ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Huerta-Cepas, Jaime; Serra, François; Bork, Peer

doi:10.1093/molbev/msw046

Cited by 1,832 publications

(1,497 citation statements)

References 29 publications

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“…They were constructed using the “sptree_raxml_all” workflow as implemented in ETE3 v3.0.0b36 (Huerta‐Cepas et al , 2016a). In brief, multiple sequence alignments were built for the 40 marker proteins using Clustal Omega v1.2.1 (Sievers et al , 2011), translated into codon alignments, concatenated, and used to infer a phylogeny by RAxML v8.1.20 (Stamatakis, 2014).…”

Section: Methodsmentioning

confidence: 99%

Subspecies in the global human gut microbiome

Costea

Coelho

Sunagawa

et al. 2017

Molecular Systems Biology

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Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large‐scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture‐independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single‐nucleotide variation clearly indicates the existence of sub‐populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies‐specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro‐inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.

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Section: Methodsmentioning

confidence: 99%

Subspecies in the global human gut microbiome

Costea

Coelho

Sunagawa

et al. 2017

Molecular Systems Biology

Self Cite

136

143

View full text Add to dashboard Cite

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“…Trees were rooted at the midpoint between the two most divergent genes. Gene duplication events shown in Figs 2b and 3a were inferred on the basis of species overlap between partitions 87 using a Python package 'ETE3' 88 . The trees were visualized using iTOL 89 .…”

Section: Go Enrichment Analysis Supplementarymentioning

confidence: 99%

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

et al. 2017

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Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.

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“…These gene structures were then extended by 120 nt upstream and 510 nt downstream, in order to include a similar length of non-coding sequence at each side (considering the AMD1 tail downstream of AMD1 main ORF stop). The phylogenetic tree of the investigated species was extracted from NCBI taxonomy 37 and standardized arbitrarily to a dichotomic tree with ETE 3 38 .…”

Section: Gene Finding and Evolutionary Analysismentioning

confidence: 99%