BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection

Forni, Giobbe; Ruggieri, Angelo; Piccinini, Giovanni; Luchetti, Andrea

doi:10.1002/ece3.7959

Cited by 5 publications

(3 citation statements)

References 49 publications

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“…We tested each gene for positive selection via branch-site models (branch-site neutral versus branch-site selection) using codeml from PAML (30), as implemented in BASE (31). We also used BUSTED from the HyPhy software suite (32, 33).…”

Section: Methodsmentioning

confidence: 99%

Convergent relaxation of molecular constraint in mammalian herbivores highlights the roles of liver and kidney functions in carnivory

Pollard,

Meyer,

Puckett

2023

Preprint

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BackgroundMammalia comprises a great diversity of diet types and associated adaptations. An understanding of the genomic mechanisms underlying these adaptations may offer insights for improving human health. Comparative genomic studies of diet that employ taxonomically restricted analyses or simplified diet classifications may suffer reduced power to detect molecular convergence associated with diet evolution. Here, we used a quantitative carnivory score and 80 mammalian species to detect significant correlations between the relative evolutionary rates of genes and changes in diet. Increases in this carnivory score indicated increasing amounts of animal protein in a species’ diet.ResultsWe identified six genes—ACADSB,CLDN16,CPB1,PNLIP,SLC13A2, andSLC14A2—that experienced significant evolutionary constraint and greater functional importance as increasingly carnivorous diets evolved. We further considered the biological functions associated with diet evolution and observed that pathways related to amino acid and lipid metabolism, biological oxidation, and small molecule transport were evolutionarily constrained in association with increased carnivory. Liver and kidney functions showed a similar pattern of greater constraint as carnivory increases.ConclusionsOur results indicate that, during adaptation to increasing carnivory, selection acts on the liver and kidneys to maintain sufficient metabolism and excretion of substances found in excess in carnivorous diets.

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Section: Methodsmentioning

confidence: 99%

Convergent relaxation of molecular constraint in mammalian herbivores highlights the roles of liver and kidney functions in carnivory

Pollard,

Meyer,

Puckett

2023

Preprint

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“…The amino acid alignments were then retro translated to nucleotides using pal2nal [ 61 ], and Gblocks was used to exclude spurious signals coming from misalignments [ 62 ]. We then inferred instances of positive selection using the branch-site model implemented in codeml [ 63 ]; all codeml analyses were carried out using BASE [ 64 ]. Separate analyses were performed using each terminal branch of our phylogeny as the foreground.…”

Section: Methodsmentioning

confidence: 99%

Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis

et al. 2022

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The evolution of automixis – i.e., meiotic parthenogenesis – requires several features, including ploidy restoration after meiosis and maintenance of fertility. Characterizing the relative contribution of novel versus pre-existing genes and the similarities in their expression and sequence evolution is fundamental to understand the evolution of reproductive novelties. Here we identify gonads-biased genes in two Bacillus automictic stick-insects and compare their expression profile and sequence evolution with a bisexual congeneric species. The two parthenogens restore ploidy through different cytological mechanisms: in Bacillus atticus, nuclei derived from the first meiotic division fuse to restore a diploid egg nucleus, while in Bacillus rossius, diploidization occurs in some cells of the haploid blastula through anaphase restitution. Parthenogens’ gonads transcriptional program is found to be largely assembled from genes that were already present before the establishment of automixis. The three species transcriptional profiles largely reflect their phyletic relationships, yet we identify a shared core of genes with gonad-biased patterns of expression in parthenogens which are either male gonads-biased in the sexual species or are not differentially expressed there. At the sequence level, just a handful of gonads-biased genes were inferred to have undergone instances of positive selection exclusively in the parthenogen species. This work is the first to explore the molecular underpinnings of automixis in a comparative framework: it delineates how reproductive novelties can be sustained by genes whose origin precedes the establishment of the novelty itself and shows that different meiotic mechanisms of reproduction can be associated with a shared molecular ground plan.

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“…An essential metric to detect the selection type driving such sequence evolution is the nucleic acid and amino acid substitution rate, namely, the nonsynonymous ( d N ) to synonymous ( d S ) substitution rate ratio (ω = d N / d S ). This measure has proven to be useful for understanding different evolutionary processes in comparative genomics ( Clark et al 2003 ; Chuang and Li 2004 ; Felsenstein and Felenstein 2004 ; Stark et al 2007 ; Egan et al 2008 ; Fedorova et al 2008 ; Sánchez et al 2011 ; Pan et al 2013 ; Parker et al 2013 ; Li et al 2014 ; Bast et al 2018 ; Glover et al 2019 ; Liu et al 2019 ; Forni et al 2021 ; Policarpo et al 2021 ). Such evolutionary analyses have profited from massive amounts of data derived from next-generation sequencing technologies, making comparative genomics analyses more attainable.…”

Section: Introductionmentioning

confidence: 99%

AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis

Ceron-Noriega,

Schoonenberg,

Butter

et al. 2023

Genome Biology and Evolution

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The detection of adaptive selection in a system approach considering all protein-coding genes allows for the identification of mechanisms and pathways that enabled adaptation to different environments. Currently, available programs for the estimation of positive selection signals can be divided into two groups. They are either easy to apply but can analyze only one gene family at a time, restricting system analysis; or they can handle larger cohorts of gene families, but require considerable prerequisite data such as orthology associations, codon alignments, phylogenetic trees, and proper configuration files. All these steps require extensive computational expertise, restricting this endeavor to specialists. Here, we introduce AlexandrusPS, a high-throughput pipeline that overcomes technical challenges when conducting transcriptome-wide positive selection analyses on large sets of nucleotide and protein sequences. The pipeline streamlines 1) the execution of an accurate orthology prediction as a precondition for positive selection analysis, 2) preparing and organizing configuration files for CodeML, 3) performing positive selection analysis using CodeML, and 4) generating an output that is easy to interpret, including all maximum likelihood and log-likelihood test results. The only input needed from the user is the CDS and peptide FASTA files of proteins of interest. The pipeline is provided in a Docker image, requiring no program or module installation, enabling the application of the pipeline in any computing environment. AlexandrusPS and its documentation are available via GitHub (https://github.com/alejocn5/AlexandrusPS).

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BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection

Cited by 5 publications

References 49 publications

Convergent relaxation of molecular constraint in mammalian herbivores highlights the roles of liver and kidney functions in carnivory

Convergent relaxation of molecular constraint in mammalian herbivores highlights the roles of liver and kidney functions in carnivory

Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis

AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis

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