GPU MrBayes V3.1: MrBayes on Graphics Processing Units for Protein Sequence Data: Table 1.

Pang, Shaoning; Stones, Rebecca J.; Ren, Mingming; Liu, Xiaoguang; Wang, Gang; Xia, Hong-ju; Haoyang, Wu; Liu, Yang; Xie, Qiang

doi:10.1093/molbev/msv129

Cited by 18 publications

(8 citation statements)

References 9 publications

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“…The concatenated sequences of 13 PCGs (without stop codons) extracted from the reported 32 mitogenomes of Carangidae species, including A. indicus , D. tabl , and A. djedaba, were used to construct phylogenetic trees with MEGA 7.0, MrBayes 3.1 (University of California, La Jolla, San Diego, CA, USA) [ 53 ], and iTOL ( ) [ 54 ], using Larimichthys crocea (GenBank accession number: EU339149) as the outgroup. Bayesian Inference (BI) was analyzed in MrBayes 3.1 [ 55 ] and maximum likelihood (ML) analysis was performed in MEGA 7.0. When performing Bayesian analysis, general time reversible (GTR) was adopted in the data substitution model and the ratio of the difference between sites was set as invgamma.…”

Section: Methodsmentioning

confidence: 99%

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Li¹,

et al. 2020

IJMS

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Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

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Section: Methodsmentioning

confidence: 99%

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Li¹,

et al. 2020

IJMS

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“…Each partition scheme was run with the GTRGAMMAI model, and 1000 rapid bootstrapping replications were set to evaluate the bootstrap support values and search for the best-scoring ML tree. The BI phylogeny was performed in MrBayes v3.1.2 [100] with the "unlink" and "prest ratepr = variable" model parameters. 10,000,000 generations were run in two independent runs of four independent Markov Chain Monte Carlo (MCMC) chains, and were sampled every 1000 generations.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae

Zhou

Yang

et al. 2021

BMC Genomics

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Background Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated. Results In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus. Conclusions The current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.

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“…We used SequenceMatrix (Vaidya G., 2011) to concatenate individual alignments in a single matrix using, and MEGA X to select the best nucleotide substitution models for individual gene alignments. We used MRBAYES (Pang, et al, 2015) as provided by the CIPRES SCIENCE platform to estimate phylogenetic relationships based on the Bayesian information criterion (BIC) and assuming a minimal mutation rate (µ) of 2×10 −10 mutations per nucleotide site per cell division, following the work of Lee et al . (Lee, et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

“…We used SequenceMatrix [53] to concatenate individual alignments in a single matrix using, and MEGA X to select the best nucleotide substitution models for individual gene alignments. We conducted Bayesian inference using MRBAYES [54] as provided by the CIPRES SCIENCE platform to estimate phylogenetic relationships based on the Bayesian information criterion (BIC) and assuming a minimal mutation rate (µ) of 2x10 -10 mutations per nucleotide site per cell division, as described by [55]. The parameters of the posterior probability model, tree branch lengths, and tree topology were obtained using the Metropoliscoupled Markov Chain Monte Carlo (MCMCMC) algorithm.…”

Section: Acquiring Genomic Phylogenetic and Phenotypic Data For Escherichia Colimentioning

confidence: 99%

CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species

Hongo

Castro

Picorelli

et al. 2021

Preprint

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The increasing availability of high-quality genomic, annotation and phenotypic data for different species contrasts with the lack of general software for comparative genomics that integrates these data types in a statistically sound framework in order to produce biologically meaningful knowledge. In this work, we present CALANGO (Comparative AnaLysis with ANnotation-based Genomic cOmponentes), a first-principles comparative genomics tool to search for annotation terms, such as GO terms or Pfam domain IDs, associated with a quantitative variable used to rank species data, after correcting for phylogenetic relatedness. This information can be used to annotate genomes at any level, including protein domains, genes, or promoters, allowing comparative analyses of genomes at several resolutions and from distinct functional and evolutionary angles. CALANGO outputs a set of HTML5 files that can be opened in any conventional web browser, featuring interactive heatmaps, scatter plots, and tables, stimulating scientific reproducibility, data sharing, and exploratory analysis. Detailed results and a reproducibility-focused data structure are also returned after each run of the tool. CALANGO provides classic association statistics used in comparative genomics, including correlation coefficients, probabilities, and phylogeny-aware linear models. To illustrate how CALANGO can be used to produce biologically meaningful, statistically sound knowledge, we present a case study of the co-evolution of Escherichia coli and their integrated bacteriophages (prophages). Through controlled in silico experiments, we demonstrate that terms from a functional annotation are both more prevalent across genomes and more abundant than the homology-based annotation terms commonly used in traditional comparative genomics studies. This result demonstrates how GO-based annotation captures information of non-homologous sequences fulfilling the same biological roles. Most homologous regions positively associated with prophage occurrence are found in genes of viral origin (e.g. capsids, lysozymes, and integrases), as expected, while the second most abundant category is virulence factors. The removal of viral genes demonstrated that most of the virulence factors associated with prophage density are located outside viral genes, suggesting a more complex biological process than the archetypal bacteriophage-mediated horizontal gene transfer of virulence factors. The functional annotation performed by CALANGO revealed several GO terms describing general and specific aspects of viral biology (e.g. "viral life cycle", "DNA integration"). We also found an association of the GO term "pathogenicity", used to annotate several non-homologous virulence factors, as well as terms describing several known virulence mechanisms in pathogenic E. coli (e.g. "Type III secretion system"). Moreover, CALANGO also detected previously unknown associations that unveil a richer scenario of the bacteriophage-host biological interaction. An interesting example is the association of GO term "response to stress", used to annotate several classes of non-homologous genes components of distinct stress response mechanisms (e.g. peroxidases, DNA repair enzymes, heat shock proteins), indicating that the horizontal transfer of such genes may be adaptive for host cells and, consequently, advantageous for the integrated prophages as well. CALANGO is provided as a fully operational, out-of-the-box R package that can be freely installed directly from CRAN. Usage examples and longer-format documentation are also available at maintainer's github page.

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GPU MrBayes V3.1: MrBayes on Graphics Processing Units for Protein Sequence Data: Table 1.

Cited by 18 publications

References 9 publications

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae

CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species

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