Combined Hybridization Capture and Shotgun Sequencing for Ancient DNA Analysis of Extinct Wild and Domestic Dromedary Camel

TY - JOUR

T1 - Combined Hybridization Capture and Shotgun Sequencing for Ancient DNA Analysis of Extinct Wild and Domestic Dromedary Camel

AU - Mohandesan, Elmira

AU - Speller, Camilla Filomena

AU - Peters, Joris

AU - Uerpmann, Margarethe

AU - Uerpmann, Hans-Peter

AU - De Cupere, Bea

AU - Hofreiter, Michael Stefan

AU - Burger, Pamela

N1 - © 2016 John Wiley & Sons.This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details. Embargo period (paper and supplementary material): 12 months.

PY - 2016/8/1

Y1 - 2016/8/1

N2 - The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17–95% length coverage and 1.27–47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1–1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.

AB - The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17–95% length coverage and 1.27–47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1–1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.

KW - Camelus dromedarius

KW - ANCIENT DNA

KW - degraded DNA

KW - mitogenome

KW - capture enrichment

KW - next generation sequencing

KW - double-stranded libraries

U2 - 10.1111/1755-0998.12551

DO - 10.1111/1755-0998.12551

M3 - Article

SN - 1755-098X

VL - 17

SP - 300

EP - 313

JO - Molecular ecology resources

JF - Molecular ecology resources

IS - 2

ER -