진선덕 (국립생태원)

한빛사논문

조회1,422

진선덕Seondeok Jin

국립생태원

Genome Biol., Published: 21 October 2015, 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

Abstract

Oksung Chung^1†, Seondeok Jin^2†, Yun Sung Cho^13†, Jeongheui Lim⁴, Hyunho Kim³, Sungwoong Jho¹, Hak-Min Kim³, JeHoon Jun¹, HyeJin Lee¹, Alvin Chon³, Junsu Ko⁵, Jeremy Edwards⁶, Jessica A. Weber⁷, Kyudong Han⁸⁹, Stephen J. O’Brien¹⁰¹¹¹², Andrea Manica¹³, Jong Bhak^1143* and Woon Kee Paek^4*

¹ Personal Genomics Institute, Genome Research Foundation, Osong 361-951, Republic of Korea

² National Institute of Ecology, Seocheon 325-813, Republic of Korea

³ The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea

⁴ National Science Museum, Daejeon 305-705, Republic of Korea

⁵ Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea

⁶ Department Chemistry and Chemical Biology, Molecular Genetics and Microbiology, and Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico, USA

⁷ Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA

⁸ Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea

⁹ DKU-Theragen institute for NGS analysis (DTiNa), Cheonan 330-714, Republic of Korea

¹⁰ Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University St. Petersburg, Petersburg 199004, Russia

¹¹ Oceanographic Center, 8000 N. Ocean Drive, Dania Beach, USA

¹² Nova Southeastern University Ft Lauderdale, Fort Lauderdale 33004, Florida, USA

¹³ Department of Zoology, Evolutionary Ecology Group, University of Cambridge, Cambridge, UK

¹⁴ Geromics, Ulsan 689-798, Republic of Korea

^* Corresponding authors: Jong Bhak, Woon K Paek

^†Equal contributors

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.

Keywords: Cinereous vulture; Old world vulture; New world vulture; Transcriptome; Genome; Next-generation sequencing

논문정보

형식Research article
게재일2015년 10월 (BRIC 등록일 2015-11-05)
연구진국내(교신)+국외 연구진
분야 생명과학 > 유전학

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