RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding

G3: Genes, Genomes, Genetics

article

Emily Humble¹  Kanchon K. Dasmahapatra³  Alvaro Martinez-Barrio⁴  Inês Gregório¹  Jaume Forcada²  Ann-Christin Polikeit¹  Simon D. Goldsworthy⁵  Michael E. Goebel⁶  Jörn Kalinowski⁷  Jochen B. W. Wolf⁸  Joseph I. Hoffman¹ 

[1] Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany;British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, United Kingdom;Department of Biology, University of York, Heslington, York, YO10 5DD, United Kingdom;Science for Life Laboratories and Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden;South Australian Research and Development Institute, 2 Hamra Avenue, West Beach, South Australia, 5024, Australia;Antarctic Ecosystem Research Division, SWFSC, NMFS, NOAA, La Jolla, California 92037-1023 USA;Centrum für Biotechnologie, CeBiTec, University of Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany;Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinstried, Germany;Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden

关键词: Key words: PacBio sequencing;    RAD sequencing;    comparative genomics;    single nucleotide polymorphism (SNP);    linkage disequilibrium (LD);    population structure;    genomic inbreeding coefficient;   

DOI  :  10.1534/g3.118.200171

学科分类：社会科学、人文和艺术（综合）

来源: Genetics Society of America

【 摘 要 】

Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal ( Arctocephalus gazella ) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog ( Canis lupus familiaris ). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.

【 授权许可】

CC BY|CC BY-NC