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

Metarhizium anisopliae Pathogenesis of Mosquito Larvae: A Verdict of Accidental Death

Metarhizium anisopliae, a fungal pathogen of terrestrial arthropods, kills the aquatic larvae of Aedes aegypti, the vector of dengue and yellow fever. The fungus kills without adhering to the host cuticle. Ingested conidia also fail to germinate and are expelled in fecal pellets. This study investigates the mechanism by which this fungus adapted to terrestrial hosts kills aquatic mosquito larvae. Genes associated with the M. anisopliae early pathogenic response (proteinases Pr1 and Pr2, and adhesins, Mad1 and Mad2) are upregulated in the presence of larvae, but the established infection process observed in terrestrial hosts does not progress and insecticidal destruxins were not detected. Protease inhibitors reduce larval mortality indicating the importance of proteases in the host interaction. The Ae. aegypti immune response to M. anisopliae appears limited, whilst the oxidative stress response gene encoding for thiol peroxidase is upregulated. Cecropin and Hsp70 genes are downregulated as larval death occurs, and insect mortality appears to be linked to autolysis through caspase activity regulated by Hsp70 and inhibited, in infected larvae, by protease inhibitors. Evidence is presented that a traditional host-pathogen response does not occur as the species have not evolved to interact. M. anisopliae retains pre-formed pathogenic determinants which mediate host mortality, but unlike true aquatic fungal pathogens, does not recognise and colonise the larval host

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

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

Growth of strain LBMH1013 in different carbon sources (colonies at 10 and 20 days of growth are shown) and at different pH (48 and 36 hours).

Growth of strain LBMH1013 in different carbon sources (colonies at 10 and 20 days of growth are shown) and at different pH (48 and 36 hours).</p