Data from: In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA

Here, we present a set of RNA-based probes for whole mitochondrial genome
in-solution enrichment, targeting a diversity of mammalian mitogenomes.
This probes set was designed from seven mammalian orders and tested to
determine the utility for enriching degraded DNA. We generated 63
mitogenomes representing five orders and 22 genera of mammals that yielded
varying coverage ranging from 0 to >5400X. Based on a threshold of
70% mitogenome recovery and at least 10× average coverage, 32 individuals
or 51% of samples were considered successful. The estimated sequence
divergence of samples from the probe sequences used to construct the array
ranged up to nearly 20%. Sample type was more predictive of mitogenome
recovery than sample age. The proportion of reads from each individual in
multiplexed enrichments was highly skewed, with each pool having one
sample that yielded a majority of the reads. Recovery across each
mitochondrial gene varied with most samples exhibiting regions with gaps
or ambiguous sites. We estimated the ability of the probes to capture
mitogenomes from a diversity of mammalian taxa not included here by
performing a clustering analysis of published sequences for 100 taxa
representing most mammalian orders. Our study demonstrates that a general
array can be cost and time effective when there is a need to screen a
modest number of individuals from a variety of taxa. We also address the
practical concerns for using such a tool, with regard to pooling samples,
generating high quality mitogenomes and detail a pipeline to remove
chimeric molecules.