TY - JOUR

T1 - SNP Discovery from Single and Multiplex Genome Assemblies of Non-model Organisms

AU - Morin, Phillip A

AU - Foote, Andrew D

AU - Hill, Christopher M

AU - Simon-Bouhet, Benoit

AU - Lang, Aimee R

AU - Louis, Marie

PY - 2018

Y1 - 2018

N2 - Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.

AB - Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.

KW - Animals

KW - Contig Mapping

KW - DNA, Bacterial

KW - Genetic Markers

KW - Genome/genetics

KW - Genomic Library

KW - High-Throughput Nucleotide Sequencing/methods

KW - Multiplex Polymerase Chain Reaction/methods

KW - Polymorphism, Single Nucleotide/genetics

KW - Sequence Alignment

KW - Single-Cell Analysis/methods

KW - Software

KW - Statistics as Topic

U2 - 10.1007/978-1-4939-7514-3_9

DO - 10.1007/978-1-4939-7514-3_9

M3 - Article

C2 - 29224072

VL - 1712

SP - 113

EP - 144

JO - Methods in Molecular Biology

JF - Methods in Molecular Biology

SN - 1064-3745

ER -