title: Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences.
abstract: Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.
authors.affiliation: Department of Ecology, Evolution and Behavior, Bell Museum of Natural History, University of Minnesota , Saint Paul, MN , USA .
authors.forename: F
authors.initials: F
authors.lastname: Keith Barker
authors.forename: Sara
authors.initials: S
authors.lastname: Oyler-McCance
authors.forename: Diana F
authors.initials: DF
authors.lastname: Tomback
mesh_terms: D000818:Animals; D029688:Brassica napus / Q000235:genetics*; D004247:DNA / Q000097:blood* / Q000302:isolation & purification; D030541:Databases, Genetic; D015723:Gene Library; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats / Q000235:genetics; D018482:Muscle, Skeletal / Q000378:metabolism; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: Microsatellite; NUMT; mitochondrial DNA; next-generation sequencing