Biology Faculty Articles
Document Type
Article
Publication Date
10-21-2015
Publication Title
Genome Biology
Keywords
Cinereous vulture, Old world vulture, New world vulture, Transcriptome, Genome, Next-generation sequencing
ISSN
1474-760X
Volume
16
Issue/No.
215
First Page
1
Last Page
13
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.
Additional Comments
National Research Foundation of Korea grant #s: 2008–2004707, 2013M3A9A5047052; UNIST research fund #: 1.140077.01; Russian Ministry of Science grant #: 11.G34.31.0068; GenBank accession #s: GDQP01000000
NSUWorks Citation
Chung, Oksung; Seondeok Jin; Yun Sung Cho; Jeongheui Lim; Hyunho Kim; Sungwoong Jho; Hak-Min Kim; JeHoon Jun; HyeJin Lee; Alvin Chon; Junsu Ko; Jeremy Edwards; Jessica A. Weber; Kyudong Han; Stephen J. O'Brien; Andrea Manica; Jong Bhak; and Woon Kee Paek. 2015. "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." Genome Biology 16, (215): 1-13. https://nsuworks.nova.edu/cnso_bio_facarticles/734
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
Comments
© 2015 Chung et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.