MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies

Abstract

Recent advances in high throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is not an easy task due to the high cost of genome sequencing, the high complexity of assembly, and the lack of standardized protocols for genome annotation. The lack of consensus in the annotation and publication of genome files hinders research by making researchers lose time in reformatting the files for their purposes but can also reduce the quality of the genetic repertoire for an evolutionary study. Thus, the use of transcriptomes obtained using the same pipeline as a proxy for the genetic content of species remains a valuable resource that is easier to obtain, cheaper, and more comparable than genomes. In a previous study, we presented the Metazoan Assemblies from Transcriptomic Ensembles database (MATEdb), a repository of high-quality transcriptomic and genomic data for the two most diverse animal phyla, Arthropoda and Mollusca. Here, we present the newest version of MATEdb (MATEdb2) that overcomes some of the previous limitations of our database: (1) we include data from all animal phyla where public data is available, (2) we provide gene annotations from genomes obtained using the same pipeline. In total, we provide proteomes inferred from high-quality transcriptomic or genomic data for almost 1000 animal species, including the longest isoforms, all isoforms, and functional annotation based on sequence homology and protein language models, as well as the embedding representations of the sequences. We believe this new version of MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open, greener, and collaborative science.

Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models

“…We applied the methodology described in MATEdb2 53 to obtain the proteome files for 961 animals and 9 outgroups containing the longest peptide sequence (or isoform) per gene (Supp. File 1).…”

“…Genome annotations were downloaded from their respective repositories. All final and intermediate files are publicly available in MATEdb2 53 . Next, we created a subset of 93 species (Supp.…”

“…All proteomes, EggNOG-mapper annotations and GOPredSim-ProtT5 per-protein embeddings and annotations are available in MATEdb2 53 . DeepGOPlus and GOPredSim-Seqvec annotations are provided in Zenodo 65–70 , together with information content, semantic similarity and other results.…”

A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids

“…High-quality genomic data from thirty-five annelid species and two outgroups (Nemertea and Mollusca) were used to infer gene repertoire evolutionary dynamics across the Annelida phylum (Supplementary Table 5), including the newly generated data described above and following the current systematic classification of the phylum 12,[77][78][79][80] . The pipeline described in the MATEdb2 database 81 was used to retrieve the longest isoform for each species. Hierarchical orthologous groups (HOGs) were inferred with OMA v2.6 82 .…”