ProtTest 3: fast selection of best-fit models of protein evolution

Darriba, Diego; Taboada, Guillermo L.; Doallo, Ramón; Posada, David

doi:10.1093/bioinformatics/btr088

Cited by 2,409 publications

(1,899 citation statements)

References 8 publications

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“…ProtTest version 3.4 (Darriba, Taboada, Doallo, & Posada, 2011) was used to choose the model MtArt + G + F for the amino acid dataset. As MtArt could not be implemented in the amino acid Bayesian analysis, we used the best scoring alternative MtRev + I + G + F model.…”

Section: Methodsmentioning

confidence: 99%

The first complete mitogenome of the South China deep‐sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods

Shen

Kou

Zhong

et al. 2017

Ecology and Evolution

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In this study, the complete mitochondrial (mt) genome sequence of the South China deep‐sea giant isopod Bathynomus sp. was determined, and this study is the first to explore in detail the mt genome of a deep‐sea member of the order Isopoda. This species belongs to the genus Bathynomus, the members of which are saprophagous residents of the deep‐sea benthic environment; based on their large size, Bathynomus is included in the “supergiant group” of isopods. The mt genome of Bathynomus sp. is 14,965 bp in length and consists of 13 protein‐coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362 bp in length, which is the smallest control region discovered in Isopoda to date. Although the overall genome organization is typical for metazoans, the mt genome of Bathynomus sp. shows a number of derived characters, such as an inversion of 10 genes when compared to the pancrustacean ground pattern. Rearrangements in some genes (e.g., cob, trnT, nad5, and trnF) are shared by nearly all isopod mt genomes analyzed thus far, and when compared to the putative isopod ground pattern, five rearrangements were found in Bathynomus sp. Two tRNAs exhibit modified secondary structures: The TΨC arm is absent from trnQ, and trnC lacks the DHU. Within the class Malacostraca, trnC arm loss is only found in other isopods. Phylogenetic analysis revealed that Bathynomus sp. (Cymothoida) and Sphaeroma serratum (Sphaeromatidea) form a single clade, although it is unclear whether Cymothoida is monophyletic or paraphyletic. Moreover, the evolutionary rate of Bathynomus sp. (dN/dS [nonsynonymous mutational rate/synonymous mutational rate] = 0.0705) is the slowest measured to date among Cymothoida, which may be associated with its relatively constant deep‐sea environment. Overall, our results may provide useful information for understanding the evolution of deep‐sea Isopoda species.

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Section: Methodsmentioning

confidence: 99%

The first complete mitogenome of the South China deep‐sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods

Shen

Kou

Zhong

et al. 2017

Ecology and Evolution

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show abstract

“…Neighbor‐joining analysis with 1,000 bootstrap replicates was performed in Mega7.0 under default setting. For maximum‐likelihood analysis, the package jModeltest 2.1.7 (Darriba, Taboada, Doallo, & Posada, 2012) and prottest 3.4 (Darriba, Taboada, Doallo, & Posada, 2011) were used to select the best‐fit model GTR + I + G and LG + I + G + F for nucleotide dataset and amino acid dataset, respectively. Maximum‐likelihood analyses were performed in Mega7.0 (Kumar, Stecher, & Tamura, 2016) with 1,000 replicates.…”

Section: Methodsmentioning

confidence: 99%

Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats

Liu

Cai

et al. 2018

Ecology and Evolution

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Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide‐rich deep‐sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group, and help to clarify generic classifications. In this study, we analyze the features and evolutionary dynamics of mt genomes from three Archivesica species (Archivesica sp., Ar. gigas and Ar. pacifica) pertaining to subfamily Pliocardinae. Sequence coverage is nearly complete for the three newly sequenced mt genomes, with only the control region and some tRNA genes missing. Gene content, base composition, and codon usage are highly conserved in these pliocardiin species. Comparative analysis revealed the vesicomyid have a relatively lower ratio of Ka/Ks, and all 13 protein‐coding genes (PGCs) are under strong purifying selection with a ratio of Ka/Ks far lower than one. Minimal changes in gene arrangement among vesicomyid species are due to the translocation trnaG in Isorropodon fossajaponicum. Additional tRNA genes were detected between trnaG and nad2 in Abyssogena mariana (trnaL3), Ab. phaseoliformis (trnaS3), and Phreagena okutanii (trnaM2), and display high similarity to other pliocardiin sequences at the same location. Single base insertion in multiple sites of this location could result in new tRNA genes, suggesting a possible tRNA arising from nongeneic sequence. Phylogenetic analysis based on 12 PCGs (excluding atp8) supports the monophyly of Pliocardiinae. These nearly complete mitogenomes provide relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group of chemosymbiotic bivalves.

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“…Appropriate protein models of substitution were selected for each gene family using the Bayesian information criterion implemented in ProtTest3 (Darriba et al, 2011). Optimum models and associated parameters for all protein families are summarized in Additional file 1-D. One hundred bootstrap replicates were then carried out with the appropriate protein model using the software programme PHYML (Guindon and Gascuel, 2003) and summarized using the majority-rule consensus method.…”

Section: Phylogenetic Methodsmentioning

confidence: 99%

The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine

Jones

Doyle

Fitzpatrick

2014

Gene

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Ergothioneine (EGT) is a histidine betaine derivative that exhibits antioxidant action in humans. EGT is primarily synthesized by fungal species and a number of bacterial species. A five-gene cluster (egtA, egtB, egtC, egtD & egtE) responsible for EGT production in Mycobacteria smegmatis has recently been identified. The first fungal biosynthetic EGT gene (NcEgt-1) has also been identified in Neurospora crassa. NcEgt-1 contains domains similar to those found in M. smegmatis egtB and egtD. EGT is biomembrane impermeable. Here we inferred the evolutionary history of the EGT cluster in prokaryotes as well as examining the phyletic distribution of Egt-1 in the fungal kingdom. A genomic survey of 2509 prokaryotes showed that the five-gene EGT cluster is only found in the Actinobacteria. Our survey identified more than 400 diverse prokaryotes that contain genetically linked orthologs of egtB and egtD. Phylogenetic analyses of Egt proteins show a complex evolutionary history and multiple incidences of horizontal gene transfer. Our analysis also identified two independent incidences of a fusion event of egtB and egtD in bacterial species. A genomic survey of over 100 fungal genomes shows that Egt-1 is found in all fungal phyla, except species that belong to the Saccharomycotina subphylum. This analysis provides a comprehensive analysis of the distribution of the key genes involved in the synthesis of EGT in prokaryotes and fungi. Our phylogenetic inferences illuminate the complex evolutionary history of the genes involved in EGT synthesis in prokaryotes. The potential to synthesize EGT is a fungal trait except for species belonging to the Saccharomycotina subphylum.

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ProtTest 3: fast selection of best-fit models of protein evolution

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 2,409 publications

References 8 publications

The first complete mitogenome of the South China deep‐sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods

The first complete mitogenome of the South China deep‐sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods

Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats

The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine

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