Metagenomics-Based Phylogeny and Phylogenomic

Phylogenetic relationships among microbial taxa in natural environments provide key insights into the mechanisms that shape community structure and functions. In this chapter, we address the current methodologies to carry out community structure profiling, using single-copy markers and the small subunit of the rRNA gene to measure phylogenetic diversity from next-generation sequencing data. Furthermore, the huge amount of data from metagenomics studies across the world has allowed us to assemble thousands of draft genomes, making necessary the comparison of whole genomes composites through phylogenomic approximations. Several computational tools are available to carry out these analyses with considerable success; we present a compendium of those open source tools, easy to use and with modest hardware requirements, with the aim that they can be applied by biologists non-specialists to study microbial diversity in a phylogenetic context

Principal Components Analysis (PCA) performed on the representatives of the <i>Herpotrichiellaceae</i> family with genome metrics as factors.

Mash genomic distance, ANI, AAI, POCP. Analysis based on Correlations. Variances were computed as SS/N-1. Missing Data deletion: Casewise. No. of active Factors: 4; No. of active cases: 93. Eigenvalues: 2.84348 .830461 .314132. 011930. NSP: Non-Separable Data. (PDF)</p

<i>Exophiala chapopotensis</i> sp. nov (LBMH1013, Holotype).

A colony in MM with benzo [a] pyrene (100 ppm) after 1 week. B, C colonies on PDA after 1 week. D conidiogenous cell and septate hyphae, E multinucleated conidia, F aseptate conidia and budding cells. Scale bar: A-C 1 cm; D, E 10 μm. The background image corresponds to the Holotype isolation site, the installation of the flare stack for local oil duct, Cuanduacán, Tabasco, México is observed. The specimen was isolated from soil.</p

Genome assembly statistics of the strain LBMH1013.

Genome assembly statistics of the strain LBMH1013.</p

Species and GenBank accession numbers of sequences used for multiple gene phylogenetic analysis in this study.^T represents ex-type cultures.

Species and GenBank accession numbers of sequences used for multiple gene phylogenetic analysis in this study.T represents ex-type cultures.</p

Maximum-likelihood tree from concatenated sequences (SSU, ITS, LSU and B-TUB).

Branch supports are represented in nodes (periwinkle circles) as SH-like approximate likelihood ratio test (SH-aLRT) (%). Bar (0.1) represents number of changes per site. The tree was edited in iTOL online Version 6.7.6. bPTP and GMYC speciation partition supports for E. chapopotensis are depicted in violet on the corresponding branch. The indigo background corresponds to Capronia representatives. Cyphellophora oxyspora was used as the outgroup.</p

Kmers frequency match between <i>Exophiala chapopotensis</i> LBMH1013 and its closest phylogenetic neighbours.

Kmers frequency match between Exophiala chapopotensis LBMH1013 and its closest phylogenetic neighbours.</p

Growth, carbon utilization and micromorphology of <i>E</i>. <i>chapopotensis</i> LBMH1013 under several conditions^b'*'.

Growth, carbon utilization and micromorphology of E. chapopotensis LBMH1013 under several conditionsb'*'.</p

Overall genome relatedness indices of the strain LBMH1013 against 92 representatives of the family <i>Herpotrichiellaceae</i>.

Overall genome relatedness indices of the strain LBMH1013 against 92 representatives of the family Herpotrichiellaceae.</p