CAFE 5 models variation in evolutionary rates among gene families

Mendes, Fábio K.; Vanderpool, Dan; Fulton, Ben; Hahn, Matthew W.

doi:10.1093/bioinformatics/btaa1022

Cited by 396 publications

(332 citation statements)

References 18 publications

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“…Family sizes within taxonomic groups were further explored with the Computational Analysis of gene Family Evolution v5 (CAFE; [ 34 ]; https://github.com/hahnlab/CAFE5 ), which uses phylogenomics and family sizes to estimate the timing of gene family evolution. Family sizes for each ABC family in each species were estimated using the ABC_scan pipeline described above.…”

Section: Methodsmentioning

confidence: 99%

Comparative and functional genomics of the ABC transporter superfamily across arthropods

et al. 2021

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Background The ATP-binding cassette (ABC) transporter superfamily is comprised predominantly of proteins which directly utilize energy from ATP to move molecules across the plasma membrane. Although they have been the subject of frequent investigation across many taxa, arthropod ABCs have been less well studied. While the manual annotation of ABC transporters has been performed in many arthropods, there has so far been no systematic comparison of the superfamily within this order using the increasing number of sequenced genomes. Furthermore, functional work on these genes is limited. Results Here, we developed a standardized pipeline to annotate ABCs from predicted proteomes and used it to perform comparative genomics on ABC families across arthropod lineages. Using Kruskal-Wallis tests and the Computational Analysis of gene Family Evolution (CAFE), we were able to observe significant expansions of the ABC-B full transporters (P-glycoproteins) in Lepidoptera and the ABC-H transporters in Hemiptera. RNA-sequencing of epithelia tissues in the Lepidoptera Helicoverpa armigera showed that the 7 P-glycoprotein paralogues differ substantially in their tissue distribution, suggesting a spatial division of labor. It also seems that functional redundancy is a feature of these transporters as RNAi knockdown showed that most transporters are dispensable with the exception of the highly conserved gene Snu, which is probably due to its role in cuticular formation. Conclusions We have performed an annotation of the ABC superfamily across > 150 arthropod species for which good quality protein annotations exist. Our findings highlight specific expansions of ABC transporter families which suggest evolutionary adaptation. Future work will be able to use this analysis as a resource to provide a better understanding of the ABC superfamily in arthropods.

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Section: Methodsmentioning

confidence: 99%

Comparative and functional genomics of the ABC transporter superfamily across arthropods

et al. 2021

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“…All protein coding gene sequences from Hymenoptera from the study of Thomas et al, 2020 were obtained from www.arthrofam.org and together with the ab initio protein predictions from our AUGUSTUS run, were parsed through the OrthoFinder pipeline (Emms and Kelley 2019) to perform comparative genomic analyses of (a) gene duplications, (b) identifying single copy orthologs, and (c) delineating orthogroups based on reciprocal DendroBLAST/DIAMOND searches and estimating gene-trees. The gene family counts identified by OrthoFinder and a rooted, binary, and ultrametric species tree (based on the species tree inferred above) were then used in iterative runs of the likelihood-based method, CAFE5 (Mendes et al, 2020) to estimate gene turnover rates (λ) and annotation error rates (ε), sensu the methods of Thomas et al, 2020.…”

Section: Methodsmentioning

confidence: 99%

“…Specifically, we used the (a) discrete state reconstruction, and (b) empirical Bayes reconstruction using 1000 simulated trees for two relevant Hymenopteran traits -(a) mode of reproduction -thelytoky (unfertilized eggs developing into females), arrhenotoky (unfertilized eggs developing into males), and sexual reproduction, (b) sociality -solitary, eusociality, and facultative sociality.Gene Family EvolutionAll protein coding gene sequences from Hymenoptera from the study ofThomas et al, 2020 were obtained from www.arthrofam.org and together with the ab initio protein predictions from our AUGUSTUS run, were parsed through the OrthoFinder pipeline (Emms and Kelley 2019) to perform comparative genomic analyses of (a) gene duplications, (b) identifying single copy orthologs, and (c) delineating orthogroups based on reciprocal DendroBLAST/DIAMOND searches and estimating gene-trees. The gene family counts identified by OrthoFinder and a rooted, binary, and ultrametric species tree (based on the species tree inferred above) were then used in iterative runs of the likelihood-based method, CAFE5(Mendes et al, 2020) to estimate gene turnover rates (λ) and annotation error rates (ε), sensu the methods ofThomas et al, 2020.…”

mentioning

confidence: 99%

Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior

Sethuraman

Tovar

Welch

et al. 2021

Preprint

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Dinocampus coccinellae (Hymenoptera: Braconidae) is a generalist parasitoid wasp that parasitizes >50 species of predatory lady beetles (Coleoptera: Coccinellidae), with thelytokous parthenogeny as its primary mode of reproduction. Here we present the first high quality genome of D. coccinellae using a combination of short and long read sequencing technologies, followed by assembly and scaffolding of chromosomal segments using Chicago+HiC technologies. We also present a first-pass ab initio genome annotation, and resolve timings of divergence and evolution of (1) solitary behavior vs eusociality, (2) arrhenotokous vs thelytokous parthenogenesis, and (3) rates of gene loss and gain among Hymenopteran lineages. Our study finds (1) at least two independent origins of eusociality and solitary behavior among Hymenoptera, (2) two independent origins of thelytokous parthenogenesis from ancestral arrhenotoky, and (3) accelerated rates of gene duplications, loss, and gain along the lineages leading to D. coccinellae. Our work both affirms the ancient divergence of Braconid wasps from ancestral Hymenopterans and accelerated rates of evolution in response to adaptations to novel hosts, including polyDNA viral co-evolution.

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“…Full absence was verified with alignment of the Arabidopsis protein sequence against the assembly. CAFE v5 (Mendes et al, 2020) was used to identify rapidly evolving gene families. Values from the newick species tree produced by OrthoFinder were multiplied by 100 to prevent issues with rounding in CAFE, and the tree was made ultrametric using OrthoFinder.…”

Section: Comparative Genomicsmentioning

confidence: 99%

Strategies of tolerance reflected in two North American maple genomes

McEvoy

Sezen

Trouern-Trend

et al. 2021

Preprint

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Maples (the genus Acer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. Among Acer species, several stand out in their importance to economic interest. Here we report the first two chromosome-scale genomes for North American species, Acer negundo and Acer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, with A. negundo at a length of 442 Mb, N50 of 32 Mb and 30,491 genes, and A. saccharum at 626 Mb, N50 of 46 Mb, and 40,074 genes. No recent whole genome duplications were detected, though A. saccharum has local gene duplication and more recent bursts of transposable elements, as well as a large-scale translocation between two chromosomes. Genomic comparison revealed that A. negundo has a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of expression from RNA-Seq obtained from A. saccharum grown in long-term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest, provided insights into genes involved in aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.

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CAFE 5 models variation in evolutionary rates among gene families

Cited by 396 publications

References 18 publications

Comparative and functional genomics of the ABC transporter superfamily across arthropods

Comparative and functional genomics of the ABC transporter superfamily across arthropods

Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior

Strategies of tolerance reflected in two North American maple genomes

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