OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

Zdobnov, Evgeny M.; Tegenfeldt, Fredrik; Kuznetsov, Dmitry; Waterhouse, Robert M.; Simão, Felipe A.; Ioannidis, Panagiotis; Seppey, Mathieu; Loetscher, Alexis; Kriventseva, Evgenia V.

doi:10.1093/nar/gkw1119

Cited by 421 publications

(369 citation statements)

References 34 publications

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“…We used a set of 1,759 BUSCO genes inferred to be saccharomyceta-specific (“saccharomyceta” is an informal taxonomic rank used by many databases, including NCBI: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=716545) and single-copy in at least 90% of 60 genomes in the OrthoDB Version 9 database (Zdobnov et al, 2017) to evaluate the completeness of the 332 genome assemblies. Briefly, for each BUSCO gene, its consensus orthologous protein sequence among the 60 reference genomes was used as query in a tBLASTn search against each genome to identify up to three putative genomic regions, and the gene structure of each putative genomic region was predicted by AUGUSTUS v 3.2.2 (Stanke and Waack, 2003).…”

Section: Methods Detailsmentioning

confidence: 99%

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Shen

Opulente

Kominek

et al. 2018

Cell

473

787

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Summary Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly a third of all known budding yeast diversity. Here we establish a robust genus-level phylogeny comprised of 12 major clades, infer the timescale of diversification from the Devonian Period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the Budding Yeast Common Ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.

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Section: Methods Detailsmentioning

confidence: 99%

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Shen

Opulente

Kominek

et al. 2018

Cell

473

787

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“…All contigs <200 bp were removed prior to final assembly submission. To test the quality of the assembly, the aves_odb9 dataset of single copy, orthologous, Avian specific genes from orthodb version 9 (Zdobnov et al., ) was selected to check their status (present, duplicated, fragment or missing) with busco version 3.0.2 (Waterhouse et al., ) in the Galgal4, Galgal5 and GRCg6a assemblies of the chicken genome and in our NumMel1 guinea fowl assembly. The assembly is publicly available in NCBI Assembly under the name of NumMel1.0 (accession GCA_002078875.2).…”

Section: Methodsmentioning

confidence: 99%

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes

Vignal

Boitard

Thébault

et al. 2019

Molecular Ecology Resources

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The helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub‐Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2,000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Today, it is still farmed in Africa, mainly as a traditional village poultry, and is also bred more intensively in other countries, mainly France and Italy. The lack of available molecular genetic markers has limited the genetic studies conducted to date on guinea fowl. We present here a first‐generation whole‐genome sequence draft assembly used as a reference for a study by a Pool‐seq approach of wild and domestic populations from Europe and Africa. We show that the domestic populations share a higher genetic similarity between each other than they do to wild populations living in the same geographical area. Several genomic regions showing selection signatures putatively related to domestication or importation to Europe were detected, containing candidate genes, most notably EDNRB 2 , possibly explaining losses in plumage coloration phenotypes in domesticated populations.

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“…As many of the transcriptome libraries were assembled using pooled individuals and developmental stages, cd‐hit v.4.6.1 (Godzik and Li, ) was used to select the longest transcript with a 98% sequence identity threshold (‑c 0.98). Single‐copy nuclear orthologues were then identified using the orthoDB Diptera gene set ( diptera_odb9 , 2799 genes) (Zdobnov et al, ) with busco (v.3) (Waterhouse et al, ) and augustus (Stanke and Morgenstern, ). Orthologous genes annotated in all samples ( n = 16) were extracted and nucleotides aligned based on reading frame using geneous v.10.2.6 with the mafft FFT‐NS‐2 algorithm (Katoh and Standley, ).…”

Section: Methodsmentioning

confidence: 99%

Identification of Y‐chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species

Choo

Nguyen

Ward

et al. 2019

Insect Molecular Biology

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Bactrocera tryoni (Queensland fruit fly) are polyphagous horticultural pests of eastern Australia. Heterogametic males contain a sex‐determining Y‐chromosome thought to be gene poor and repetitive. Here, we report 39 Y‐chromosome scaffolds (~700 kb) from B. tryoni identified using genotype‐by‐sequencing data and whole‐genome resequencing. Male diagnostic PCR assays validated eight Y‐scaffolds, and one (Btry4096) contained a novel gene with five exons that encode a predicted 575 amino acid protein. The Y‐gene, referred to as typo‐gyf, is a truncated Y‐chromosome paralogue of X‐chromosome gene gyf (1773 aa). The Y‐chromosome contained ~41 copies of typo‐gyf, and expression occurred in male flies and embryos. Analysis of 13 tephritid transcriptomes confirmed typo‐gyf expression in six additional Bactrocera species, including Bactrocera latifrons, Bactrocera dorsalis and Bactrocera zonata. Molecular dating estimated typo‐gyf evolved within the past 8.02 million years (95% highest posterior density 10.56–5.52 million years), after the split with Bactrocera oleae. Phylogenetic analysis also highlighted complex evolutionary histories among several Bactrocera species, as discordant nuclear (116 genes) and mitochondrial (13 genes) topologies were observed. B. tryoni Y‐sequences may provide useful sites for future transgene insertions, and typo‐gyf could act as a Y‐chromosome diagnostic marker for many Bactrocera species, although its function is unknown.

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OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

Cited by 421 publications

References 34 publications

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes

Identification of Y‐chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species

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