Jung A Kim1, Beom-Soon Choi2, Nam-Soo Kim2, Seung-Gu Kang3, Jin-Young Park1, Yong-Gu Yeo4, Ju-Hee Bae4, Ju-Hee Lee4, Taeyoung Um5, Ik-Young Choi6,7, Junghwa An8. 1. National Institute of Biological Resources, Incheon, Republic of Korea. 2. Research Institute, NBIT Co., Ltd., Chuncheon, Republic of Korea. 3. Research Center for Endangered Species, National Institute of Ecology, Yeongyang-gun, Republic of Korea. 4. Conservation and Health Center, Seoul Zoo, Gwcheon, Republic of Korea. 5. Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea. 6. Research Institute, NBIT Co., Ltd., Chuncheon, Republic of Korea. choii@kangwon.ac.kr. 7. Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea. choii@kangwon.ac.kr. 8. National Institute of Biological Resources, Incheon, Republic of Korea. safety@korea.kr.
Abstract
BACKGROUND: The family Columbidae is known as the pigeon family and contains approximately 351 species and 50 genera. Compared to the wealth of biological and genomic information on these Columba livia var. domesteca, information on Columba rupestris and Streptopelia orientalis has been rather limited. The C. rupestris population size is decreasing in Korea. OBJECTIVES: Whole-genome sequencing and identification of population characterization of each species based genome variation on 9 Korean pigeon and dove samples, namely, six hill pigeon (C. rupestris), one rock pigeon (C. livia var. domestica) and two oriental turtle dove (S. orientalis) samples. RESULTS: The whole genome of 9 genotypes were sequenced and mapped to the C. livia reference genome. Sequence alignment showed over 96% identity in C. rupestris and 94% identity in S. orientalis to the reference genome (GenBank assembly accession: GCA_001887795.1). Sequence variations, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations, revealed that intergenus (Columba vs. Streptopelia) variations were approximately four times higher than intragenus variations (C. livia vs. C. rupestris). Of the two Columba species, C. livia var. domestica is closer to S. orientalis than C. rupestris. Pairwise sequentially Markovian coalescent (PSMC) demographic history analysis revealed that the three species underwent a common population bottleneck between 105 and 120 Kya; since then, the effective population sizes of the rock pigeon and oriental turtle dove have increased. CONCLUSION: The effective population size of the hill pigeon, an Endangered Species of Grade II in Korea, has increased slowly from the second severe bottleneck that occurred approximately 0.5-1.4 × 104 years ago. Our results showed no relationship between copy number variation in the Norrie disease protein (NDP) regulatory regions and plumage color patterns. We report the first comparative analysis of three pigeon genomes.
BACKGROUND: The family Columbidae is known as the pigeon family and contains approximately 351 species and 50 genera. Compared to the wealth of biological and genomic information on these Columba livia var. domesteca, information on Columba rupestris and Streptopelia orientalis has been rather limited. The C. rupestris population size is decreasing in Korea. OBJECTIVES: Whole-genome sequencing and identification of population characterization of each species based genome variation on 9 Korean pigeon and dove samples, namely, six hill pigeon (C. rupestris), one rock pigeon (C. livia var. domestica) and two oriental turtle dove (S. orientalis) samples. RESULTS: The whole genome of 9 genotypes were sequenced and mapped to the C. livia reference genome. Sequence alignment showed over 96% identity in C. rupestris and 94% identity in S. orientalis to the reference genome (GenBank assembly accession: GCA_001887795.1). Sequence variations, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations, revealed that intergenus (Columba vs. Streptopelia) variations were approximately four times higher than intragenus variations (C. livia vs. C. rupestris). Of the two Columba species, C. livia var. domestica is closer to S. orientalis than C. rupestris. Pairwise sequentially Markovian coalescent (PSMC) demographic history analysis revealed that the three species underwent a common population bottleneck between 105 and 120 Kya; since then, the effective population sizes of the rock pigeon and oriental turtle dove have increased. CONCLUSION: The effective population size of the hill pigeon, an Endangered Species of Grade II in Korea, has increased slowly from the second severe bottleneck that occurred approximately 0.5-1.4 × 104 years ago. Our results showed no relationship between copy number variation in the Norrie disease protein (NDP) regulatory regions and plumage color patterns. We report the first comparative analysis of three pigeon genomes.
Authors: Beth Shapiro; Dean Sibthorpe; Andrew Rambaut; Jeremy Austin; Graham M Wragg; Olaf R P Bininda-Emonds; Patricia L M Lee; Alan Cooper Journal: Science Date: 2002-03-01 Impact factor: 47.728
Authors: William M Muir; Gane Ka-Shu Wong; Yong Zhang; Jun Wang; Martien A M Groenen; Richard P M A Crooijmans; Hendrik-Jan Megens; Huanmin Zhang; Ron Okimoto; Addie Vereijken; Annemieke Jungerius; Gerard A A Albers; Cindy Taylor Lawley; Mary E Delany; Sean MacEachern; Hans H Cheng Journal: Proc Natl Acad Sci U S A Date: 2008-11-03 Impact factor: 11.205
Authors: Michael D Shapiro; Zev Kronenberg; Cai Li; Eric T Domyan; Hailin Pan; Michael Campbell; Hao Tan; Chad D Huff; Haofu Hu; Anna I Vickrey; Sandra C A Nielsen; Sydney A Stringham; Hao Hu; Eske Willerslev; M Thomas P Gilbert; Mark Yandell; Guojie Zhang; Jun Wang Journal: Science Date: 2013-01-31 Impact factor: 47.728
Authors: Carson Holt; Michael Campbell; David A Keays; Nathaniel Edelman; Aurélie Kapusta; Emily Maclary; Eric T Domyan; Alexander Suh; Wesley C Warren; Mark Yandell; M Thomas P Gilbert; Michael D Shapiro Journal: G3 (Bethesda) Date: 2018-05-04 Impact factor: 3.154