go_batch: A snakemake pipeline to assemble mitochondrial and ribosomal sequences from genome skims

Abstract

AbstractLow coverage “genome-skims” are often used to assemble organelle genomes and ribosomal gene sequences for cost effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet degraded DNA often hinders PCR based analysis. However, with improvements to molecular techniques and sequencing technology, it is possible to use ancient DNA methods to generate libraries and sequence short fragments from degraded DNA to generate genome skims from museum collections.Here we introduce “go_batch”, a bioinformatic pipeline written in snakemake designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically,go_batchallows the batch assembly and annotation of mitochondrial genomes and nuclear ribosomal genes from low-coverage skims. The utility of the pipeline is demonstrated by analysing a novel genome skimming dataset from both recent and historical sollariellid gastropod samples.We demonstrate thatgo_batchcan recover previously unattainable mitochondrial genomes and ribosomal genes from sollariellid gastropods. In addition, phylogenetic analysis of these gene sequences helped resolve complex taxonomic relationships.The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet.