51
|
Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB, Arif M, Li X, Lin L, Yu J, Ma T, Xu F, Han P, Jiang H, Mardinoglu A, Zhang C, von Feilitzen K, Xu X, Wang J, Yang H, Bolund L, Zhong W, Fagerberg L, Lindskog C, Pontén F, Mulder J, Luo Y, Uhlen M. Genome-wide annotation of protein-coding genes in pig. BMC Biol 2022; 20:25. [PMID: 35073880 PMCID: PMC8788080 DOI: 10.1186/s12915-022-01229-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/07/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND There is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here, a new annotation strategy is introduced based on dimensionality reduction and density-based clustering of whole-body co-expression patterns. This strategy has been used to explore the gene expression landscape in pig, and we present a whole-body map of all protein-coding genes in all major pig tissues and organs. RESULTS An open-access pig expression map ( www.rnaatlas.org ) is presented based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups. A new UMAP-based classification scheme is introduced, in which all protein-coding genes are stratified into tissue expression clusters based on body-wide expression profiles. The distribution and tissue specificity of all 22,342 protein-coding pig genes are presented. CONCLUSIONS Here, we present a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering. A genome-wide resource of the transcriptome map across all major tissues and organs in pig is presented, and the data is available as an open-access resource ( www.rnaatlas.org ), including a comparison to the expression of human orthologs.
Collapse
Affiliation(s)
- Max Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Per Oksvold
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jinrong Huang
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - María Bueno Álvez
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xiangyu Li
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jiaying Yu
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Tao Ma
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | | | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Lars Bolund
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Wen Zhong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Mathias Uhlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
52
|
Yang Y, Yan J, Fan X, Chen J, Wang Z, Liu X, Yi G, Liu Y, Niu Y, Zhang L, Wang L, Li S, Li K, Tang Z. The genome variation and developmental transcriptome maps reveal genetic differentiation of skeletal muscle in pigs. PLoS Genet 2021; 17:e1009910. [PMID: 34780471 PMCID: PMC8629385 DOI: 10.1371/journal.pgen.1009910] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/29/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Natural and artificial directional selections have resulted in significantly genetic and phenotypic differences across breeds in domestic animals. However, the molecular regulation of skeletal muscle diversity remains largely unknown. Here, we conducted transcriptome profiling of skeletal muscle across 27 time points, and performed whole-genome re-sequencing in Landrace (lean-type) and Tongcheng (obese-type) pigs. The transcription activity decreased with development, and the high-resolution transcriptome precisely captured the characterizations of skeletal muscle with distinct biological events in four developmental phases: Embryonic, Fetal, Neonatal, and Adult. A divergence in the developmental timing and asynchronous development between the two breeds was observed; Landrace showed a developmental lag and stronger abilities of myoblast proliferation and cell migration, whereas Tongcheng had higher ATP synthase activity in postnatal periods. The miR-24-3p driven network targeting insulin signaling pathway regulated glucose metabolism. Notably, integrated analysis suggested SATB2 and XLOC_036765 contributed to skeletal muscle diversity via regulating the myoblast migration and proliferation, respectively. Overall, our results provide insights into the molecular regulation of skeletal muscle development and diversity in mammals.
Collapse
Affiliation(s)
- Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Junyu Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiaxing Chen
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Zishuai Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Xiaoqin Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- Guangxi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | | | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - ShuaiCheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
- * E-mail: (SCL); (KL); (ZLT)
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen, China
- * E-mail: (SCL); (KL); (ZLT)
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- Guangxi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen, China
- * E-mail: (SCL); (KL); (ZLT)
| |
Collapse
|
53
|
Ma H, Jiang J, He J, Liu H, Han L, Gong Y, Li B, Yu Z, Tang S, Zhang Y, Duan Y, Yin Y, Zeng Q, Yi J, He X, Zeng Y, Kim KS, Xu K, Liang F, He J. Long-read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds. Mol Ecol Resour 2021; 22:1508-1520. [PMID: 34758184 DOI: 10.1111/1755-0998.13550] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]
Abstract
Advances in long-read sequencing technology and genome assembly provide an opportunity to improve the pig genome and reveal the full range of structural variations (SVs) between local Chinese and European pigs. To date, little is known about the genomes of some unique Chinese indigenous breeds, such as the Ningxiang pig. Here, we report the sequencing and assembly of a highly contiguous Ningxiang pig genome (NX) via an integration of PacBio single-molecule real-time sequencing, Illumina next-generation sequencing, BioNano optical mapping and Hi-C (chromosome conformation capture) approaches. The assembled genome comprises 2.44 Gb with a contig N50 of 26.1 Mb and 418 contigs in total. These contigs are organized into 121 scaffolds with a scaffold N50 of 139.0 Mb. More than 99.1% of the assembled sequence could be localized to 19 pseudochromosomes and is annotated with 20,914 protein-coding genes and 34.04% repetitive sequences. Comparisons between the NX and European Duroc assemblies revealed many SVs in genes involved in the immune system, nervous system, lipid metabolism and environmental adaptation. The genetic variants include 47 Chinese domestic pig-specific SVs and the associated 74 genes may contribute to the differences in domestic traits compared to European pigs. Moreover, single nucleotide polymorphisms (SNPs) identified from whole genome resequencing data of 73 Chinese pigs, representing 17 geographically isolated breeds, showed their specific genetic variations, population structure and evolutionary patterns. Finally, we explore transcriptional regulation in the first intron of the MYL4 gene, as the genomic SV (281-bp deletion) in Ningxiang pig promotes its subcutaneous fat compared to European pig breeds. This work identifies a set of Asian-specific SVs and SNPs, which will be important resources for modern pig breeding and genetic conservation.
Collapse
Affiliation(s)
- Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Juan Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | | | | | - Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Shengguo Tang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Yehui Duan
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, PR China
| | - Yulong Yin
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, PR China
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China.,Ningxiang Pig Farm of Dalong Livestock Technology Co., Ltd, Ningxiang, PR China
| | | | - Xinglong He
- Bureau of Animal Husbandry, Veterinary and Fisheries in Ningxiang City, Ningxiang, PR China
| | - Yongbo Zeng
- Bureau of Animal Husbandry, Veterinary and Fisheries in Ningxiang City, Ningxiang, PR China
| | - Kung Seok Kim
- Department of Natural Resources Ecology and Management, Iowa State University, Ames, Iowa, USA
| | - Kang Xu
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, PR China
| | - Fan Liang
- Grandomics Biosciences, Wuhan, PR China
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| |
Collapse
|
54
|
Zhu X, Zhang H, Tang Q. pyRSD-CoEv: A python package for selective sweep detection and co-evolutionary gene cluster identification. Anim Genet 2021; 53:161-165. [PMID: 34729801 DOI: 10.1111/age.13151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/14/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
Genes undergo distinct selective sweeps, and also interact and coevolve, forming the bases of complex phenotypic traits. Therefore, the identification of genes that coevolve or are under artificial selective sweeps is of great importance. However, previous computational methods have been designed for either populations of closely related breeds or individuals of distinct species. Approaches intended specifically for closely related individuals without replicate (i.e. each breed/strain is represented by only one individual) are long overdue. We present a free, powerful, open source package, pyRSD-CoEv, that allows the identification of genes undergoing coevolution and/or selection-based sweeps. pyRSD-CoEv includes two main analysis workflows for genomic variant data: (i) the identification of selective sweeps using relative homozygous single nucleotide variant density (RSD); and (ii) the identification of coevolutionary gene clusters based on correlated evolutionary rates. The python package pyRSD-CoEv is written using python 3.7 and is freely available from the github website at https://github.com/QianZiTang/pyRSD-CoEv. It runs on Linux.
Collapse
Affiliation(s)
- Xingxing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haoyu Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| |
Collapse
|
55
|
Ai H, Zhang M, Yang B, Goldberg A, Li W, Ma J, Brandt D, Zhang Z, Nielsen R, Huang L. Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes. Mol Biol Evol 2021; 38:5051-5065. [PMID: 34343337 PMCID: PMC8557463 DOI: 10.1093/molbev/msab230] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We resequenced 80 Eurasian pigs from nine different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex-biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y chromosomes.
Collapse
Affiliation(s)
- Huashui Ai
- National Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi Province, P.R. China
| | - Mingpeng Zhang
- National Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi Province, P.R. China
| | - Bin Yang
- National Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi Province, P.R. China
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Wanbo Li
- National Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi Province, P.R. China
| | - Junwu Ma
- National Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi Province, P.R. China
| | - Debora Brandt
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Zhiyan Zhang
- National Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi Province, P.R. China
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Lusheng Huang
- National Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi Province, P.R. China
| |
Collapse
|
56
|
Adetula AA, Fan X, Zhang Y, Yao Y, Yan J, Chen M, Tang Y, Liu Y, Yi G, Li K, Tang Z. Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs ( Sus-scrofa). RNA Biol 2021; 18:439-450. [PMID: 34314293 PMCID: PMC8677025 DOI: 10.1080/15476286.2021.1954380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/08/2022] Open
Abstract
RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs. The RNA editing events at the miRNA binding sites were generated. The biological function of the differentially edited gene in skeletal muscle was further characterized in pig muscle-derived satellite cells. RNA editome analysis revealed a total of 171,909 A-to-I RNA editing sites (RESs), and examination of its features showed that these A-to-I editing sites were mainly located in SINE retrotransposons PRE-1/Pre0_SS element. Analysis of differentially edited sites (DESs) revealed a total of 4,552 DESs across tissues between Duroc and Luchuan pigs, and functional category enrichment analysis of differentially edited gene (DEG) sets highlighted a significant association and enrichment of tissue-developmental pathways including TGF-beta, PI3K-Akt, AMPK, and Wnt signaling pathways. Moreover, we found that RNA editing events at the miRNA binding sites in the 3'-UTR of HSPA12B mRNA could prevent the miRNA-mediated mRNA downregulation of HSPA12B in the muscle-derived satellite (MDS) cell, consistent with the results obtained from the Luchuan skeletal muscle. This study represents the most systematic attempt to characterize the significance of RNA editing in regulating gene expression, particularly in skeletal muscle, constituting a new layer of regulation to understand the genetic mechanisms behind phenotype variance in animals.Abbreviations: A-to-I: Adenosine-to-inosine; ADAR: Adenosine deaminase acting on RNA; RES: RNA editing site; DEG: Differentially edited gene; DES: Differentially edited site; FDR: False discovery rate; GO: Gene Ontology; KEGG: Kyoto Encyclopaedia of Genes and Genomes; MDS cell: musclederived satellite cell; RPKM: Reads per kilobase of exon model in a gene per million mapped reads; UTR: Untranslated coding regions.
Collapse
Affiliation(s)
- Adeyinka A. Adetula
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongsheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yilong Yao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junyu Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Muya Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| |
Collapse
|
57
|
Wang D, Yang L, Ning C, Liu JF, Zhao X. Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs. BMC Genomics 2021; 22:736. [PMID: 34641784 PMCID: PMC8507312 DOI: 10.1186/s12864-021-08030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Background Reference sequences play a vital role in next-generation sequencing (NGS), impacting mapping quality during genome analyses. However, reference genomes usually do not represent the full range of genetic diversity of a species as a result of geographical divergence and independent demographic events of different populations. For the mitochondrial genome (mitogenome), which occurs in high copy numbers in cells and is strictly maternally inherited, an optimal reference sequence has the potential to make mitogenome alignment both more accurate and more efficient. In this study, we used three different types of reference sequences for mitogenome mapping, i.e., the commonly used reference sequence (CU-ref), the breed-specific reference sequence (BS-ref) and the sample-specific reference sequence (SS-ref), respectively, and compared the accuracy of mitogenome alignment and SNP calling among them, for the purpose of proposing the optimal reference sequence for mitochondrial DNA (mtDNA) analyses of specific populations Results Four pigs, representing three different breeds, were high-throughput sequenced, subsequently mapping reads to the reference sequences mentioned above, resulting in a largest mapping ratio and a deepest coverage without increased running time when aligning reads to a BS-ref. Next, single nucleotide polymorphism (SNP) calling was carried out by 18 detection strategies with the three tools SAMtools, VarScan and GATK with different parameters, using the bam results mapping to BS-ref. The results showed that all eighteen strategies achieved the same high specificity and sensitivity, which suggested a high accuracy of mitogenome alignment by the BS-ref because of a low requirement for SNP calling tools and parameter choices. Conclusions This study showed that different reference sequences representing different genetic relationships to sample reads influenced mitogenome alignment, with the breed-specific reference sequences being optimal for mitogenome analyses, which provides a refined processing perspective for NGS data. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08030-1.
Collapse
Affiliation(s)
- Dan Wang
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Liu Yang
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| |
Collapse
|
58
|
Wang Z, Ye S, Yao C, Wang J, Mao J, Xu L, Liu Y, Fu C, Lu G, Li S. Antiviral Activity of Canine RIG-I against Canine Influenza Virus and Interactions between Canine RIG-I and CIV. Viruses 2021; 13:v13102048. [PMID: 34696478 PMCID: PMC8540569 DOI: 10.3390/v13102048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
RIG-I functions as a virus sensor that induces a cellular antiviral response. Although it has been investigated in other species, there have been no further studies to date on canine RIG-I against canine influenza virus (CIV). In the present study, we cloned the RIG-I gene of beagle dogs and characterized its expression, subcellular localization, antiviral response, and interactions with CIV proteins. RIG-I was highly expressed and mainly localized in the cytoplasm, with low levels detected in the nucleus. The results revealed that overexpression of the CARD domain of RIG-I and knockdown of RIG-I showed its ability to activate the RLR pathway and induced the expression of downstream interferon-stimulated genes. Moreover, overexpression of canine RIG-I suppressed the replication of CIV. The association between RIG-I and CIV was evaluated with the luciferase assay and by indirect immunofluorescence and bimolecular fluorescence complementation analyses. The results showed that CIV nonstructural protein 1 (NS1) can strongly suppress the RIG-I–mediated innate immune response, and the novel interactions between CIV matrix proteins (M1 and M2) and canine RIG-I were disclosed. These findings provide a basis for investigating the antiviral mechanism of canine RIG-I against CIV, which can lead to effective strategies for preventing CIV infection in dogs.
Collapse
Affiliation(s)
- Zhen Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
| | - Shaotang Ye
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
| | - Congwen Yao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
| | - Ji Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
| | - Jianwei Mao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
| | - Liang Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
| | - Yongbo Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Fu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510642, China;
| | - Gang Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Z.W.); (S.Y.); (C.Y.); (J.W.); (J.M.); (L.X.); (Y.L.); (G.L.)
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China
- Guangdong Technological Engineering Research Center for Pet, South China Agricultural University, Guangzhou 510642, China
- Correspondence:
| |
Collapse
|
59
|
Zhao P, Du H, Jiang L, Zheng X, Feng W, Diao C, Zhou L, Liu GE, Zhang H, Chamba Y, Zhang Q, Li B, Liu JF. PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene. Genome Biol Evol 2021; 12:1751-1764. [PMID: 33151306 PMCID: PMC7643367 DOI: 10.1093/gbe/evaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/22/2022] Open
Abstract
Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single-nucleotide polymorphism information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5–0.2 Ma and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO, and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.
Collapse
Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Maryland
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yangzom Chamba
- College of Animal Science and Technology, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
| | - Qin Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, PR China
| | - Bugao Li
- Department of Animal Sciences and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
60
|
Wang K, Hu H, Tian Y, Li J, Scheben A, Zhang C, Li Y, Wu J, Yang L, Fan X, Sun G, Li D, Zhang Y, Han R, Jiang R, Huang H, Yan F, Wang Y, Li Z, Li G, Liu X, Li W, Edwards D, Kang X. The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Mol Biol Evol 2021; 38:5066-5081. [PMID: 34329477 PMCID: PMC8557422 DOI: 10.1093/molbev/msab231] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional ∼66.5 Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression level are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based GWAS identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size QTL located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
Collapse
Affiliation(s)
- Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, 6009 WA, Australia
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Jingyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chenxi Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yiyi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Junfeng Wu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Lan Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Xuewei Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Hetian Huang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Fengbin Yan
- Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yanbin Wang
- Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, 6009 WA, Australia
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| |
Collapse
|
61
|
Chu JSC, Peng B, Tang K, Yi X, Zhou H, Wang H, Li G, Leng J, Chen N, Feng X. Eight soybean reference genome resources from varying latitudes and agronomic traits. Sci Data 2021; 8:164. [PMID: 34210987 PMCID: PMC8249447 DOI: 10.1038/s41597-021-00947-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/30/2021] [Indexed: 01/18/2023] Open
Abstract
Comparative analysis of multiple reference genomes representing diverse genetic backgrounds is critical for understanding the role of key alleles important in domestication and genetic breeding of important crops such as soybean. To enrich the genetic resources for soybean, we describe the generation, technical assessment, and preliminary genomic variation analysis of eight de novo reference-grade soybean genome assemblies from wild and cultivated accessions. These resources represent soybeans cultured at different latitudes and exhibiting different agronomical traits. Of these eight soybeans, five are from new accessions that have not been sequenced before. We demonstrate the usage of these genomes to identify small and large genomic variations affecting known genes as well as screening for genic PAV regions for identifying candidates for further functional studies.
Collapse
Affiliation(s)
- Jeffrey Shih-Chieh Chu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Wuhan Frasergen Bioinformatics Inc., East Lake High-Tech Zone, Wuhan, China
| | - Bo Peng
- Wuhan Frasergen Bioinformatics Inc., East Lake High-Tech Zone, Wuhan, China
| | - Kuanqiang Tang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xingxing Yi
- Wuhan Frasergen Bioinformatics Inc., East Lake High-Tech Zone, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huangkai Zhou
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Inc., East Lake High-Tech Zone, Wuhan, China
| | - Guang Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jiantian Leng
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Nansheng Chen
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.
| | - Xianzhong Feng
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| |
Collapse
|
62
|
Novel functional sequences uncovered through a bovine multiassembly graph. Proc Natl Acad Sci U S A 2021; 118:2101056118. [PMID: 33972446 DOI: 10.1073/pnas.2101056118] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many genomic analyses start by aligning sequencing reads to a linear reference genome. However, linear reference genomes are imperfect, lacking millions of bases of unknown relevance and are unable to reflect the genetic diversity of populations. This makes reference-guided methods susceptible to reference-allele bias. To overcome such limitations, we build a pangenome from six reference-quality assemblies from taurine and indicine cattle as well as yak. The pangenome contains an additional 70,329,827 bases compared to the Bos taurus reference genome. Our multiassembly approach reveals 30 and 10.1 million bases private to yak and indicine cattle, respectively, and between 3.3 and 4.4 million bases unique to each taurine assembly. Utilizing transcriptomes from 56 cattle, we show that these nonreference sequences encode transcripts that hitherto remained undetected from the B. taurus reference genome. We uncover genes, primarily encoding proteins contributing to immune response and pathogen-mediated immunomodulation, differentially expressed between Mycobacterium bovis-infected and noninfected cattle that are also undetectable in the B. taurus reference genome. Using whole-genome sequencing data of cattle from five breeds, we show that reads which were previously misaligned against the Bos taurus reference genome now align accurately to the pangenome sequences. This enables us to discover 83,250 polymorphic sites that segregate within and between breeds of cattle and capture genetic differentiation across breeds. Our work makes a so-far unused source of variation amenable to genetic investigations and provides methods and a framework for establishing and exploiting a more diverse reference genome.
Collapse
|
63
|
Martin FJ, Gall A, Szpak M, Flicek P. Accessing Livestock Resources in Ensembl. Front Genet 2021; 12:650228. [PMID: 33995484 PMCID: PMC8115729 DOI: 10.3389/fgene.2021.650228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
Genome assembly is cheaper, more accurate and more automated than it has ever been. This is due to a combination of more cost-efficient chemistries, new sequencing technologies and better algorithms. The livestock community has been at the forefront of this new wave of genome assembly, generating some of the highest quality vertebrate genome sequences. Ensembl's goal is to add functional and comparative annotation to these genomes, through our gene annotation, genomic alignments, gene trees, regulatory, and variation data. We run computationally complex analyses in a high throughput and consistent manner to help accelerate downstream science. Our livestock resources are continuously growing in both breadth and depth. We annotate reference genome assemblies for newly sequenced species and regularly update annotation for existing genomes. We are the only major resource to support the annotation of breeds and other non-reference assemblies. We currently provide resources for 13 pig breeds, maternal and paternal haplotypes for hybrid cattle and various other non-reference or wild type assemblies for livestock species. Here, we describe the livestock data present in Ensembl and provide protocols for how to view data in our genome browser, download via it our FTP site, manipulate it via our tools and interact with it programmatically via our REST API.
Collapse
Affiliation(s)
- Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Michal Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| |
Collapse
|
64
|
Donaldson B, Villagomez DAF, King WA. Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective. Animals (Basel) 2021; 11:1257. [PMID: 33925534 PMCID: PMC8146943 DOI: 10.3390/ani11051257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.
Collapse
Affiliation(s)
- Brendan Donaldson
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | | | - W. Allan King
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Karyotekk Inc., Box 363 OVC, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
65
|
Zhou R, Li ST, Yao WY, Xie CD, Chen Z, Zeng ZJ, Wang D, Xu K, Shen ZJ, Mu Y, Bao W, Jiang W, Li R, Liang Q, Li K. The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication. Mol Ecol Resour 2021; 21:2077-2092. [PMID: 33825319 DOI: 10.1111/1755-0998.13396] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/17/2021] [Accepted: 03/29/2021] [Indexed: 01/27/2023]
Abstract
There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.
Collapse
Affiliation(s)
- Rong Zhou
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shang-Tong Li
- National Institute of Biological Sciences (NIBS, Beijing, China
| | - Wen-Ye Yao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chun-Di Xie
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Zhi-Jie Zeng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Di Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhao-Ji Shen
- Guangdong Provincial key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,Fulcrum gene science and technology (Beijing) Ltd, Beijing, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
66
|
A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nat Commun 2021; 12:2217. [PMID: 33850120 PMCID: PMC8044108 DOI: 10.1038/s41467-021-22448-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Although major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model. Here, we systematically characterize cis-regulatory elements and their functions in 12 diverse tissues from four pig breeds by adopting similar strategies as the ENCODE and Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, and ChIP-seq. In total, we generate 199 datasets and identify more than 220,000 cis-regulatory elements in the pig genome. Surprisingly, we find higher conservation of cis-regulatory elements between human and pig genomes than those between human and mouse genomes. Furthermore, the differences of topologically associating domains between the pig and human genomes are associated with morphological evolution of the head and face. Beyond generating a major new benchmark resource for pig epigenetics, our study provides basic comparative epigenetic data relevant to using pigs as models in human biomedical research.
Collapse
|
67
|
Kulus M, Kranc W, Wojtanowicz-Markiewicz K, Celichowski P, Światły-Błaszkiewicz A, Matuszewska E, Sujka-Kordowska P, Konwerska A, Zdun M, Bryl R, Wieczorkiewicz M, Kulus J, Stelmach B, Stefańska K, Budna-Tukan J, Petitte JN, Mozdziak P, Ratajczak K, Matysiak J, Jaśkowski JM, Nowicki M, Kempisty B. New Gene Markers Expressed in Porcine Oviductal Epithelial Cells Cultured Primary In Vitro Are Involved in Ontological Groups Representing Physiological Processes of Porcine Oocytes. Int J Mol Sci 2021; 22:ijms22042082. [PMID: 33669854 PMCID: PMC7923230 DOI: 10.3390/ijms22042082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
Changes that occur within oviducts after fertilization are dependent on post-ovulation events, including oocyte-oviduct interactions. Although general processes are well-defined, the molecular basis are poorly understood. Recently, new marker genes involved in ‘cell development’, ‘cell growth’, ‘cell differentiation’ and ‘cell maturation’ processes have been identified in porcine oocytes. The aim of the study was to assess the expression profile of genes in primary in vitro cultured oviductal epithelial cells (OECs), clustered in Gene Ontology groups which enveloped markers also identified in porcine oocytes. OECs (from 45 gilts) were surgically removed and cultured in vitro for ≤ 30 days, and then subjected to molecular analyses. The transcriptomic and proteomic profiles of cells cultured during 7, 15 and 30 days were investigated. Additionally, morphological/histochemical analyzes were performed. The results of genes expression profiles were validated after using RT-qPCR. The results showed a significant upregulation of UNC45B, NOX4, VLDLR, ITGB3, FMOD, SGCE, COL1A2, LOX, LIPG, THY1 and downregulation of SERPINB2, CD274, TXNIP, CELA1, DDX60, CRABP2, SLC5A1, IDO1, ANPEP, FST. Detailed knowledge of the molecular pathways occurring in the OECs and the gametes that contact them may contribute both to developments of basic science of physiology, and new possibilities in advanced biotechnology of assisted reproduction.
Collapse
Affiliation(s)
- Magdalena Kulus
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.W.-M.); (K.R.)
| | - Wiesława Kranc
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (W.K.); (R.B.)
| | - Katarzyna Wojtanowicz-Markiewicz
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.W.-M.); (K.R.)
| | - Piotr Celichowski
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.C.); (P.S.-K.); (A.K.); (K.S.); (J.B.-T.); (M.N.)
| | - Agata Światły-Błaszkiewicz
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 60-780 Poznan, Poland; (A.Ś.-B.); (E.M.); (J.M.)
| | - Eliza Matuszewska
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 60-780 Poznan, Poland; (A.Ś.-B.); (E.M.); (J.M.)
| | - Patrycja Sujka-Kordowska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.C.); (P.S.-K.); (A.K.); (K.S.); (J.B.-T.); (M.N.)
- Department of Anatomy and Histology, University of Zielona Gora, 65-046 Zielona Gora, Poland
| | - Aneta Konwerska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.C.); (P.S.-K.); (A.K.); (K.S.); (J.B.-T.); (M.N.)
| | - Maciej Zdun
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.Z.); (M.W.)
| | - Rut Bryl
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (W.K.); (R.B.)
| | - Maria Wieczorkiewicz
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.Z.); (M.W.)
| | - Jakub Kulus
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (J.K.); (J.M.J.)
| | - Bogusława Stelmach
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, 60-535 Poznan, Poland;
| | - Katarzyna Stefańska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.C.); (P.S.-K.); (A.K.); (K.S.); (J.B.-T.); (M.N.)
| | - Joanna Budna-Tukan
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.C.); (P.S.-K.); (A.K.); (K.S.); (J.B.-T.); (M.N.)
| | - James N. Petitte
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA; (J.N.P.); (P.M.)
| | - Paul Mozdziak
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA; (J.N.P.); (P.M.)
| | - Kornel Ratajczak
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.W.-M.); (K.R.)
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 60-780 Poznan, Poland; (A.Ś.-B.); (E.M.); (J.M.)
| | - Jędrzej M. Jaśkowski
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (J.K.); (J.M.J.)
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.C.); (P.S.-K.); (A.K.); (K.S.); (J.B.-T.); (M.N.)
| | - Bartosz Kempisty
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.W.-M.); (K.R.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (W.K.); (R.B.)
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.C.); (P.S.-K.); (A.K.); (K.S.); (J.B.-T.); (M.N.)
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA; (J.N.P.); (P.M.)
- Correspondence:
| |
Collapse
|
68
|
Du H, Zheng X, Zhao Q, Hu Z, Wang H, Zhou L, Liu JF. Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of Meishan Pigs by Whole Genome Sequencing. Front Genet 2021; 12:550676. [PMID: 33613628 PMCID: PMC7890942 DOI: 10.3389/fgene.2021.550676] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 01/15/2021] [Indexed: 12/17/2022] Open
Abstract
Structural variants (SVs) represent essential forms of genetic variation, and they are associated with various phenotypic traits in a wide range of important livestock species. However, the distribution of SVs in the pig genome has not been fully characterized, and the function of SVs in the economic traits of pig has rarely been studied, especially for most domestic pig breeds. Meishan pig is one of the most famous Chinese domestic pig breeds, with excellent reproductive performance. Here, to explore the genome characters of Meishan pig, we construct an SV map of porcine using whole-genome sequencing data and report 33,698 SVs in 305 individuals of 55 globally distributed pig breeds. We perform selective signature analysis using these SVs, and a number of candidate variants are successfully identified. Especially for the Meishan pig, 64 novel significant selection regions are detected in its genome. A 140-bp deletion in the Indoleamine 2,3-Dioxygenase 2 (IDO2) gene, is shown to be associated with reproduction traits in Meishan pig. In addition, we detect two duplications only existing in Meishan pig. Moreover, the two duplications are separately located in cytochrome P450 family 2 subfamily J member 2 (CYP2J2) gene and phospholipase A2 group IVA (PLA2G4A) gene, which are related to the reproduction trait. Our study provides new insights into the role of selection in SVs' evolution and how SVs contribute to phenotypic variation in pigs.
Collapse
Affiliation(s)
- Heng Du
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qiqi Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengzheng Hu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haifei Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
69
|
Du H, Diao C, Zhao P, Zhou L, Liu JF. Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads. Brief Bioinform 2021; 22:6082823. [PMID: 33429431 DOI: 10.1093/bib/bbaa399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/20/2020] [Accepted: 12/08/2020] [Indexed: 11/12/2022] Open
Abstract
With the rapid progress of sequencing technologies, various types of sequencing reads and assembly algorithms have been designed to construct genome assemblies. Although recent studies have attempted to evaluate the appropriate type of sequencing reads and algorithms for assembling high-quality genomes, it is still a challenge to set the correct combination for constructing animal genomes. Here, we present a comparative performance assessment of 14 assembly combinations-9 software programs with different short and long reads of Duroc pig. Based on the results of the optimization process for genome construction, we designed an integrated hybrid de novo assembly pipeline, HSCG, and constructed a draft genome for Duroc pig. Comparison between the new genome and Sus scrofa 11.1 revealed important breakpoints in two S. scrofa 11.1 genes. Our findings may provide new insights into the pan-genome analysis studies of agricultural animals, and the integrated assembly pipeline may serve as a guide for the assembly of other animal genomes.
Collapse
Affiliation(s)
- Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
70
|
Wang Y, Bi D, Qin G, Song R, Yao J, Cao C, Zheng Q, Hou N, Wang Y, Zhao J. Cytosine Base Editor (hA3A-BE3-NG)-Mediated Multiple Gene Editing for Pyramid Breeding in Pigs. Front Genet 2020; 11:592623. [PMID: 33304388 PMCID: PMC7701296 DOI: 10.3389/fgene.2020.592623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/26/2020] [Indexed: 12/26/2022] Open
Abstract
Pig is an important agricultural economic animal, providing large amount of meat products. With the development of functional genomics and bioinformatics, lots of genes and functional single nucleotide polymorphisms (SNPs) related to disease resistance and (or) economic traits in pigs have been identified, which provides the targets for genetic improvement by genome editing. Base editors (BEs), combining Cas9 nickase and cytidine or adenine deaminase, achieve all four possible transition mutations (C-to-T, A-to-G, T-to-C, and G-to-A) efficiently and accurately without double strand breaks (DSBs) under the protospacer adjacent motif (PAM) sequence of NGG. However, the NGG PAM in canonical CRISPR-Cas9 can only cover approximately 8.27% in the whole genome which limits its broad application. In the current study, hA3A-BE3-NG system was constructed with the fusion of SpCas9-NG variant and hA3A-BE3 to create C-to-T conversion at NGN PAM sites efficiently. The editing efficiency and scope of hA3A-BE3-NG were confirmed in HEK293T cells and porcine fetal fibroblast (PFF) cells. Results showed that the efficiency of hA3A-BE3-NG was much higher than that of hA3A-BE3 on NGH (H = A, C, or T) PAM sites (21.27 vs. 2.81% at average). Further, nonsense and missense mutations were introduced efficiently and precisely via hA3A-BE3-NG in multiple pig economic trait-related genes (CD163, APN, MSTN, and MC4R) in PFF cells by one transfection. The current work indicates the potential applications of hA3A-BE3-NG for pyramid breeding studies in livestock.
Collapse
Affiliation(s)
- Yu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dengfeng Bi
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Science and Technology of China, Hefei, China
| | - Guosong Qin
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ruigao Song
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Yao
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chunwei Cao
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiantao Zheng
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Naipeng Hou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanfang Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jianguo Zhao
- State Key Laboratory of Stem cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
71
|
Lee J, Park N, Lee D, Kim J. Evolutionary and Functional Analysis of Korean Native Pig Using Single Nucleotide Polymorphisms. Mol Cells 2020; 43:728-738. [PMID: 32868490 PMCID: PMC7468586 DOI: 10.14348/molcells.2020.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 11/27/2022] Open
Abstract
Time and cost-effective production of next-generation sequencing data has enabled the performance of population-scale comparative and evolutionary studies for various species, which are essential for obtaining the comprehensive insight into molecular mechanisms underlying species- or breed-specific traits. In this study, the evolutionary and functional analysis of Korean native pig (KNP) was performed using single nucleotide polymorphism (SNP) data by comparative and population genomic approaches with six different mammalian species and five pig breeds. We examined the evolutionary history of KNP SNPs, and the specific genes of KNP based on the uniqueness of non-synonymous SNPs among the used species and pig breeds. We discovered the evolutionary trajectory of KNP SNPs within the used mammalian species as well as pig breeds. We also found olfaction-associated functions that have been characterized and diversified during evolution, and quantitative trait loci associated with the unique traits of KNP. Our study provides new insight into the evolution of KNP and serves as a good example for a better understanding of domestic animals in terms of evolution and domestication using the combined approaches of comparative and population genomics.
Collapse
Affiliation(s)
- Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
- These authors contributed equally to this work.
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
- These authors contributed equally to this work.
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| |
Collapse
|
72
|
Li Z, Simianer H. Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction. PLoS Genet 2020; 16:e1008995. [PMID: 32833967 PMCID: PMC7470747 DOI: 10.1371/journal.pgen.1008995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 09/03/2020] [Accepted: 07/15/2020] [Indexed: 11/19/2022] Open
Abstract
Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic prediction. A Saccharomyces cerevisiae dataset with whole-genome SNPs, pan-genomic ORFs, and the copy numbers of those ORFs is used to test the effectiveness of ORF data as a predictor in three prediction models for 35 traits. Our results show that the ORF-based heritability can capture more genetic effects than SNP-based heritability for all traits. Compared to SNP-based genomic prediction (GBLUP), pan-genomic ORF-based genomic prediction (OBLUP) is distinctly more accurate for all traits, and the predictive abilities on average are more than doubled across all traits. For four traits, the copy number of ORF-based prediction(CBLUP) is more accurate than OBLUP. When using different numbers of isolates in training sets in ORF-based prediction, the predictive abilities for all traits increased as more isolates are added in the training sets, suggesting that with very large training sets the prediction accuracy will be in the range of the square root of the heritability. We conclude that pan-genomic ORFs have the potential to be a supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction.
Collapse
Affiliation(s)
- Zhengcao Li
- Animal Breeding and Genetics Group, Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- * E-mail:
| | - Henner Simianer
- Animal Breeding and Genetics Group, Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| |
Collapse
|
73
|
Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z. Pan-Genome of Wild and Cultivated Soybeans. Cell 2020; 182:162-176.e13. [PMID: 32553274 DOI: 10.1016/j.cell.2020.05.023] [Citation(s) in RCA: 403] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022]
Abstract
Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.
Collapse
Affiliation(s)
- Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengcheng Li
- Berry Genomics Corporation, Beijing 100015, China
| | - Yanting Shen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hua Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo-An Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Zhi Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao Shi
- Berry Genomics Corporation, Beijing 100015, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yan Li
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
74
|
Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience 2020; 9:5858065. [PMID: 32543654 PMCID: PMC7448572 DOI: 10.1093/gigascience/giaa051] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 01/05/2023] Open
Abstract
Background The domestic pig (Sus scrofa) is important both as a food source and
as a biomedical model given its similarity in size, anatomy, physiology, metabolism,
pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a
purebred Duroc female pig established using older clone-based sequencing methods was
incomplete, and unresolved redundancies, short-range order and orientation errors, and
associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created
with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the
same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0).
Both assemblies are of substantially higher (>90-fold) continuity and accuracy than
Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read
assemblies provide an unprecedented view of the genetic make-up of this important
agricultural and biomedical model species. We propose that the improved Duroc assembly
(Sscrofa11.1) become the reference genome for genomic research in pigs.
Collapse
Affiliation(s)
- Amanda Warr
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Nabeel Affara
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Hamid Beiki
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lel Eory
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Heather A Finlayson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Carlos G Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Richard Hall
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | | | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.,Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane QLD 4104, Australia
| | - Osagie Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kristi Kim
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Haibou Liu
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Nancy Manchanda
- Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Dan J Nonneman
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Gary A Rohrer
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | - Laurie A Rund
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Carole A Sargent
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | | | - Ben M Skinner
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Richard Talbot
- Edinburgh Genomics, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Elizabeth Tseng
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Christopher K Tuggle
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA.,Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Timothy P L Smith
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| |
Collapse
|
75
|
Diffusion Kurtosis Imaging of Leptin Intervention in Early Hypoxic-Ischemic Brain Edema. Neuroscience 2020; 431:176-183. [PMID: 32068083 DOI: 10.1016/j.neuroscience.2020.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 02/07/2020] [Indexed: 11/22/2022]
Abstract
The role of leptin in neuroprotection has recently been recognized. However, there are few reports on the use of imaging methods to dynamically evaluate the neuroprotection role of leptin. Diffusion kurtosis imaging (DKI), which is a method used to measure non-Gaussian water diffusion, can reflect the real water diffusion in brain tissues. In this study, a newborn piglet model was used to dynamically evaluate the leptin intervention in early hypoxic-ischemic brain edema via DKI. Thirty-two Yorkshire newborn piglets were divided into three groups: the hypoxic-ischemic encephalopathy (HIE) group, the leptin group, and the control group. DKI scanning was performed at time points of 3, 6, 9, 12, 16, and 24 h after hypoxic-ischemic exposure. After scanning, arterial blood was extracted from all piglets to measure NSE and S100β levels. Then, the brain was completely extracted for pathological examination. In the lesion areas, the MK, Ka, and Kr values in the leptin group were significantly lower than those in the HIE group, the MD, Da, and Dr values showed an opposite trend. The lesion areas in the leptin group were smaller than those of in the HIE group. In addition, the pathological results showed that less cell and organelle injury occurred in the leptin group. Our findings indicate that leptin can effectively reduce hypoxic-ischemic brain edema, and DKI can be more sensitive than conventional diffusivity metrics for visualizing the microstructural changes of HIE. This provides a new clue for the treatment and evaluation of HIE.
Collapse
|
76
|
Golicz AA, Bayer PE, Bhalla PL, Batley J, Edwards D. Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications. Trends Genet 2019; 36:132-145. [PMID: 31882191 DOI: 10.1016/j.tig.2019.11.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/09/2019] [Accepted: 11/12/2019] [Indexed: 02/01/2023]
Abstract
The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities.
Collapse
Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia.
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
| |
Collapse
|
77
|
Møhlenberg M, Terczynska-Dyla E, Thomsen KL, George J, Eslam M, Grønbæk H, Hartmann R. The role of IFN in the development of NAFLD and NASH. Cytokine 2019; 124:154519. [DOI: 10.1016/j.cyto.2018.08.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 02/07/2023]
|
78
|
Lin Y, Tang Q, Li Y, He M, Jin L, Ma J, Wang X, Long K, Huang Z, Li X, Gu Y, Li M. Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs. PeerJ 2019; 7:e8009. [PMID: 31737448 PMCID: PMC6855203 DOI: 10.7717/peerj.8009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/07/2019] [Indexed: 11/20/2022] Open
Abstract
Crossbreeding is widely used aimed at improving crossbred performance for poultry and livestock. Alleles that are specific to different purebreds will yield a large number of heterozygous single-nucleotide polymorphisms (SNPs) in crossbred individuals, which are supposed to have the power to alter gene function or regulate gene expression. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is generally used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, little is known about the breed-of-origin effects from purebreds on DLY pigs. In this study, we first estimated the distribution of heterozygous SNPs in three kinds of three-way crossbred pigs via whole genome sequencing data originated from three purebreds. The result suggested that DLY is a more effective strategy for three-way crossbreeding as it could yield more stably inherited heterozygous SNPs. We then sequenced a DLY pig family and identified 95, 79, 132 and 42 allele-specific expression (ASE) genes in adipose, heart, liver and skeletal muscle, respectively. Principal component analysis and unrestricted clustering analyses revealed the tissue-specific pattern of ASE genes, indicating the potential roles of ASE genes for development of DLY pigs. In summary, our findings provided a lot of candidate SNP markers and ASE genes for DLY three-way crossbreeding system, which may be valuable for pig breeding and production in the future.
Collapse
Affiliation(s)
- Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yiren Gu
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| |
Collapse
|
79
|
‘Cell cycle’ and ‘cell death’- related genes are differentially expressed during long – term in vitro real-time cultivation of porcine oviductal epithelial cells. ACTA ACUST UNITED AC 2019. [DOI: 10.2478/acb-2019-0012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Abstract
Alterations in cells depend on their genetic material, its activation and translation of the products. The genes responsible for the cell cycle processes and apoptosis of porcine oviductal cells have been presented in our study. The processes occurring in the reproductive system of females are extremely complex and require in-depth knowledge. Thanks to in vitro studies on the fallopian tube epithelium cells, we can get closer to understanding the biochemical and morphological changes occurring in mammalian organisms. Our research was conducted on fallopian tubes obtained from commercially bred pigs and its aim was to assess the expression profile of genes responsible for the most important processes of cellular life. Cell cultures were carried out for 30 days, with the obtained cells subjected to molecular analysis. We have shown significant regulation of “cell death” and “cell cycle” genes, some of which are related to the reproductive system. The alterations in transcriptomic profile and mutual relations between the genes were analyzed and related to the literature findings. The knowledge gained could help in identifying new potential markers of the in vitro occurrence of processes described by the ontology groups of interest.
Running title: pig, oocytes, microarray assays, in vitro maturation (IVM)
Collapse
|
80
|
Zhang L, Huang Y, Wang M, Guo Y, Liang J, Yang X, Qi W, Wu Y, Si J, Zhu S, Li Z, Li R, Shi C, Wang S, Zhang Q, Tang Z, Wang L, Li K, Fei JF, Lan G. Development and Genome Sequencing of a Laboratory-Inbred Miniature Pig Facilitates Study of Human Diabetic Disease. iScience 2019; 19:162-176. [PMID: 31376679 PMCID: PMC6677790 DOI: 10.1016/j.isci.2019.07.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/11/2019] [Accepted: 07/13/2019] [Indexed: 01/10/2023] Open
Abstract
Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism.
Collapse
Affiliation(s)
- Li Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuemeng Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Meng Wang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Yafen Guo
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
| | - Xiurong Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenjing Qi
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yanjun Wu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinglei Si
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Siran Zhu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhe Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Chao Shi
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Shuo Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qunjie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Zhonglin Tang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ji-Feng Fei
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
| |
Collapse
|
81
|
|
82
|
Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data. SCIENCE CHINA-LIFE SCIENCES 2019; 63:750-763. [PMID: 31290097 DOI: 10.1007/s11427-019-9551-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/03/2019] [Indexed: 01/23/2023]
Abstract
Pigs were domesticated independently in the Near East and China, indicating that a single reference genome from one individual is unable to represent the full spectrum of divergent sequences in pigs worldwide. Therefore, 12 de novo pig assemblies from Eurasia were compared in this study to identify the missing sequences from the reference genome. As a result, 72.5 Mb of non-redundant sequences (∼3% of the genome) were found to be absent from the reference genome (Sscrofa11.1) and were defined as pan-sequences. Of the pan-sequences, 9.0 Mb were dominant in Chinese pigs, in contrast with their low frequency in European pigs. One sequence dominant in Chinese pigs contained the complete genic region of the tazarotene-induced gene 3 (TIG3) gene which is involved in fatty acid metabolism. Using flanking sequences and Hi-C based methods, 27.7% of the sequences could be anchored to the reference genome. The supplementation of these sequences could contribute to the accurate interpretation of the 3D chromatin structure. A web-based pan-genome database was further provided to serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.
Collapse
|
83
|
Walker ME, Matthan NR, Lamon-Fava S, Solano-Aguilar G, Jang S, Lakshman S, Molokin A, Urban JF, Faits T, Johnson WE, Lichtenstein AH. A Western-Type Dietary Pattern Induces an Atherogenic Gene Expression Profile in the Coronary Arteries of the Ossabaw Pig. Curr Dev Nutr 2019; 3:nzz023. [PMID: 31049488 PMCID: PMC6488722 DOI: 10.1093/cdn/nzz023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/27/2019] [Accepted: 03/28/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Current cardiovascular risk reduction guidance focuses on shifts in dietary patterns, rather than single foods or nutrients. Experimental studies are needed to identify the mechanisms by which food-based diets affect the development and progression of atherosclerosis. OBJECTIVES The aim of this study was to investigate the effect of 2 food-based dietary patterns and statin therapy on the transcriptome of the left anterior descending coronary artery of the Ossabaw pig. METHODS Pigs were randomly assigned to 1 of 4 groups and fed isocaloric diets for 6 mo; Heart Healthy-style diet (HHD) (high in unsaturated fat, unrefined grain, fruits/vegetables) or Western-style diet (WD) (high in saturated fat, cholesterol, refined grain), with or without atorvastatin. A 2-factor edge R analysis was used to determine differential gene expression in the left anterior descending coronary artery. RESULTS Relative to the HHD, the WD resulted in the differential expression of 143 genes, of which 139 genes were upregulated and 4 genes were downregulated (all log fold change ≥0.6, false discovery rate <0.10). The WD, compared with the HHD, resulted in the statistically significant upregulation of 8 atherosclerosis-associated pathways implicated in immune and inflammatory processes. There were no genes with significant differential expression attributable to statin therapy. CONCLUSIONS These data suggest that a WD induces alterations in the transcriptome of the coronary artery consistent with an inflammatory atherogenic phenotype in the Ossabaw pig with no significant modification by concurrent statin therapy.
Collapse
Affiliation(s)
- Maura E Walker
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Nirupa R Matthan
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Stefania Lamon-Fava
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Gloria Solano-Aguilar
- USDA, ARS, Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, MD
| | - Saebyeol Jang
- USDA, ARS, Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, MD
| | - Sukla Lakshman
- USDA, ARS, Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, MD
| | - Aleksey Molokin
- USDA, ARS, Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, MD
| | - Joseph F Urban
- USDA, ARS, Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, MD
| | - Tyler Faits
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - W Evan Johnson
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Alice H Lichtenstein
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA
| |
Collapse
|
84
|
Wang W, Zhang X, Zhou X, Zhang Y, La Y, Zhang Y, Li C, Zhao Y, Li F, Liu B, Jiang Z. Deep Genome Resequencing Reveals Artificial and Natural Selection for Visual Deterioration, Plateau Adaptability and High Prolificacy in Chinese Domestic Sheep. Front Genet 2019; 10:300. [PMID: 31001329 PMCID: PMC6454055 DOI: 10.3389/fgene.2019.00300] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/19/2019] [Indexed: 01/02/2023] Open
Abstract
Sheep were one of the earliest domesticated animals. Both artificial and natural selection during domestication has resulted in remarkable changes in behavioral, physiological, and morphological phenotypes; however, the genetic mechanisms underpinning these changes remain unclear, particularly for indigenous Chinese sheep. In the present study, we performed pooled whole-genome resequencing of 338 sheep from five breeds representative of indigenous Chinese breeds and compared them to the wild ancestors of domestic sheep (Asian mouflon, Ovis orientalis) for detection of genome-wide selective sweeps. Comparative genomic analysis between domestic sheep and Asian mouflon showed that selected regions were enriched for genes involved in bone morphogenesis, growth regulation, and embryonic and neural development in domestic sheep. Moreover, we identified several vision-associated genes with funtional mutations, such as PDE6B (c.G2994C/p.A982P and c.C2284A/p.L762M mutations), PANK2, and FOXC1/GMSD in all five Chinese native breeds. Breed-specific selected regions were determined including genes such as CYP17 for hypoxia adaptability in Tibetan sheep and DNAJB5 for heat tolerance in Duolang sheep. Our findings provide insights into the genetic mechanisms underlying important phenotypic changes that have occurred during sheep domestication and subsequent selection.
Collapse
Affiliation(s)
- Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Yangzi Zhang
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Yongfu La
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yu Zhang
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Youzhang Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| |
Collapse
|
85
|
Ma X, Wang Z, Li W, Zhang Y, Zhou X, Liu Y, Ren Z, Pei X, Zhou K, Zhang W, He K, Zhang F, Liu J, Ma W, Xiao G, Yang D. Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:762-775. [PMID: 30220108 PMCID: PMC6419577 DOI: 10.1111/pbi.13013] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 05/21/2023]
Abstract
Upland cotton (Gossypium hirsutum) is the world's largest source of natural fibre and dominates the global textile industry. Hybrid cotton varieties exhibit strong heterosis that confers high fibre yields, yet the genome-wide effects of artificial selection that have influenced Upland cotton during its breeding history are poorly understood. Here, we resequenced Upland cotton genomes and constructed a variation map of an intact breeding pedigree comprising seven elite and 19 backbone parents. Compared to wild accessions, the 26 pedigree accessions underwent strong artificial selection during domestication that has resulted in reduced genetic diversity but stronger linkage disequilibrium and higher extents of selective sweeps. In contrast to the backbone parents, the elite parents have acquired significantly improved agronomic traits, with an especially pronounced increase in the lint percentage. Notably, identify by descent (IBD) tracking revealed that the elite parents inherited abundant beneficial trait segments and loci from the backbone parents and our combined analyses led to the identification of a core genomic segment which was inherited in the elite lines from the parents Zhong 7263 and Ejing 1 and that was strongly associated with lint percentage. Additionally, SNP correlation analysis of this core segment showed that a non-synonymous SNP (A-to-G) site in a gene encoding the cell wall-associated receptor-like kinase 3 (GhWAKL3) protein was highly correlated with increased lint percentage. Our results substantially increase the valuable genomics resources available for future genetic and functional genomics studies of cotton and reveal insights that will facilitate yield increases in the molecular breeding of cotton.
Collapse
Affiliation(s)
- Xiongfeng Ma
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhenyu Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Wei Li
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Yuzhou Zhang
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical ChemistryNational Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of ChinaCollege of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Xiaojian Zhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Yangai Liu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhongying Ren
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Xiaoyu Pei
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Kehai Zhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Wensheng Zhang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Kunlun He
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Fei Zhang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Junfang Liu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Wenyu Ma
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Guanghui Xiao
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical ChemistryNational Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of ChinaCollege of Life SciencesShaanxi Normal UniversityXi'anChina
- Present address:
College of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Daigang Yang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
- Present address:
Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| |
Collapse
|
86
|
Taylor ME, Snelling T, Smith DF, Drickamer K. Absence of a human ortholog of rodent Kupffer cell galactose-binding receptor encoded by the CLEC4f gene. Glycobiology 2019; 29:332-345. [PMID: 30590594 PMCID: PMC6422238 DOI: 10.1093/glycob/cwy113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 01/21/2023] Open
Abstract
The murine CLEC4f gene encodes the Kupffer cell receptor, a galactose-binding receptor containing a C-type carbohydrate-recognition domain. Orthologs have been identified in nearly 100 species. The receptors from rat and mouse have previously been characterized and data presented here show that functional CLEC4f protein is expressed in domestic cattle (Bos taurus). However, the human CLEC4f gene does not encode a functional receptor because a mutation in the splice acceptor site of the final exon prevents appropriate splicing and a missense mutation disrupts the sugar-binding site. Transcriptomic and PCR analysis of transcripts confirms the absence of a spliced transcript containing the final exon and only background levels of transcripts are detected in human tissues. These mutations are also present in the CLEC4f gene in Neanderthals. In contrast to humans, closely related species, including chimpanzees, do have CLEC4f genes that encode full-length receptors. Affinity chromatography and glycan array results demonstrate that the chimpanzee, bovine and murine proteins all bind to galactose, but they show preferences for different subsets of galactose-containing glycans. In non-human primates, the receptor is expressed in spleen rather than in liver. The results indicate that the CLEC4f protein probably has distinct functions in different species. Absence of the receptor precludes using it for targeting of glycoconjugates to cells in human liver. The fact that CLEC4f protein is expressed in spleen in non-human primates and the close evolutionary relationship of the CLEC4f protein to langerin (CD207) suggest that it may function in the immune system, possibly as a pathogen receptor.
Collapse
Affiliation(s)
| | - Tom Snelling
- Department of Life Sciences, Imperial College, London, UK
| | - David F Smith
- Emory Comprehensive Glycomics Core, Emory University, Atlanta, GA, USA
| | - Kurt Drickamer
- Department of Life Sciences, Imperial College, London, UK
| |
Collapse
|
87
|
Ye J, He J, Li N. Molecular identification and characterization of pig's Cdh16 gene. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2018.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
88
|
The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcγR) in the Göttingen minipig. Immunogenetics 2018; 71:123-136. [PMID: 30564855 PMCID: PMC6327001 DOI: 10.1007/s00251-018-01099-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/24/2018] [Indexed: 12/21/2022]
Abstract
Safety and efficacy of therapeutic antibodies are often dependent on their interaction with Fc receptors for IgG (FcγRs). The Göttingen minipig represents a valuable species for biomedical research but its use in preclinical studies with therapeutic antibodies is hampered by the lack of knowledge about the porcine FcγRs. Genome analysis and sequencing now enabled the localization of the previously described FcγRIIIa in the orthologous location to human FCGR3A. In addition, we identified nearby the gene coding for the hitherto undescribed putative porcine FcγRIIa. The 1′241 bp long FCGR2A cDNA translates to a 274aa transmembrane protein containing an extracellular region with high similarity to human and cattle FcγRIIa. Like in cattle, the intracellular part does not contain an immunoreceptor tyrosine-based activation motif (ITAM) as in human FcγRIIa. Flow cytometry of the whole blood and single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) of Göttingen minipigs revealed the expression profile of all porcine FcγRs which is compared to human and mouse. The new FcγRIIa is mainly expressed on platelets making the minipig a good model to study IgG-mediated platelet activation and aggregation. In contrast to humans, minipig blood monocytes were found to express inhibitory FcγRIIb that could lead to the underestimation of FcγR-mediated effects of monocytes observed in minipig studies with therapeutic antibodies.
Collapse
|
89
|
Wang H, Feng H, Sun J, Zhou Y, Zhu G, Wu S, Bao W. Age-associated changes in DNA methylation and expression of the TNFα gene in pigs. Genes Genet Syst 2018; 93:191-198. [PMID: 30473548 DOI: 10.1266/ggs.18-00016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA methylation is an important mediator of gene expression regulation and has been shown to be closely linked to aging. Immune-related genes tend to be influenced by DNA methylation at different ages. To explore DNA methylation changes in the porcine TNFα gene and analyze their potential effects on gene expression, we measured the methylation level of the TNFα promoter and TNFα mRNA expression in the spleen of Meishan piglets at six developmental stages (1, 7, 14, 21, 28 and 35 days old) by bisulfite sequencing PCR and quantitative PCR. The results revealed a trend for TNFα promoter methylation level to increase and mRNA expression to decrease with age. Correlation analysis showed a significant negative association between methylation level and mRNA expression (Pearson's r = -0.775, P = 4.87E-07). In addition, the transcription factor Sp1 was revealed to bind with the TNFα promoter and regulate TNFα expression. DNA methylation in the TNFα promoter was found to decrease the promoter's activity, and methylation inhibition could enhance the expression level of TNFα, providing functional evidence that promoter methylation controls TNFα expression. Together, our data provide insights into age-associated changes in promoter methylation of the TNFα gene in the spleen and contribute to our understanding of regulatory mechanisms for TNFα expression in the immune system of pigs.
Collapse
Affiliation(s)
- Haifei Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University
| | - Haiyue Feng
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University
| | - Juan Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University
| | - Yajing Zhou
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University.,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University.,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University
| |
Collapse
|
90
|
Zhao P, Yu Y, Feng W, Du H, Yu J, Kang H, Zheng X, Wang Z, Liu GE, Ernst CW, Ran X, Wang J, Liu JF. Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization. Gigascience 2018; 7:5001425. [PMID: 29790964 PMCID: PMC6007440 DOI: 10.1093/gigascience/giy058] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
Background Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with its unique features is still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to the phenotypic traits of Meishan via large-scale sequencing. Results We found that the unique domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures, during which 300 protein-coding genes have underwent positive selection. Notably, enrichment of the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with the high fertility of Meishan pigs. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling, which may have resulted in the wrinkled skin and face of Meishan pigs. Particularly, three population-specific synonymous single-nucleotide variants occurred in PYROXD1, MC1R, and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs. Conclusions These findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs and offer a plausible method for their utilization of Meishan pigs as valuable genetic resources in pig breeding and as an animal model for human wrinkled skin disease research.
Collapse
Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jian Yu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Huimin Kang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhiquan Wang
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, T6G 2C8, Canada
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705-2350, USA
| | | | - Xueqin Ran
- School of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jiafu Wang
- School of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
91
|
Tang Q, Gu Y, Zhou X, Jin L, Guan J, Liu R, Li J, Long K, Tian S, Che T, Hu S, Liang Y, Yang X, Tao X, Zhong Z, Wang G, Chen X, Li D, Ma J, Wang X, Mai M, Jiang A, Luo X, Lv X, Gladyshev VN, Li X, Li M. Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives. Gigascience 2018; 6:1-9. [PMID: 29149296 PMCID: PMC5729692 DOI: 10.1093/gigascience/gix105] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 10/24/2017] [Indexed: 01/22/2023] Open
Abstract
Background Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. Findings We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression-based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. Conclusions These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments.
Collapse
Affiliation(s)
- Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115 USA
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiuqiang Guan
- Yak Research Institute, Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Rui Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Kereng Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuemei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Zhijun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Guosong Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Department of Animal Science, Texas A & M University, College Station, Texas, 77843 USA
| | - Xiaohui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Miaomiao Mai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - An'an Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolin Luo
- Yak Research Institute, Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xuebin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115 USA
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
92
|
Chen M, Wang J, Wang Y, Wu Y, Fu J, Liu JF. Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle. BMC Genet 2018; 19:31. [PMID: 29776331 PMCID: PMC5960162 DOI: 10.1186/s12863-018-0622-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 04/30/2018] [Indexed: 12/31/2022] Open
Abstract
Background Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. Result In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure. Conclusions Our results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies. Electronic supplementary material The online version of this article (10.1186/s12863-018-0622-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Minhui Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ying Wu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jinluan Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
93
|
Abstract
Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar. A total of 15,040 lncRNA transcripts were identified among these samples. We found that the temporal expression pattern of lncRNAs was more restricted than observed for protein-coding genes. Time-series analysis showed two large modules for protein-coding genes and lncRNAs. The up-regulated module was enriched for genes related to immune and inflammatory function, while the down-regulated module was enriched for cell proliferation processes such as cell division and DNA replication. Co-expression networks indicated the functional relatedness between protein-coding genes and lncRNAs, which were enriched for similar functions over the series of time points examined. We identified numerous differentially expressed protein-coding genes and lncRNAs in all five developmental stages. Notably, ceruloplasmin precursor (CP), a protein-coding gene participating in antioxidant and iron transport processes, was differentially expressed in all stages. This study provides the first catalog of the developing pig spleen, and contributes to a fuller understanding of the molecular mechanisms underpinning mammalian spleen development.
Collapse
|
94
|
Dawson HD, Chen C, Gaynor B, Shao J, Urban JF. The porcine translational research database: a manually curated, genomics and proteomics-based research resource. BMC Genomics 2017; 18:643. [PMID: 28830355 PMCID: PMC5568366 DOI: 10.1186/s12864-017-4009-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs. RESULTS The process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5' and 3') unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes. CONCLUSIONS This database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.
Collapse
Affiliation(s)
- Harry D Dawson
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA.
| | - Celine Chen
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Brady Gaynor
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab, Beltsville, MD, 20705, USA
| | - Joseph F Urban
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| |
Collapse
|
95
|
Origin and dispersal of early domestic pigs in northern China. Sci Rep 2017; 7:5602. [PMID: 28798357 PMCID: PMC5552793 DOI: 10.1038/s41598-017-06056-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/07/2017] [Indexed: 11/30/2022] Open
Abstract
It is widely accepted that modern pigs were domesticated independently at least twice, and Chinese native pigs are deemed as direct descendants of the first domesticated pigs in the corresponding domestication centers. By analyzing mitochondrial DNA sequences of an extensive sample set spanning 10,000 years, we find that the earliest pigs from the middle Yellow River region already carried the maternal lineages that are dominant in both younger archaeological populations and modern Chinese pigs. Our data set also supports early Neolithic pig utilization and a long-term in situ origin for northeastern Chinese pigs during 8,000–3,500 BP, suggesting a possibly independent domestication in northeast China. Additionally, we observe a genetic replacement in ancient northeast Chinese pigs since 3,500 BP. The results not only provide increasing evidence for pig origin in the middle Yellow River region but also depict an outline for the process of early pig domestication in northeast China.
Collapse
|
96
|
Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data. Sci Rep 2017; 7:2376. [PMID: 28539617 PMCID: PMC5443785 DOI: 10.1038/s41598-017-02600-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/13/2017] [Indexed: 12/23/2022] Open
Abstract
Simple sequence repeats (SSRs) are used as polymorphic molecular markers in many species. They contribute very important functional variations in a range of complex traits; however, little is known about the variation of most SSRs in pig populations. Here, using genome resequencing data, we identified ~0.63 million polymorphic SSR loci from more than 100 individuals. Through intensive analysis of this dataset, we found that the SSR motif composition, motif length, total length of alleles and distribution of alleles all contribute to SSR variability. Furthermore, we found that CG-containing SSRs displayed significantly lower polymorphism and higher cross-species conservation. With a rigorous filter procedure, we provided a catalogue of 16,527 high-quality polymorphic SSRs, which displayed reliable results for the analysis of phylogenetic relationships and provided valuable summary statistics for 30 individuals equally selected from eight local Chinese pig breeds, six commercial lean pig breeds and Chinese wild boars. In addition, from the high-quality polymorphic SSR catalogue, we identified four loci with potential loss-of-function alleles. Overall, these analyses provide a valuable catalogue of polymorphic SSRs to the existing pig genetic variation database, and we believe this catalogue could be used for future genome-wide genetic analysis.
Collapse
|