Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

摘要: The advent of next-generation sequencing technologies (NGSTs) has transformed the way in which scientists approach a myriad biological questions (Hawkins et al. 2010). Even with NGSTs' growing familiarity and broad range applications such as ChIP-seq, RNA-seq, genome-wide association studies, NGSTs still have potential to influence field population genetics phylogenetics new methods obtain genomic sequences rare, difficult sample, or extinct species (Millar 2008). ability uncover phylogenetic history recently rapidly improved due reduced cost increased sequence capacity (Gilbert 2007, 2008; Miller 2008, 2009); however, obstacles do remain. difficulties applying problems not lie technology itself, but preparative procedures for isolation large, orthologous DNA regions across multiple divergent (Summerer 2009). This problem is exacerbated museum specimens, where quality varies greatly between samples contamination levels are often high Generation whole genome even complete mitochondrial (mtDNA) sequences, cost-effective most laboratories large amount required adequate coverage single individual. Capture hybridization routinely used genomic-scale enrichments modern target from same 2009; Mamanova 2010) also recovery fossil specimens by largely removing contaminants final product (Krause However, capture techniques been applied assembling data sets taxa (e.g., millions years genetic divergence), lack appropriate probes exploration conditions allow heterologous capture. Enrichment PCR (which standard previous studies) requires closely related reference painstaking efforts design many oligonucleotide primers amplify very short interest. Capture targeted loci promises be more flexible, cost-effective, efficient than other enrichment degraded samples. Here we describe application selection recover 13 Sunda colugo (Galeopterus variegatus) varying ages (47–170 yr old) that represent major geographical locations throughout Southeast Asian mainland archipelago (Supplemental Fig. S1; Table 1). Colugos arboreal mammals widely distributed Asia extensive gliding membrane (patagium) any known mammal. allows them glide distances, longest recorded being 136 m (Lim 2007). rarely kept captivity elusive wild 2007), factors obscured their evolutionary decades. Under current taxonomy, colugos comprise unique mammalian order (Dermoptera) classified two species: Philippine (Cynocephalus volans) (Wilson Reeder 2005). recent mtDNA nuclear provide compelling evidence geographically widespread fact represents (Janecka 2008) suggest further sampling may identify additional populations and/or species. Because extreme difficulty obtaining fresh tissue colugos, explored this question using collections devised comprehensive method capture, selection, fragments NGST. Table 1. USNM