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bioRxiv2024

srahunter: A User-Friendly Tool for Efficient Retrieval and Management of SRA Data

Easy access and use of vast datasets are paramount for advancing scientific discovery in steadily expanding studies based on high-throughput sequencing (HTS). The Sequence Read Archive (SRA) is a publicly accessible repository currently holding a huge amount of HTS reads, as part of the International Nucleotide Sequence Database Collaboration (INSDC). However, accessing, downloading, and managing data and metadata efficiently can be challenging. Here, we introduce srahunter, a tool designed to simplify data and metadata acquisition from SRA. Developed with Python, srahunter leverages the core functionalities of SRA Toolkit and Entrez Direct, to enable automated downloading, smart data management, and user-friendly metadata integration through an interactive HTML table https://github.com/GitEnricoNeko/srahunter. Compared to existing tools, srahunter increases the efficiency of metadata retrieval by reducing the technical barriers to SRA data and streamlining the handling of SRA datasets, and can therefore accelerate the development of genomics and multiple omics research.

bioinformatics↗

bioRxiv2019

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

Mussels are ecologically and economically relevant edible marine bivalves, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other species. Here we show that the Mediterranean mussel Mytilus galloprovincialis has a complex pan-genomic architecture, which includes a core set of 45,000 genes shared by all individuals plus a surprisingly high number of dispensable genes ([~]15,000). The latter are subject to presence/absence variation (PAV), i.e., they may be entirely missing in a given individual and, when present, they are frequently found as a single copy. The enrichment of dispensable genes in survival functions suggests an adaptive value for PAV, which might be the key to explain the extraordinary capabilities of adaptation and invasiveness of this species. Our study underpins a unique metazoan pan-genome architecture only previously described in prokaryotes and in a few non-metazoan eukaryotes, but that might also characterize other marine invertebrates.\n\nSignificance statementIn animals, intraspecific genomic diversity is generally thought to derive from relatively small-scale variants, such as single nucleotide polymorphisms, small indels, duplications, inversions and translocations. On the other hand, large-scale structural variations which involve the loss of genomic regions encoding protein-coding genes in some individuals (i.e. presence/absence variation, PAV) have been so far only described in bacteria and, occasionally, in plants and fungi. Here we report the first evidence of a pan-genome in the animal kingdom, revealing that 25% of the genes of the Mediterranean mussel are subject to PAV. We show that this unique feature might have an adaptive value, due to the involvement of dispensable genes in functions related with defense and survival.

genetics↗