Evidence map›Paper›PMID 33165812›Full record

ArticleScience China. Life sciences2021

Modes of genetic adaptations underlying functional innovations in the rumen.

Xiangyu Pan, Yudong Cai, Zongjun Li, Xianqing Chen, Rasmus Heller, Nini Wang, Yu Wang, Chen Zhao, Yong Wang, Han Xu and 30 more

Abstract read
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In one paragraph

Article in Science China. Life sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.

0numbers the graph read from it
0cells of the map it votes in
21citing papers in PubMed
4.5field-weighted citation impact, top 5% 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

21 citing papers in PubMed, 40 citations in OpenAlex.

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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

40 authors at 15 institutions in 3 countries.

Xiangyu Pan *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Yudong Cai *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Zongjun Li *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Xianqing Chen *School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
Rasmus Heller *Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark.
Nini Wang *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Yu WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Chen ZhaoKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Yong WangUniversity of Chinese Academy of Sciences, Beijing, 100049, China.
Han XuKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Songhai LiMarine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
Ming LiKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Cunyuan LiCollege of Life Sciences, Shihezi University, Shihezi, 832003, China.
Shengwei HuCollege of Life Sciences, Shihezi University, Shihezi, 832003, China.
Hui LiKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Kun WangSchool of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
Lei ChenSchool of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
Bin WeiKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Zhuqing ZhengKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 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, 712100, China.
Yue YangSchool of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
Tingting ZhangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Zhuoting HouSchool of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
Yueyang YanKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Xiaoyang LvCollege of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
Wei SunCollege of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
Xinyu LiKey Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
Shisheng HuangSchool of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China.
Lixiang LiuCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
Shengyong MaoCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
Wenqing LiuCollege of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, 712100, China.
Jinlian HuaCollege of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, 712100, China.
Zhipeng LiDepartment of Special Economic Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
Guojie ZhangCenter for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
Yulin ChenKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Xihong WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Qiang QiuSchool of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
Brian P DalrympleSchool of Animal Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, 6009, Australia.
Wen WangSchool of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China. wwang@mail.kiz.ac.cn.
Yu JiangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China. yu.jiang@nwafu.edu.cn.
Northwest A&F University · CNNorthwestern Polytechnical University · CNNanjing Agricultural University · CNShihezi University · CNYangzhou University · CNAcademy of Mathematics and Systems Science · CNChinese Academy of Agricultural Sciences · CNChinese Academy of Sciences · CNInstitute of Deep-Sea Science and Engineering · CNKunming Institute of Zoology · CNShanghaiTech University · CNThird Affiliated Hospital of Guangzhou Medical University · CNUniversity of Chinese Academy of Sciences · CNUniversity of Copenhagen · DKUniversity of Western Australia · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We analyzed 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations. We identified genes with relatively high expression in the rumen, of which many appeared to be recruited from other tissues. These genes show functional enrichment in ketone body metabolism, regulation of microbial community, and epithelium absorption, which are the most prominent biological processes involved in rumen innovations. Several modes of genetic change underlying rumen functional innovations were uncovered, including coding mutations, genes newly evolved, and changes of regulatory elements. We validated that the key ketogenesis rate-limiting gene (HMGCS2) with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals. Two newly evolved genes (LYZ1 and DEFB1) are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium. Furthermore, we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment. These results greatly improve our understanding of rumen evolution and organ evo-devo in general.

Indexed as

Adaptation, PhysiologicalAmino Acid SequenceAnimalsCamelusCetaceaCluster AnalysisEpitheliumGene Expression ProfilingGenomicsMicrobiotaModels, GeneticPhylogenyRumenRuminantsSequence Homology, Amino Acidcomparative genomicscomparative transcriptomicsevo-devoevolution of organsrumen innovations

Identifiers

PMID33165812
OpenAlexW3105438192

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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.