A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections

Low 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 poor preservation resulting in degraded DNA often hinders
PCR based analyses. However, it is possible to generate libraries and
sequence the short fragments typical of degraded DNA to generate
genome-skims from museum collections. Here we introduce a snakemake
toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo,
designed to unlock the genomic potential of historical museum specimens
using genome skimming. Specifically, skim2mito and skim2rrna perform the
batch assembly, annotation and phylogenetic analysis of mitochondrial
genomes and nuclear ribosomal genes, respectively, from low-coverage
genome skims. The third pipeline gene2phylo takes a set of gene alignments
and performs phylogenetic analysis of individual genes, partitioned
analysis of concatenated alignments and a phylogenetic analysis based on
gene trees. We benchmark our pipelines with simulated data, followed by
testing with a novel genome skimming dataset from both recent and
historical solariellid gastropod samples. We show that the toolkit can
recover mitochondrial and ribosomal genes from poorly preserved museum
specimens of the gastropod family Solariellidae, and the phylogenetic
analysis is consistent with our current understanding of 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.