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Review
. 2021 Oct 13;9(10):2143.
doi: 10.3390/microorganisms9102143.

Myxobacterial Genomics and Post-Genomics: A Review of Genome Biology, Genome Sequences and Related 'Omics Studies

David E Whitworth  1 , Natashia Sydney  1 , Emily J Radford  1
Affiliations
Review

Myxobacterial Genomics and Post-Genomics: A Review of Genome Biology, Genome Sequences and Related 'Omics Studies

David E Whitworth et al. Microorganisms. .

Abstract

Myxobacteria are fascinating and complex microbes. They prey upon other members of the soil microbiome by secreting antimicrobial proteins and metabolites, and will undergo multicellular development if starved. The genome sequence of the model myxobacterium Myxococcus xanthus DK1622 was published in 2006 and 15 years later, 163 myxobacterial genome sequences have now been made public. This explosion in genomic data has enabled comparative genomics analyses to be performed across the taxon, providing important insights into myxobacterial gene conservation and evolution. The availability of myxobacterial genome sequences has allowed system-wide functional genomic investigations into entire classes of genes. It has also enabled post-genomic technologies to be applied to myxobacteria, including transcriptome analyses (microarrays and RNA-seq), proteome studies (gel-based and gel-free), investigations into protein-DNA interactions (ChIP-seq) and metabolism. Here, we review myxobacterial genome sequencing, and summarise the insights into myxobacterial biology that have emerged as a result. We also outline the application of functional genomics and post-genomic approaches in myxobacterial research, highlighting important findings to emerge from seminal studies. The review also provides a comprehensive guide to the genomic datasets available in mid-2021 for myxobacteria (including 24 genomes that we have sequenced and which are described here for the first time).

Keywords: comparative genomics; functional genomics; genome evolution; genome organisation; pan-genome; proteomics; taxonomy; transcriptomics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
An exponential increase in myxobacterial genome sequencing. The numbers of genome sequences from cultured strains (black columns) and MAGs (grey columns) available at the end of each year are shown. The columns for 2021 only include genomes and MAGs published in the first six months of the year.
Figure 2
Figure 2
Phylogenetic tree showing the number of genome sequences and MAGs available for sequenced myxobacterial taxa. The tree was produced using 16S rRNA gene sequences from the type strain of each myxobacterial genus (Appendix A). Looking down the tree, families are alternately shaded grey and white. Numbers denote sequenced genomes/MAGs and are shown for each genus, family, order [in square brackets] and class (curved brackets). The Haliangiales and Nanncystales orders each comprise a single family (Haliangiaceae and Nannocystaceae, respectively), while the Myxococcia class contains a single class [Myxococcales]. Not all sequenced organisms/MAGs are taxonomically defined down to the genus, family or order levels (Supplementary Table S1).
Figure 3
Figure 3
Sources of samples from which myxobacterial 444 MAGs have been derived. The ten sources which have yielded the largest numbers of MAGs are indicated.
Figure 4
Figure 4
The relationship between genome size (Mbp) and %GC for myxobacterial genome sequences (black) and MAGs (grey).
Figure 5
Figure 5
The Corallococcus exiguus pan-genome. The number of core genes (left) and total number of genes (right) for the pan-genome are shown as a function of the number of genomes included (V1–V10). Boxes show the median number of genes ± 1 standard deviation, whiskers show ± 2 standard deviations.
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