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Genome Biol. 2015 Oct 21;16:215. doi: 10.1186/s13059-015-0780-4.

The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.

Chung O1, Jin S2, Cho YS3,4, Lim J5, Kim H6, Jho S7, Kim HM8, Jun J9, Lee H10, Chon A11, Ko J12, Edwards J13, Weber JA14, Han K15,16, O'Brien SJ17,18,19, Manica A20, Bhak J21,22,23, Paek WK24.

Author information

1
Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. okokookk219@gmail.com.
2
National Institute of Ecology, Seocheon, 325-813, Republic of Korea. withbirds@daum.net.
3
Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. joys0406@gmail.com.
4
The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. joys0406@gmail.com.
5
National Science Museum, Daejeon, 305-705, Republic of Korea. jeongheuilim@gmail.com.
6
The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. pgi.kimhh@gmail.com.
7
Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. sungwoong.jho@gmail.com.
8
The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. howmany2@gmail.com.
9
Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. junjh0701@gmail.com.
10
Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. leehj08111@gmail.com.
11
The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. chon.alvin@gmail.com.
12
Theragen BiO Institute, TheragenEtex, Suwon, 443-270, Republic of Korea. junsu.ko@therabio.kr.
13
Department Chemistry and Chemical Biology, Molecular Genetics and Microbiology, and Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico, USA. jeremy.scott.edwards@gmail.com.
14
Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA. weberj@unm.edu.
15
Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea. kyudong.han@gmail.com.
16
DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 330-714, Republic of Korea. kyudong.han@gmail.com.
17
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University St. Petersburg, Petersburg, 199004, Russia. lgdchief@gmail.com.
18
Oceanographic Center, 8000 N. Ocean Drive, Dania Beach, USA. lgdchief@gmail.com.
19
Nova Southeastern University Ft Lauderdale, Fort Lauderdale, Florida, 33004, USA. lgdchief@gmail.com.
20
Department of Zoology, Evolutionary Ecology Group, University of Cambridge, Cambridge, UK. am315@cam.ac.uk.
21
Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. jongbhak@genomics.org.
22
The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. jongbhak@genomics.org.
23
Geromics, Ulsan, 689-798, Republic of Korea. jongbhak@genomics.org.
24
National Science Museum, Daejeon, 305-705, Republic of Korea. paekwk@naver.com.

Abstract

BACKGROUND:

The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.

RESULTS:

We sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene.

CONCLUSIONS:

We present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures.

PMID:
26486310
PMCID:
PMC4618389
DOI:
10.1186/s13059-015-0780-4
[Indexed for MEDLINE]
Free PMC Article

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