DOI: 10.5061/dryad.gq883
title: Data from: In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA

description: 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 &gt;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.
description: chimera_IDThis script sorts capture sequences that hit to non-closest-relative (NCR) MMA probes.combiner-2.0The FASTA file is sequences from MMA capture. The Blast output is the output of blasting those sequences against the MMA probeset, minus closest relative to the target species (non-closest-relative, or NCR, probeset). This program appends the length of the query sequence (found in the FASTA file) onto the end of that sequence's line in the blast table so that the chimera detection decision rules can be followed in chimera_ID.pysequenceGetter-4.0This script gets a subset of a FASTA file based on a CSV file of BLAST hits.AllProbes_goodThis file contains all 8,178 probes used for RNA bait synthesis.H3FTPWM01454 Sequencing reads for some of newly generated mitogenomes, a text file is provided with demultiplexing information and for this run.H3HWW5Q01Second 454 run containing novel mitogenomes. Details for demultiplexing are provided in a separate text file.WMG_Alignment26Ind_FINAL01.09.14All mitochondrial genomes used for array design. 16 are published sequences and 10 are novel mitogenomes.Dryad_ModernSquirrelDemuxThis file contains the 454 barcode information to demultiplex the samples from the two 454 sff files.pero_in.454.fastaThis file contains 454 generated fastq reads for the Peromyscus samples used for the probe development. Both individuals included in the concatenated reference sequence are within this file, with USNM 569292 represented as 92. Sample USNM 569298 is represented as reads ID'd as 98.Enrichment AssembliesThese are all 63 assemblies, in bam format with the resulting consensus sequences as fasta. All sequences are labelled by capture pool ID in table 2.