Evidence map›Paper›PMID 37310928›Full record

ArticleGenome research2023

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes.

Ran Li, Mian Gong, Xinmiao Zhang, Fei Wang, Zhenyu Liu, Lei Zhang, Qimeng Yang, Yuan Xu, Mengsi Xu, Huanhuan Zhang and 25 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.

0numbers the graph read from it
0cells of the map it votes in
74citing papers in PubMed
–field-weighted citation impact
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

74 citing papers in PubMed, 116 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026
    Review
  6. Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Review
  13. Article
  14. Article
  15. Article
  16. The Function of the Lysophospholipase 1 (Animals : an open access journal from MDPI · 2025
    Article
  17. Review
  18. Article
  19. Article
  20. Evolution of Duplicated Hox Gene Clusters in Land Snails and Slugs.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025
    Article

14 more citing papers are in PubMed but not listed here.

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

35 authors at 12 institutions in 6 countries.

Ran Li *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Mian Gong *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Xinmiao Zhang *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Fei Wang *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Zhenyu Liu *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Lei Zhang *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Qimeng YangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Yuan XuKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Mengsi XuState Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China.
Huanhuan ZhangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Yunfeng ZhangState Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China.
Xuelei DaiKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Yuanpeng GaoKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Zhuangbiao ZhangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Wenwen FangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Yuta YangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Weiwei FuKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Chunna CaoKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Peng YangState Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China.
Zeinab Amiri GhanatsamanDepartment of Animal Science, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Shiraz 7155863511, Iran.
Niloufar Jafarpour NegariDepartment of Animal Science, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran.
Hojjat Asadollahpour NanaeiReproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran 1983969412, Iran.
Xiangpeng YueState Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
Yuxuan SongKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Xianyong LanKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Weidong DengFaculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
Xihong WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Chuanying PanKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Ruidong XiangFaculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, 3052 Victoria, Australia.
Eveline M Ibeagha-AwemuSherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec J1M 0C8, Canada.
Pat J S Heslop-HarrisonDepartment of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom.ORCID 0000-0002-3105-2167
Benjamin D RosenAnimal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA.
Johannes A LenstraFaculty of Veterinary Medicine, Utrecht University, Utrecht 3508 TD, The Netherlands.ORCID 0000-0003-1745-7739
Shangquan GanState Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China; yu.jiang@nwafu.edu.cn shangquangan@gdou.edu.cn.
Yu JiangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; yu.jiang@nwafu.edu.cn shangquangan@gdou.edu.cn.
Northwest A&F University · CNXinjiang Academy of Agricultural and Reclamation Science · CNAgriculture and Agri-Food Canada · CAMinistry of Agriculture and Rural Affairs · CNNorth West Agriculture and Forestry University · CNRoyan Institute · IRShahid Bahonar University of Kerman · IRSoil Conservation and Watershed Management Research · IRThe University of Melbourne · AUUniversity of Leicester · GBUtrecht University · NLYunnan Agricultural University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5' untranslated region (5' UTR) of

Indexed as

Genome-Wide Association StudyTail5' Untranslated RegionsAllelesAnimalsPhenotypeSheep5' Untranslated Regions

Identifiers

PMID37310928
PMCPMC10078295
OpenAlexW4361018486

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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Registered trials

None linked

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.