
|
||
data-add-to-bibliography-url="/add-to-bibliography/"
|
||
data-get-article-ids-by-search-url="/get-article-ids-by-search/"
|
||
data-mybib-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/mybibliography/">
|
||
|
||
<input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S">
|
||
|
||
|
||
|
||
<div class="action-panel-control-wrap bibliographies-controls">
|
||
<div class="choice-group">
|
||
<ul class="bibliographies-action-add radio-group-items">
|
||
<li>
|
||
<input name="bibliography" id="my-bibliography" class="my-bibliography" type="radio" checked/>
|
||
<label for="my-bibliography">My Bibliography</label>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="bibliographies-retry-load-on-error usa-input-error-message selection-validation-message">
|
||
Unable to load your delegates due to an error<br>
|
||
<a href="#">Please try again</a>
|
||
</div>
|
||
|
||
<div class="action-panel-actions">
|
||
<button class="action-panel-submit"
|
||
type="submit"
|
||
data-loading-label="Adding..."
|
||
data-pinger-ignore>
|
||
Add
|
||
</button>
|
||
<button class="action-panel-cancel"
|
||
aria-label="Close 'Add to bibliography' panel"
|
||
ref="linksrc=close_bibliography_panel"
|
||
aria-controls="bibliography-action-panel"
|
||
aria-expanded="false"
|
||
data-ga-category="save_share"
|
||
data-ga-action="mybib"
|
||
data-ga-label="cancel">
|
||
Cancel
|
||
</button>
|
||
</div>
|
||
</form>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
<div id="saved-search-action-panel" class="saved-search-action-panel action-panel " aria-hidden="true"
|
||
data-saved-search-open-panel-enabled="false"
|
||
data-saved-search-open-panel-url-hash="#open-saved-search-panel">
|
||
<div class="inner-wrap">
|
||
<h2 class="action-panel-heading">
|
||
Your saved search
|
||
</h2>
|
||
|
||
<form id="saved-search-action-panel-form"
|
||
class="saved-search-action-panel-form action-panel-content action-form"
|
||
data-create-saved-search-url="/create-saved-search/"
|
||
data-try-search-terms-url="/try-search-term/"
|
||
data-saved-search-root-url="https://www.ncbi.nlm.nih.gov/myncbi/searches/">
|
||
|
||
<input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S">
|
||
|
||
<div class="action-panel-control-wrap">
|
||
<label for="saved-search-name" class="action-panel-label saved-search-name-label required-field-asterisk">
|
||
Name of saved search:
|
||
</label>
|
||
<input maxlength="200"
|
||
type="text"
|
||
name="saved-search-name"
|
||
id="saved-search-name"
|
||
class="saved-search-name"
|
||
value=""
|
||
required
|
||
pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/">
|
||
</div>
|
||
|
||
<div class="action-panel-control-wrap">
|
||
<label for="saved-search-term" class="action-panel-label required-field-asterisk">
|
||
Search terms:
|
||
</label>
|
||
<textarea name="saved-search-term" id="saved-search-term" class="saved-search-term" required></textarea>
|
||
</div>
|
||
<div class="test-search-term-wrap">
|
||
<a href="#" class="try-search-term">Test search terms</a>
|
||
</div>
|
||
<div class="choice-group action-panel-extra-margin-top">
|
||
<span class="action-panel-label" id="fieldset-label">
|
||
Would you like email updates of new search results?
|
||
</span>
|
||
<fieldset id="saved-search-alert" aria-describedby="fieldset-label">
|
||
<legend class="usa-sr-only">Saved Search Alert Radio Buttons</legend>
|
||
<ul class="radio-group-items">
|
||
<li>
|
||
<input type="radio" id="saved-search-alert-yes" class="saved-search-alert-yes" name="saved-search-alert" value="yes" checked>
|
||
<label for="saved-search-alert-yes" class="action-panel-label">Yes</label>
|
||
</li>
|
||
<li>
|
||
<input aria-label="No radio input" type="radio" id="saved-search-alert-no" class="saved-search-alert-no" name="saved-search-alert" value="no">
|
||
<label for="saved-search-alert-no" class="action-panel-label">No</label>
|
||
</li>
|
||
</ul>
|
||
</fieldset>
|
||
</div>
|
||
|
||
<div class="alert-schedule-wrap">
|
||
<div class="action-panel-control-wrap">
|
||
<label class="action-panel-label">
|
||
Email:
|
||
</label>
|
||
<span aria-label="Email address" id="saved-search-email" class="action-panel-label"><span class="action-panel-label-bold"></span> (<a class="myncbi-account-settings" href="https://www.ncbi.nlm.nih.gov/account/settings/">change</a>)</span>
|
||
</div>
|
||
<div class="action-panel-control-wrap action-panel-extra-margin-top">
|
||
<label for="saved-search-frequency" class="action-panel-label">
|
||
Frequency:
|
||
</label>
|
||
<select id="saved-search-frequency" class="no-border-panel-selector saved-search-frequency">
|
||
<option value="monthly">Monthly</option>
|
||
<option value="weekly">Weekly</option>
|
||
<option value="daily">Daily</option>
|
||
</select>
|
||
</div>
|
||
<div class="action-panel-control-wrap saved-search-monthly-additional">
|
||
<label for="saved-search-monthly-on-day" class="action-panel-label">
|
||
Which day?
|
||
</label>
|
||
<select id="saved-search-monthly-on-day" class="no-border-panel-selector">
|
||
<option value="Sunday">The first Sunday</option>
|
||
<option value="Monday">The first Monday</option>
|
||
<option value="Tuesday">The first Tuesday</option>
|
||
<option value="Wednesday">The first Wednesday</option>
|
||
<option value="Thursday">The first Thursday</option>
|
||
<option value="Friday">The first Friday</option>
|
||
<option value="Saturday">The first Saturday</option>
|
||
<option value="day">The first day</option>
|
||
<option value="weekday">The first weekday</option>
|
||
</select>
|
||
</div>
|
||
<div class="action-panel-control-wrap saved-search-weekly-additional">
|
||
<label for="saved-search-weekly-on-day" class="action-panel-label">
|
||
Which day?
|
||
</label>
|
||
<select id="saved-search-weekly-on-day" class="no-border-panel-selector saved-search-weekly-on-day">
|
||
<option value="Sunday">Sunday</option>
|
||
<option value="Monday">Monday</option>
|
||
<option value="Tuesday">Tuesday</option>
|
||
<option value="Wednesday">Wednesday</option>
|
||
<option value="Thursday">Thursday</option>
|
||
<option value="Friday">Friday</option>
|
||
<option value="Saturday">Saturday</option>
|
||
</select>
|
||
</div>
|
||
<div class="action-panel-control-wrap">
|
||
<label for="saved-search-report" class="action-panel-label">
|
||
Report format:
|
||
</label>
|
||
<select id="saved-search-report" class="no-border-panel-selector saved-search-report">
|
||
<option value="DocSum">Summary</option>
|
||
<option value="DocSumText">Summary (text)</option>
|
||
<option value="Abstract">Abstract</option>
|
||
<option value="AbstractText">Abstract (text)</option>
|
||
<option value="MEDLINE">PubMed</option>
|
||
</select>
|
||
</div>
|
||
<div class="action-panel-control-wrap">
|
||
<label for="saved-search-amount" class="action-panel-label">
|
||
Send at most:
|
||
</label>
|
||
<select id="saved-search-amount" class="no-border-panel-selector saved-search-amount">
|
||
<option value="1">1 item</option>
|
||
<option value="5" selected>5 items</option>
|
||
<option value="10">10 items</option>
|
||
<option value="20">20 items</option>
|
||
<option value="50">50 items</option>
|
||
<option value="100">100 items</option>
|
||
<option value="200">200 items</option>
|
||
</select>
|
||
</div>
|
||
<div>
|
||
<input type="checkbox" id="saved-search-send-if-no-result" class="saved-search-send-if-no-result" name="saved-search-send-if-no-result">
|
||
<label for="saved-search-send-if-no-result" class="action-panel-label smaller-checkbox">
|
||
Send even when there aren't any new results
|
||
</label>
|
||
</div>
|
||
<div class="action-panel-control-wrap option-text-in-email-wrap">
|
||
<label for="saved-search-email-text" class="action-panel-label">
|
||
Optional text in email:
|
||
</label>
|
||
<textarea name="saved-search-email-text"
|
||
id="saved-search-email-text"
|
||
class="saved-search-email-text"></textarea>
|
||
</div>
|
||
|
||
</div>
|
||
|
||
<div class="action-panel-actions">
|
||
<button class="action-panel-submit"
|
||
type="submit"
|
||
data-loading-label="Saving..."
|
||
data-ga-category="save_share"
|
||
data-ga-action="alert"
|
||
data-ga-label="save">
|
||
Save
|
||
</button>
|
||
<button class="action-panel-cancel"
|
||
aria-label="Close 'Your saved search' panel"
|
||
ref="linksrc=close_saved_search_panel"
|
||
aria-controls="saved-search-action-panel"
|
||
aria-expanded="false"
|
||
data-ga-category="save_share"
|
||
data-ga-action="alert"
|
||
data-ga-label="cancel">
|
||
Cancel
|
||
</button>
|
||
</div>
|
||
</form>
|
||
</div>
|
||
</div>
|
||
|
||
<div id="citation-manager-action-panel" class="citation-manager-action-panel action-panel" aria-hidden="true">
|
||
<div class="inner-wrap">
|
||
<h2 class="action-panel-heading">
|
||
Create a file for external citation management software
|
||
</h2>
|
||
<form id="citation-manager-action-panel-form"
|
||
class="action-panel-content action-form"
|
||
action="/results-export-ids/"
|
||
data-by-search-action="/results-export-search-data/"
|
||
data-by-ids-action="/results-export-ids/"
|
||
method="post"
|
||
data-by-search-method="post"
|
||
data-by-ids-method="post">
|
||
|
||
<input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S">
|
||
|
||
|
||
|
||
<input name="results-format" type="hidden" value="pubmed"/>
|
||
|
||
<div class="action-panel-actions">
|
||
<button class="action-panel-submit"
|
||
type="submit"
|
||
data-loading-label="Sending..."
|
||
data-ga-category="save_share"
|
||
data-ga-action="citation_manager"
|
||
data-ga-label="save">
|
||
Create file
|
||
</button>
|
||
<button class="action-panel-cancel"
|
||
aria-label="Close 'Send citations to citation manager' panel"
|
||
ref="linksrc=close_citation_manager_panel"
|
||
aria-controls="citation-manager-action-panel"
|
||
aria-expanded="false"
|
||
data-ga-category="save_share"
|
||
data-ga-action="citation_manager"
|
||
data-ga-label="cancel">
|
||
Cancel
|
||
</button>
|
||
</div>
|
||
</form>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
<div id="rss-action-panel" class="rss-action-panel action-panel " aria-hidden="true">
|
||
<div class="inner-wrap">
|
||
<h2 class="action-panel-heading">
|
||
Your RSS Feed
|
||
</h2>
|
||
|
||
<form id="rss-action-panel-form"
|
||
class="rss-action-panel-form action-panel-content action-form"
|
||
data-create-rss-feed-url="/create-rss-feed-url/"
|
||
data-search-form-term-value="">
|
||
|
||
<input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S">
|
||
|
||
<div class="action-panel-control-wrap">
|
||
<label for="rss-name" class="action-panel-label required-field-asterisk">
|
||
Name of RSS Feed:
|
||
</label>
|
||
<input maxlength="200"
|
||
placeholder="Name"
|
||
type="text"
|
||
name="rss-name"
|
||
id="rss-name"
|
||
class="rss-name"
|
||
value=''
|
||
required
|
||
pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/">
|
||
</div>
|
||
|
||
<div class="rss-limit-wrap">
|
||
<div class="action-panel-control-wrap action-panel-extra-margin-top">
|
||
<label for="rss-limit" class="action-panel-label">
|
||
Number of items displayed:
|
||
</label>
|
||
<select id="rss-limit" class="no-border-panel-selector rss-limit">
|
||
<option value="5">5</option>
|
||
<option value="10">10</option>
|
||
<option value="15" selected="selected">15</option>
|
||
<option value="20">20</option>
|
||
<option value="50">50</option>
|
||
<option value="100">100</option>
|
||
</select>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="action-panel-actions">
|
||
<button class="action-panel-submit"
|
||
type="submit"
|
||
data-loading-label="Creating..."
|
||
data-ga-category="save_share"
|
||
data-ga-action="alert"
|
||
data-ga-label="save">
|
||
Create RSS
|
||
</button>
|
||
<button class="action-panel-cancel"
|
||
aria-label="Close 'Your RSS' panel"
|
||
ref="linksrc=close_rss_panel"
|
||
aria-controls="rss-action-panel"
|
||
aria-expanded="false"
|
||
data-ga-category="save_share"
|
||
data-ga-action="alert"
|
||
data-ga-label="cancel">
|
||
Cancel
|
||
</button>
|
||
</div>
|
||
|
||
<div class="action-panel-control-wrap rss-link-copy-wrap">
|
||
<label for="rss-link" class="usa-sr-only">RSS Link</label>
|
||
<input placeholder="Your RSS Feed Link" type="text" name="rss-link" id="rss-link" class="rss-link" title="RSS Link">
|
||
<button
|
||
type="button"
|
||
disabled
|
||
class="rss-link-copy-button disabled"
|
||
data-ga-category="save_share"
|
||
data-ga-action="rss"
|
||
data-ga-label="copy">
|
||
Copy
|
||
</button>
|
||
</div>
|
||
</form>
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
|
||
<div class="article-page" id="article-page" data-article-pmid="39548374">
|
||
<aside class="page-sidebar">
|
||
<div class="inner-wrap">
|
||
|
||
<div class="full-text-links">
|
||
<div class="full-view">
|
||
<h3 class="title">
|
||
Full text links
|
||
</h3>
|
||
<div class="full-text-links-list">
|
||
<a class="link-item
|
||
|
||
dialog-focus"
|
||
href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10858-2"
|
||
target="_blank"
|
||
rel="noopener"
|
||
|
||
ref="linksrc=fulltextorjournal_fulltext&is_pmc=False&PrId=3196&itool=Abstract-def&log$=linkouticon&uid=39548374&db=pubmed&nlmid=100965258"
|
||
title="See full text options at BioMed Central"
|
||
|
||
data-ga-category="full_text"
|
||
data-ga-action="BioMed Central"
|
||
data-ga-label="39548374"
|
||
><img src="https://cdn.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--s3-service-broker-live-ddda94b7-dbb0-4917-917d-776dae91ebba.s3.amazonaws.com-bmc-linkout-fulltext.png" alt="BioMed Central full text link"><span class="text">
|
||
|
||
BioMed Central
|
||
|
||
</span></a><a class="link-item
|
||
pmc
|
||
"
|
||
href="https://pmc.ncbi.nlm.nih.gov/articles/pmid/39548374/"
|
||
target="_blank"
|
||
rel="noopener"
|
||
|
||
ref="linksrc=fulltextorjournal_fulltext&is_pmc=True&PrId=3494&itool=Abstract-def&log$=linkouticon&uid=39548374&db=pubmed&nlmid=100965258"
|
||
title="Free full text at PubMed Central"
|
||
|
||
data-ga-category="full_text"
|
||
data-ga-action="PMC"
|
||
data-ga-label="39548374"
|
||
><span class="text">
|
||
|
||
Free PMC article
|
||
|
||
</span></a>
|
||
</div>
|
||
|
||
</div>
|
||
|
||
<div class="short-view">
|
||
<a href="#" class="full-text-links-button full-text-links-dialog-trigger">
|
||
Full text links
|
||
</a>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
<div class="actions-buttons sidebar"><h3 class="title">Actions</h3><div class="inner-wrap"><button class="citation-button citation-dialog-trigger"
|
||
aria-label="Open dialog with citation text in different styles"
|
||
data-ga-category="save_share"
|
||
data-ga-action="cite"
|
||
data-ga-label="open"
|
||
data-all-citations-url="/39548374/citations/"
|
||
data-citation-style="nlm"
|
||
data-pubmed-format-link="/39548374/export/"><span class="button-label">Cite</span></button><link type="text/css" href="ncbi-overlay-block/src/overlay-block.css"><div class="collections-button-container" data-article-id="39548374" data-article-db="pubmed"><button class="collections-button collections-dialog-trigger"
|
||
aria-label="Save article in MyNCBI collections."
|
||
data-ga-category="collections_button"
|
||
data-ga-action="click"
|
||
data-ga-label="collections_button"
|
||
data-collections-open-dialog-enabled="false"
|
||
data-collections-open-dialog-url="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39548374%2F%23open-collections-dialog"
|
||
data-in-collections="false"><span class="button-label">Collections</span></button><div class="overlay" role="dialog"><div id="collections-action-dialog"
|
||
class="dialog collections-dialog"
|
||
aria-hidden="true"><div class="title">Add to Collections</div><div class="collections-action-panel action-panel"><form id="collections-action-dialog-form"
|
||
class="collections-action-panel-form action-panel-content action-form action-panel-smaller-selectors"
|
||
data-existing-collections-url="/list-existing-collections/"
|
||
data-add-to-existing-collection-url="/add-to-existing-collection/"
|
||
data-create-and-add-to-new-collection-url="/create-and-add-to-new-collection/"
|
||
data-myncbi-max-collection-name-length="100"
|
||
data-collections-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/"><input type="hidden" name="csrfmiddlewaretoken" value="yaUKOAqv7cNrKNhZ0ir74j7XGDNMSlyKnIUXs0WNMesd5RV5RFR4ghC9d7S8Zz4S"><div class="choice-group" role="radiogroup"><ul class="radio-group-items"><li><input type="radio"
|
||
id="collections-action-dialog-new"
|
||
class="collections-new"
|
||
name="collections"
|
||
value="new"
|
||
data-ga-category="collections_button"
|
||
data-ga-action="click"
|
||
data-ga-label="collections_radio_new"><label for="collections-action-dialog-new">Create a new collection</label></li><li><input type="radio"
|
||
id="collections-action-dialog-existing"
|
||
class="collections-existing"
|
||
name="collections"
|
||
value="existing"
|
||
checked="true"
|
||
data-ga-category="collections_button"
|
||
data-ga-action="click"
|
||
data-ga-label="collections_radio_existing"><label for="collections-action-dialog-existing">Add to an existing collection</label></li></ul></div><div class="controls-wrapper"><div class="action-panel-control-wrap new-collections-controls"><label for="collections-action-dialog-add-to-new" class="action-panel-label required-field-asterisk">
|
||
Name your collection:
|
||
</label><input
|
||
type="text"
|
||
name="add-to-new-collection"
|
||
id="collections-action-dialog-add-to-new"
|
||
class="collections-action-add-to-new"
|
||
pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/"
|
||
maxlength="100"
|
||
data-ga-category="collections_button"
|
||
data-ga-action="create_collection"
|
||
data-ga-label="non_favorties_collection"><div class="collections-new-name-too-long usa-input-error-message selection-validation-message">
|
||
Name must be less than 100 characters
|
||
</div></div><div class="action-panel-control-wrap existing-collections-controls"><label for="collections-action-dialog-add-to-existing" class="action-panel-label">
|
||
Choose a collection:
|
||
</label><select id="collections-action-dialog-add-to-existing"
|
||
class="action-panel-selector collections-action-add-to-existing"
|
||
data-ga-category="collections_button"
|
||
data-ga-action="select_collection"
|
||
data-ga-label="($('.collections-action-add-to-existing').val() === 'Favorites') ? 'Favorites' : 'non_favorites_collection'"></select><div class="collections-retry-load-on-error usa-input-error-message selection-validation-message">
|
||
Unable to load your collection due to an error<br><a href="#">Please try again</a></div></div></div><div class="action-panel-actions"><button class="action-panel-submit"
|
||
type="submit"
|
||
data-loading-label="Adding..."
|
||
data-pinger-ignore
|
||
data-ga-category="collections_button"
|
||
data-ga-action="click"
|
||
data-ga-label="add">
|
||
Add
|
||
</button><button class="action-panel-cancel"
|
||
aria-label="Close 'Add to Collections' panel"
|
||
ref="linksrc=close_collections_panel"
|
||
aria-controls="collections-action-panel"
|
||
aria-expanded="false"
|
||
data-ga-category="collections_button"
|
||
data-ga-action="click"
|
||
data-ga-label="cancel">
|
||
Cancel
|
||
</button></div></form></div></div></div></div><button class="more-actions-button more-actions-dialog-trigger"
|
||
title="Open dialog with more actions to take"
|
||
ref="linksrc=more_actions_btn"></button><div class="display-options" data-format-key="format"
|
||
data-default-format-value="abstract"
|
||
data-current-format-value="abstract" role="region"><button
|
||
class="trigger usa-button"
|
||
title="Change format"
|
||
data-ga-category="display_options"
|
||
data-ga-action="display_options_dialog"><span class="button-label">Display options</span></button><div class="dropdown" hidden><div class="title">
|
||
Display options
|
||
</div><div class="content"><div class="format-container"><span class="option-label">
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Analyses of Xenorhabdus griffiniae genomes reveal two distinct sub-species that display intra-species variation due to prophages
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Analyses of Xenorhabdus griffiniae genomes reveal two distinct sub-species that display intra-species variation due to prophages
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<span class="authors-list-item "><span class="full-name">Jennifer K Heppert</span><span class="citation-separator"> et al.</span></span>
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Nematodes of the genus Steinernema and their Xenorhabdus bacterial symbionts are lethal entomopathogens that are useful in the biocontrol of insect pests, as sources of diverse natural products, and as research models for mutualism and parasitism. Xenorhabdus play a central role in all aspects of the Steinernema lifecycle, and a deeper understanding of their genomes therefore has the potential to spur advances in each of these applications.
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Here, we report a comparative genomics analysis of Xenorhabdus griffiniae, including the symbiont of Steinernema hermaphroditum nematodes, for which genetic and genomic tools are being developed. We sequenced and assembled circularized genomes for three Xenorhabdus strains: HGB2511, ID10 and TH1. We then determined their relationships to other Xenorhabdus and delineated their species via phylogenomic analyses, concluding that HGB2511 and ID10 are Xenorhabdus griffiniae while TH1 is a novel species. These additions to the existing X. griffiniae landscape further allowed for the identification of two subspecies within the clade. Consistent with other Xenorhabdus, the analysed X. griffiniae genomes each encode a wide array of antimicrobials and virulence-related proteins. Comparative genomic analyses, including the creation of a pangenome, revealed that a large amount of the intraspecies variation in X. griffiniae is contained within the mobilome and attributable to prophage loci. In addition, CRISPR arrays, secondary metabolite potential and toxin genes all varied among strains within the X. griffiniae species.
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Our findings suggest that phage-related genes drive the genomic diversity in closely related Xenorhabdus symbionts, and that these may underlie some of the traits most associated with the lifestyle and survival of entomopathogenic nematodes and their bacteria: virulence and competition. This study establishes a broad knowledge base for further exploration of not only the relationships between X. griffiniae species and their nematode hosts but also the molecular mechanisms that underlie their entomopathogenic lifestyle.
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<strong class="sub-title">
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Keywords:
|
||
</strong>
|
||
|
||
Xenorhabdus griffiniae; Bacterial subspeciation; CRISPR loci; Entomopathogenic bacteria; Insect toxins; Nematode-bacterium symbiosis; Pangenome; Prophage.
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<p class="copyright" id="copyright">
|
||
© 2024. The Author(s).
|
||
</p>
|
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|
||
|
||
<p class="disclaimer" id="disclaimer">
|
||
<a href="/disclaimer/" target="_blank" data-ga-category="literature_resources"
|
||
data-ga-action="disclaimer_link" data-ga-label="under_abstract">PubMed Disclaimer</a>
|
||
</p>
|
||
|
||
<div class="conflict-of-interest" id="conflict-of-interest">
|
||
<h2 class="title">
|
||
Conflict of interest statement
|
||
</h2>
|
||
|
||
<div class="statement">
|
||
|
||
|
||
|
||
<p xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:p1="http://pubmed.gov/pub-one"><bold>Declarations</bold> <bold>Ethics approval and consent to participate</bold> Not applicable. <bold>Consent for publication</bold> Not applicable. <bold>Competing interests</bold> The authors declare no competing interests.</p>
|
||
|
||
|
||
</div>
|
||
</div>
|
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|
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|
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|
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<div class="figures" id="figures">
|
||
<h2 class="title">
|
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Figures
|
||
</h2>
|
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|
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<div class="figures-list" id="slides-container"
|
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href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b306/11566119/126c28bc7f95/12864_2024_10858_Fig1_HTML.jpg"
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data-image-alt="Fig. 1"
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data-pmc-id="PMC11566119"
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<img class="figure-thumb" itemprop="thumbnail"
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id="article-image-0"
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src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b306/11566119/72620ca957ba/12864_2024_10858_Fig1_HTML.gif"
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alt="Fig. 1" />
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|
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|
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|
||
|
||
|
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<strong class="figure-label">
|
||
<p> Fig. 1 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Phylogenomic reconstruction of type strains… </p></div>
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||
</div>
|
||
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<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
|
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|
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|
||
|
||
<strong class="figure-label">
|
||
<p> Fig. 1 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Phylogenomic reconstruction of type strains of <i> Xenorhabdus </i> and other strains closely related to… </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
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|
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<figcaption id="figure-caption-0" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
|
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|
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|
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|
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|
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|
||
<strong class="figure-label">
|
||
Fig. 1
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents">Phylogenomic reconstruction of type strains of <i>Xenorhabdus</i> and other strains closely related to <i>Xenorhabdus griffiniae</i>. <b>A</b> This neighbour joining tree was reconstructed using genomic distances calculated with the same formula (Genome Distance BLAST Phylogeny distance formula <i>d5)</i> used for species delineation by digital DNA-DNA hybridisation (dDDH) analyses. Orange and aqua lines correlate with dDDH boundaries for species (> 70%) and subspecies (> 80%), respectively. Strains of <i>X. griffiniae</i> formed two subspecies, those from India-Indonesia (red) and those from Kenya (green). <b>B</b> Bayesian phylogenetic tree created using one-to-one orthologs from <i>Xenorhabdus</i> type strains, <i>X. griffiniae</i> strains, and <i>Photorhabdus asymbiotica</i> as an outgroup. Posterior probabilities are equal to 1 (100%) unless otherwise indicated at a given node. Strains of <i>X. griffiniae</i> formed two separate clades, those isolated from <i>S. hermaphroditum</i> nematodes found in Indonesia (ID10) and India (HGB2511) (red) and those isolated from nematodes found in Kenya (green)</div>
|
||
|
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|
||
|
||
|
||
</figcaption>
|
||
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|
||
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|
||
<a class="figure-link"
|
||
href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b306/11566119/4809a0b43299/12864_2024_10858_Fig2_HTML.jpg"
|
||
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||
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||
role="button"
|
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||
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|
||
data-image-alt="Fig. 2"
|
||
data-pmc-id="PMC11566119"
|
||
data-figure-id="Fig2">
|
||
<img class="figure-thumb" itemprop="thumbnail"
|
||
id="article-image-1"
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||
src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b306/11566119/f8bb682b74c2/12864_2024_10858_Fig2_HTML.gif"
|
||
alt="Fig. 2" />
|
||
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||
<div class="caption-wrap">
|
||
|
||
|
||
|
||
|
||
|
||
<strong class="figure-label">
|
||
<p> Fig. 2 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Graphical representations of a pangenome… </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
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<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<strong class="figure-label">
|
||
<p> Fig. 2 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Graphical representations of a pangenome of the <i> Xenorhabdus griffiniae </i> clade. <b> A </b> Sunburst chart… </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
||
|
||
<figcaption id="figure-caption-1" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<strong class="figure-label">
|
||
Fig. 2
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents">Graphical representations of a pangenome of the <i>Xenorhabdus griffiniae</i> clade. <b>A</b> Sunburst chart of a pangenome of seven close known relatives of the <i>X. griffiniae</i> type strain coupled to a heatmap of their average nucleotide identities (ANI). The pangenome contained 27,337 genes that were clustered into 5,113 groups of orthologs known as gene clusters (GC). The genomes from which each of the GCs was constituted are depicted in the sunburst chart as follows. Each concentric ring represents a genome and each radius represents a GC. For each radius, a dark shade across a concentric ring denotes that the GC is composed of genes from that genome. For the ANI heatmap, shades of red represent pairwise ANI values between 95% (blush) and 100% (rose), the threshold values for conspecific strains. <b>B</b> Loci encoding type six secretions systems (T6SS) found only in <i>X. griffiniae</i> genomes, of those analysed here. Each genome encoded two different T6SS, XG1-T6SS and XG2-T6SS. The core T6SS-encoding genes are indicated (<i>tssA-M</i>). Other genes are in grey. Pairwise percentage nucleotide identities for shown genomic loci that encode XG1-T6SS and XG2-T6SS ranged between 98–100% and 80–100%, respectively</div>
|
||
|
||
|
||
|
||
|
||
</figcaption>
|
||
|
||
|
||
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||
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|
||
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|
||
data-pmc-id="PMC11566119"
|
||
data-figure-id="Fig3">
|
||
<img class="figure-thumb" itemprop="thumbnail"
|
||
id="article-image-2"
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src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b306/11566119/b0b7d673f840/12864_2024_10858_Fig3_HTML.gif"
|
||
alt="Fig. 3" />
|
||
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||
|
||
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|
||
<div class="caption-wrap">
|
||
|
||
|
||
|
||
|
||
|
||
<strong class="figure-label">
|
||
<p> Fig. 3 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Loci of prophages and gene… </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
||
<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<strong class="figure-label">
|
||
<p> Fig. 3 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Loci of prophages and gene clusters encoding complete type six secretion systems (T6SS)… </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
||
|
||
<figcaption id="figure-caption-2" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<strong class="figure-label">
|
||
Fig. 3
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents">Loci of prophages and gene clusters encoding complete type six secretion systems (T6SS) and xenorhabdicin (<i>xnp1</i>) in complete genomes of four <i>Xenorhabdus griffiniae</i> strains. Genomes <i>of X. griffiniae</i> and XN45 and VH1 were not included in this analysis as they were not circularised, which often results in a prophage locus being split over multiple contigs</div>
|
||
|
||
|
||
|
||
|
||
</figcaption>
|
||
|
||
|
||
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|
||
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|
||
<a class="figure-link"
|
||
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|
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|
||
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|
||
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|
||
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|
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|
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|
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src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b306/11566119/f004c53e8808/12864_2024_10858_Fig4_HTML.gif"
|
||
alt="Fig. 4" />
|
||
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|
||
|
||
|
||
|
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|
||
<strong class="figure-label">
|
||
<p> Fig. 4 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Stacked bar charts depicting the… </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
||
<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<strong class="figure-label">
|
||
<p> Fig. 4 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Stacked bar charts depicting the Clusters of Orthologs Groups of proteins (COGs) of… </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
||
|
||
<figcaption id="figure-caption-3" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
|
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|
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|
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|
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|
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<strong class="figure-label">
|
||
Fig. 4
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents">Stacked bar charts depicting the Clusters of Orthologs Groups of proteins (COGs) of the core and unique genes among four closely related <i>Xenorhabdus</i> strains. The core pangenome bar shows the COGs of genes that are common to all genomes in the pangenome. The subsequent bars show the COGs of the unique genes from the HGB2511, ID10, Kalro, and TH1 genomes derived from the previously described pangenome analysis of <i>X. griffiniae</i> strains and <i>Xenorhabdus</i> sp. TH1 (Fig. 2A). The circularised Kalro genome was used to represent the XN45, VH1 and Xg97 genomes as these four genomes are highly similar (> 99.83% pairwise ANI values). The numbers on top of each bar are the total number of genes in each category, followed by the percentage of those genes without COG designation in parentheses</div>
|
||
|
||
|
||
|
||
|
||
</figcaption>
|
||
|
||
|
||
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|
||
|
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|
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|
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|
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|
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|
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|
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|
||
|
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|
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|
||
<strong class="figure-label">
|
||
<p> Fig. 5 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Neighbour-joining phylogenomic tree depicting the… </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
||
<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
|
||
|
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|
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|
||
|
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|
||
|
||
<strong class="figure-label">
|
||
<p> Fig. 5 </p>
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Neighbour-joining phylogenomic tree depicting the evolution of gene content among strains of <i> Xenorhabdus… </i> </p></div>
|
||
|
||
|
||
|
||
|
||
</div>
|
||
|
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<figcaption id="figure-caption-4" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
|
||
|
||
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|
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|
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|
||
<strong class="figure-label">
|
||
Fig. 5
|
||
</strong>
|
||
|
||
|
||
|
||
<div class="figure-caption-contents">Neighbour-joining phylogenomic tree depicting the evolution of gene content among strains of <i>Xenorhabdus griffiniae</i>. Three species are depicted in this tree, <i>Xenorhabdus</i> sp. BG5, <i>Xenorhabdus</i> sp. TH1 and <i>X. griffiniae</i>. For <i>X. griffiniae,</i> its India-Indonesia and Kenya subspecies are in red and green, respectively. The emergence of both subspecies was likely associated with net gene gains. Gene content analysis was conducted in COUNT applying Wagner parsimony</div>
|
||
|
||
|
||
|
||
|
||
</figcaption>
|
||
|
||
|
||
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<p> Fig. 6 </p>
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<div class="figure-caption-contents"><p> Genomic loci encoding phage tail-like… </p></div>
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<p> Fig. 6 </p>
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<div class="figure-caption-contents"><p> Genomic loci encoding phage tail-like particles from <i> Xenorhabdus griffiniae. </i> <b> A </b> The xenorhabdicin-encoding genomic… </p></div>
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Fig. 6
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<div class="figure-caption-contents">Genomic loci encoding phage tail-like particles from <i>Xenorhabdus griffiniae.</i>
|
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<b>A</b> The xenorhabdicin-encoding genomic loci (<i>xnp1</i>) in six strains of <i>X. griffiniae</i> and <i>Xenorhabdus</i> sp. TH1 and a cartoon of the corresponding xenorhabdicin particle. <b>B</b> Genomic loci (<i>pvc</i>) encoding an extracellular contractile injection system, the <i>Photorhabdus</i> Virulence Cassette (PVC) in <i>P. asymbiotica</i> ATCC43949, <i>X. griffiniae</i> ID10 and HGB2511. The genome coordinates of the loci are shown for the circularised genome assemblies. For XN45 and VH1, the shown coordinates are for contigs JACWFC010000129 and JADEUF010000065, respectively</div>
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<p> Fig. 7 </p>
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<div class="figure-caption-contents"><p> Graphical representation of predicted products… </p></div>
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<p> Fig. 7 </p>
|
||
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|
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<div class="figure-caption-contents"><p> Graphical representation of predicted products of genes contained within prophage loci of <i> Xenorhabdus… </i> </p></div>
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Fig. 7
|
||
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|
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|
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|
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|
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<div class="figure-caption-contents">Graphical representation of predicted products of genes contained within prophage loci of <i>Xenorhabdus griffiniae</i> ID10. The genes could be categorized into three broad categories; annotated cargo genes, viral replication genes and those whose products are unknown</div>
|
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<p> Fig. 8 </p>
|
||
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|
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|
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|
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|
||
<div class="figure-caption-contents"><p> CRISPR-Cas regions of <i> Xenorhabdus </i> strains.… </p></div>
|
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<p> Fig. 8 </p>
|
||
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|
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|
||
|
||
|
||
<div class="figure-caption-contents"><p> CRISPR-Cas regions of <i> Xenorhabdus </i> strains. <b> A </b> - <b> C </b> Comparison of three CRISPR-Cas related… </p></div>
|
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Fig. 8
|
||
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|
||
|
||
|
||
|
||
<div class="figure-caption-contents">CRISPR-Cas regions of <i>Xenorhabdus</i> strains. <b>A</b>-<b>C</b> Comparison of three CRISPR-Cas related genomic regions in selected strains, anchored for synteny in the diagram using <i>gntR</i> (<b>A</b>), <i>eda</i> (<b>B</b>), or <i>nhaB</i> (<b>C</b>). ORFs are indicated by solid block arrows (blue for <i>cas</i> genes, with the locus tag number of <i>cas3</i> provided) with annotated gene names indicated above, and identical colours indicating homology. CRISPR repeat arrays (red vertical stripe block arrows) for each region (1a, 1b, 2) had variable number of repeats (noted in parentheses). Start coordinates for each are shown underneath. Degenerate repeat arrays are indicated by brackets. A conserved sequence [1aii; vertical red line] containing a repeat, a spacer, and a degenerate repeat) was identified at the end of <i>cas2,</i> in all strains except BMMCB, which lacks this gene (<b>A</b>). Another [1bi] was apparent at the end of <i>cas3</i> in the <i>eda</i> locus of HGB2511, ID10, and TH1 (<b>B</b>)<i>.</i>
|
||
<b>D</b>-<b>F</b> The spacer sequences of each CRISPR array found at <i>gntR</i> (<b>D</b>), <i>eda</i> (<b>E</b>), or <i>nhaB</i> (<b>F</b>) were compared for identity to each other or other loci among the analysed strains. Each box represents a spacer, and different colours indicate different sequences. Spacers represented by black boxes and white lettering have 100% identity to “target” loci outside of the array, either within the same genome or within one of the other genomes analysed here. <i>gntR:</i> DNA-binding transcriptional repressor; <i>bleo/gloA</i>: bleomycin resistance/glyoxalase; <i>tn</i>: transposase; <i>lpp:</i> lipoprotein; <i>mem</i>: membrane protein: DUF4056: domain of unknown function 4056 gene; <i>eda:</i> 4-hydroxy-2-oxoglutarate aldolase; <i>nhaB</i>: Na( +):H( +) antiporter NhaB; <i>dsbB:</i> protein thiolquinone oxidoreductase; <i>cdiA</i>: Deoxyribonuclease CdiA; <i>palA/fhbA</i>: filamentous hemagglutinin; <i>luxR</i>: LuxR family transcriptional regulator; <i>cro/CI</i>: HTH cro/C1-type domain-containing protein; <i>symE</i>: Type I addiction module toxin, SymE family; <i>potA</i>: spermidine preferential ABC transporter ATP binding subunit; <i>araC:</i> AraC family transcriptional regulator; <i>fyuA:</i> Putative TonB-dependent siderophore receptor; <i>mfs</i>: putative MFS transporter, signal transducer; <i>cbbBC</i>: Molybdopterin-binding oxidoreductase; <i>res</i>: Type III restriction endonuclease subunit R; <i>mod</i>: site-specific DNA-methyltransferase (adenine-specific). The circularised Kalro genome was used to represent the XN45, VH1 and Xg97 genomes as these four genomes are highly similar (> 99.83% pairwise ANI values)</div>
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|
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<p> Fig. 9 </p>
|
||
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|
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|
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||
|
||
<div class="figure-caption-contents"><p> Genomic loci of known biosynthetic… </p></div>
|
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<p> Fig. 9 </p>
|
||
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|
||
|
||
|
||
|
||
<div class="figure-caption-contents"><p> Genomic loci of known biosynthetic gene clusters in the <i> X. griffiniae </i> ID10 genome… </p></div>
|
||
|
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|
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|
||
Fig. 9
|
||
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|
||
|
||
|
||
|
||
<div class="figure-caption-contents">Genomic loci of known biosynthetic gene clusters in the <i>X. griffiniae</i> ID10 genome and predicted chemical structures of the natural products whose biosynthesis they encode. The <i>paxABC</i>, <i>darABCDE</i> and <i>xabABCD</i> BGCs were predicted to encode the production of potentially novel derivatives of PAX peptides (8), darobactin (5) and xenoamicin (4), respectively, that differed from known structures in amino acid building blocks at positions highlighted in red. Safracin (1), gameXpeptide C (2), benzobactin (3), photoxenobactin (6), type 2 bovienimide (7), rhabduscin (9), 3-isopropyl-4-oxo-2-oxetanecarboxylic acid (10), arylpolyene (11)</div>
|
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<p> Fig. 10 </p>
|
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<div class="figure-caption-contents"><p> Comparative entomopathogenicity of <i> Xenorhabdus </i> bacteria… </p></div>
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<p> Fig. 10 </p>
|
||
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|
||
<div class="figure-caption-contents"><p> Comparative entomopathogenicity of <i> Xenorhabdus </i> bacteria to <i> Manduca sexta </i> larvae. Lines represent survival curves… </p></div>
|
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Fig. 10
|
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|
||
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||
<div class="figure-caption-contents">Comparative entomopathogenicity of <i>Xenorhabdus</i> bacteria to <i>Manduca sexta</i> larvae. Lines represent survival curves for <i>n</i>=10 insect larvae injected with approximately 1000 cells of each strain. Values have been corrected with Abbott's formula within the table below</div>
|
||
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Bhat AH, Chaubey AK, Askary TH. Global distribution of entomopathogenic nematodes, Steinernema and Heterorhabditis. Egyptian J Biol Pest Control. 2020;30:31.
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Edmunds C, Wilding CS, Rae R. Pathogenicity and environmental tolerance of commercial and UK native entomopathogenic nematodes (Steinernema and Heterorhabditis spp.) to the larvae of mosquitoes (Aedes aegypti and Ochlerotatus detritus). Int J Pest Management. 2021;67:232–40.
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Kovtun A. New locality records for Steinernema and Heterorhabditis (Nematoda: Rhabditida: Steinernematidae, Heterorhabditidae) fauna of Ukraine. Quarantine Plant Protect. 2023;2:39–45.
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Ali M, Allouf N, Ahmad M. First report of entomopathogenic nematode Steinernema affine (Nematoda: Steinernematidae) in Syria and its virulence against Galleria mellonella L. (Lepidoptera: Pyralidae). Egyptian J Biol Pest Control. 2022;32:101.
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