Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

Comte, Nicolas; Morel, Benoît; Hasic, Damir; Guéguen, Laurent; Boussau, Bastien; Daubin, Vincent; Penel, Simon; Scornavacca, Céline; Gouy, Manolo; Stamatakis, Alexandros; Tannier, Éric; Parsons, David

doi:10.1093/bioinformatics/btaa615

Cited by 27 publications

(16 citation statements)

References 15 publications

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“…From a set of homologous sequences, true orthologous groups are identified through a reconciliation software, Treerecs ( 41 ) and additional homemade scripts (steps 3–5). Using tree reconciliation instead of annotations or tools such as OMA or Eggnogg ( 58 , 59 ) may be advantageous when working with non-model species, unknown genes, and recent duplication events.…”

Section: Resultsmentioning

confidence: 99%

“…However, for multigenic families that include paralogs that have recently diverged, the gene members cannot be separated solely based on the relative lengths of the tree branches. We therefore included a phylogenetic reconciliation method, Treerecs ( 41 ), to identify genes sharing a common evolutionary history in our species of interest. To identify duplication events, Treerecs reconciles each gene tree to the user-provided species tree or cladogram.…”

Section: Methodsmentioning

confidence: 99%

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DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes

Picard

Ganivet

Allatif

et al. 2020

Nucleic Acids Research

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Adaptive evolution has shaped major biological processes. Finding the protein-coding genes and the sites that have been subjected to adaptation during evolutionary time is a major endeavor. However, very few methods fully automate the identification of positively selected genes, and widespread sources of genetic innovations such as gene duplication and recombination are absent from most pipelines. Here, we developed DGINN, a highly-flexible and public pipeline to Detect Genetic INNovations and adaptive evolution in protein-coding genes. DGINN automates, from a gene's sequence, all steps of the evolutionary analyses necessary to detect the aforementioned innovations, including the search for homologs in databases, assignation of orthology groups, identification of duplication and recombination events, as well as detection of positive selection using five methods to increase precision and ranking of genes when a large panel is analyzed. DGINN was validated on nineteen genes with previously-characterized evolutionary histories in primates, including some engaged in host-pathogen arms-races. Our results confirm and also expand results from the literature, including novel findings on the Guanylate-binding protein family, GBPs. This establishes DGINN as an efficient tool to automatically detect genetic innovations and adaptive evolution in diverse datasets, from the user's gene of interest to a large gene list in any species range.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes

Picard

Ganivet

Allatif

et al. 2020

Nucleic Acids Research

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“…1 F ) using the cost parameters which only considers gene duplication/loss (duplication cost [2]; transfer cost [1,000]; loss cost [1]). TREERECS ( Comte et al 2020 ) was also adopted to confirm the robustness of enrichment/depletion patterns for the duplication/loss events (duplication cost [2]; loss cost [1]) ( supplementary fig. S4 , Supplementary Material online).…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics Reveals Recent Adaptive Evolution in Himalayan Giant Honeybee Apis laboriosa

Lin

Lan

Zheng

et al. 2021

Genome Biology and Evolution

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The Himalayan giant honeybee, Apis laboriosa, is the largest individual honeybee with major ecological and economic importance in high-latitude environments. However, our understanding of its environmental adaptations is circumscribed by the paucity of genomic data for Apis laboriosa. Here, we provide a draft genome of wild Apis laboriosa for the first time, along with a comparison to its closely related species, Apis dorsata. The draft genome of Apis laboriosa based on the de novo assembly is 226.1 Mbp in length with a scaffold N50 size of 3.34 Mbp, a GC content of 32.2%, a repeat content of 6.86%, and a gene family number of 8,404. Comparative genomics analysis revealed that the genes in Apis laboriosa genome have undergone stronger positive selection (2.5 times) and more recent duplication/loss events (6.1 times) than those in the Apis dorsata genome. Our study implies the potential molecular mechanisms underlying the high-altitude adaptation of Apis laboriosa, and will catalyze future comparative studies to understand the environmental adaptation of modern honeybees.

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“…Evolutionary scenario for gene duplication/loss was built minimizing the duplication and loss score with standard parameters in Treerecs (Comte et al, 2020), using contracted versions of the gene and species trees (Supplementary Material 4).…”

Section: Reconciliation Between the Gene Phylogeny And Species Phylogenymentioning

confidence: 99%

Evolution of Matrix Gla and Bone Gla Protein Genes in Jawed Vertebrates

Leurs

Martinand‐Mari²,

Ventéo³

et al. 2021

Front. Genet.

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Matrix Gla protein (Mgp) and bone Gla protein (Bgp) are vitamin-K dependent proteins that bind calcium in their γ-carboxylated versions in mammals. They are recognized as positive (Bgp) or negative (Mgp and Bgp) regulators of biomineralization in a number of tissues, including skeletal tissues of bony vertebrates. The Mgp/Bgp gene family is poorly known in cartilaginous fishes, which precludes the understanding of the evolution of the biomineralization toolkit at the emergence of jawed vertebrates. Here we took advantage of recently released genomic and transcriptomic data in cartilaginous fishes and described the genomic loci and gene expression patterns of the Mgp/Bgp gene family. We identified three genes, Mgp1, Mgp2, and Bgp, in cartilaginous fishes instead of the single previously reported Mgp gene. We describe their genomic loci, resulting in a dynamic evolutionary scenario for this gene family including several events of local (tandem) duplications, but also of translocation events, along jawed vertebrate evolution. We describe the expression patterns of Mgp1, Mgp2, and Bgp in embryonic stages covering organogenesis in the small-spotted catshark Scyliorhinus canicula and present a comparative analysis with Mgp/Bgp family members previously described in bony vertebrates, highlighting ancestral features such as early embryonic, soft tissues, and neuronal expressions, but also derived features of cartilaginous fishes such as expression in fin supporting fibers. Our results support an ancestral function of Mgp in skeletal mineralization and a later derived function of Bgp in skeletal development that may be related to the divergence of bony vertebrates.

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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

Cited by 27 publications

References 15 publications

DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes

DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes

Comparative Genomics Reveals Recent Adaptive Evolution in Himalayan Giant Honeybee Apis laboriosa

Evolution of Matrix Gla and Bone Gla Protein Genes in Jawed Vertebrates

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