Evidence map›Paper›PMID 26486310›Full record

ArticleGenome biology2015

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.

Oksung Chung, Seondeok Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, JeHoon Jun, HyeJin Lee, Alvin Chon and 8 more

Open access · goldAbstract read
In one paragraph

Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed
4.2field-weighted citation impact, top 6% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

23 citing papers in PubMed, 58 citations in OpenAlex.

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  13. New genome assembly of the barn owl (Ecology and evolution · 2020
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors at 9 institutions in 4 countries.

Oksung ChungPersonal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. okokookk219@gmail.com.
Seondeok JinNational Institute of Ecology, Seocheon, 325-813, Republic of Korea. withbirds@daum.net.
Yun Sung ChoPersonal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. joys0406@gmail.com.
Jeongheui LimNational Science Museum, Daejeon, 305-705, Republic of Korea. jeongheuilim@gmail.com.
Hyunho KimThe Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. pgi.kimhh@gmail.com.
Sungwoong JhoPersonal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. sungwoong.jho@gmail.com.
Hak-Min KimThe Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. howmany2@gmail.com.
JeHoon JunPersonal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. junjh0701@gmail.com.
HyeJin LeePersonal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. leehj08111@gmail.com.
Alvin ChonThe Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. chon.alvin@gmail.com.
Junsu KoTheragen BiO Institute, TheragenEtex, Suwon, 443-270, Republic of Korea. junsu.ko@therabio.kr.
Jeremy EdwardsDepartment 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.
Jessica A WeberDepartment of Biology, University of New Mexico, Albuquerque, New Mexico, USA. weberj@unm.edu.
Kyudong HanDepartment of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea. kyudong.han@gmail.com.
Stephen J O'BrienTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University St. Petersburg, Petersburg, 199004, Russia. lgdchief@gmail.com.
Andrea ManicaDepartment of Zoology, Evolutionary Ecology Group, University of Cambridge, Cambridge, UK. am315@cam.ac.uk.
Jong BhakPersonal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. jongbhak@genomics.org.
Woon Kee PaekNational Science Museum, Daejeon, 305-705, Republic of Korea. paekwk@naver.com.
Genome Research Foundation · KRUlsan National Institute of Science and Technology · KRNational Science Museum · KRUniversity of New Mexico · USDankook University · KRNational Institute of Ecology · KROcean Institute · USTheragen · KRUniversity of Cambridge · GB

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe 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.

resultsWe 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.

conclusionsWe 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.

Indexed as

Evolution, MolecularAdaptation, BiologicalAnimalsDigestive System Physiological PhenomenaFalconiformesGenetic VariationGenomeImmunitySequence Analysis, DNATranscriptome

Identifiers

PMID26486310
PMCPMC4618389
OpenAlexW2152553362

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LicenceCC BY
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.