1
|
You X, Fang Q, Chen C, Cao J, Fu S, Zhang T, Wang S, He X, He J, Zhou Y, Wang B, Wang L, Wang Z, Sun T, Yang X, Te R, Jian J, Zhou H, Dai Y, Liu Y. A near complete genome assembly of the East Friesian sheep genome. Sci Data 2024; 11:762. [PMID: 38992134 PMCID: PMC11239650 DOI: 10.1038/s41597-024-03581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
Advancements in sequencing have enabled the assembly of numerous sheep genomes, significantly advancing our understanding of the link between genetic variation and phenotypic traits. However, the genome of East Friesian sheep (Ostfriesisches Milchschaf), a key high-yield milk breed, remains to be fully assembled. Here, we constructed a near-complete and gap-free East Friesian genome assembly using PacBio HiFi, ultra-long ONT and Hi-C sequencing. The resulting genome assembly spans approximately 2.96 Gb, with a contig N50 length of 104.1 Mb and only 164 unplaced sequences. Remarkably, our assembly has captured 41 telomeres and 24 centromeres. The assembled sequence is of high quality on completeness (BUSCO score: 97.1%) and correctness (QV: 69.1). In addition, a total of 24,580 protein-coding genes were predicted, of which 97.2% (23,891) carried at least one conserved functional domain. Collectively, this assembly provides not only a near T2T gap-free genome, but also provides a valuable genetic resource for comparative genome studies of sheep and will serve as an important tool for the sheep research community.
Collapse
Affiliation(s)
| | | | - Chunhai Chen
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Junwei Cao
- Inner Mongolia Agricultural University, Hohhot, China
| | | | - Teng Zhang
- Inner Mongolia University, Hohhot, China
| | - Shenyuan Wang
- Inner Mongolia Agricultural University, Hohhot, China
| | | | | | - Yang Zhou
- Inner Mongolia University, Hohhot, China
| | | | | | - Zheng Wang
- Inner Mongolia University, Hohhot, China
| | | | - Xukui Yang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | | | - Jianbo Jian
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Huanmin Zhou
- Inner Mongolia University, Hohhot, China.
- Inner Mongolia Agricultural University, Hohhot, China.
| | | | - Yongbin Liu
- Inner Mongolia University, Hohhot, China.
- BGI Genomics, Shenzhen, China.
| |
Collapse
|
2
|
Ho DV, Tormey D, Odell A, Newton AA, Schnittker RR, Baumann DP, Neaves WB, Schroeder MR, Sigauke RF, Barley AJ, Baumann P. Post-meiotic mechanism of facultative parthenogenesis in gonochoristic whiptail lizard species. eLife 2024; 13:e97035. [PMID: 38847388 PMCID: PMC11161175 DOI: 10.7554/elife.97035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
Facultative parthenogenesis (FP) has historically been regarded as rare in vertebrates, but in recent years incidences have been reported in a growing list of fish, reptile, and bird species. Despite the increasing interest in the phenomenon, the underlying mechanism and evolutionary implications have remained unclear. A common finding across many incidences of FP is either a high degree of homozygosity at microsatellite loci or low levels of heterozygosity detected in next-generation sequencing data. This has led to the proposal that second polar body fusion following the meiotic divisions restores diploidy and thereby mimics fertilization. Here, we show that FP occurring in the gonochoristic Aspidoscelis species A. marmoratus and A. arizonae results in genome-wide homozygosity, an observation inconsistent with polar body fusion as the underlying mechanism of restoration. Instead, a high-quality reference genome for A. marmoratus and analysis of whole-genome sequencing from multiple FP and control animals reveals that a post-meiotic mechanism gives rise to homozygous animals from haploid, unfertilized oocytes. Contrary to the widely held belief that females need to be isolated from males to undergo FP, females housed with conspecific and heterospecific males produced unfertilized eggs that underwent spontaneous development. In addition, offspring arising from both fertilized eggs and parthenogenetic development were observed to arise from a single clutch. Strikingly, our data support a mechanism for facultative parthenogenesis that removes all heterozygosity in a single generation. Complete homozygosity exposes the genetic load and explains the high rate of congenital malformations and embryonic mortality associated with FP in many species. Conversely, for animals that develop normally, FP could potentially exert strong purifying selection as all lethal recessive alleles are purged in a single generation.
Collapse
Affiliation(s)
- David V Ho
- Department of Biology, Johannes Gutenberg UniversityMainzGermany
- Institute of Quantitative and Computational Biosciences, Johannes Gutenberg UniversityMainzGermany
| | - Duncan Tormey
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Aaron Odell
- Department of Biology, Johannes Gutenberg UniversityMainzGermany
| | | | | | - Diana P Baumann
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | | | | | - Anthony J Barley
- School of Mathematical and Natural Sciences, Arizona State University–West Valley CampusGlendaleUnited States
| | - Peter Baumann
- Department of Biology, Johannes Gutenberg UniversityMainzGermany
- Institute of Quantitative and Computational Biosciences, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular BiologyMainzGermany
| |
Collapse
|
3
|
Moawad AS, Wang F, Zheng Y, Chen C, Saleh AA, Hou J, Song C. Evolution of Endogenous Retroviruses in the Subfamily of Caprinae. Viruses 2024; 16:398. [PMID: 38543763 PMCID: PMC10975924 DOI: 10.3390/v16030398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 05/23/2024] Open
Abstract
The interest in endogenous retroviruses (ERVs) has been fueled by their impact on the evolution of the host genome. In this study, we used multiple pipelines to conduct a de novo exploration and annotation of ERVs in 13 species of the Caprinae subfamily. Through analyses of sequence identity, structural organization, and phylogeny, we defined 28 ERV groups within Caprinae, including 19 gamma retrovirus groups and 9 beta retrovirus groups. Notably, we identified four recent and potentially active groups prevalent in the Caprinae genomes. Additionally, our investigation revealed that most long noncoding genes (lncRNA) and protein-coding genes (PC) contain ERV-derived sequences. Specifically, we observed that ERV-derived sequences were present in approximately 75% of protein-coding genes and 81% of lncRNA genes in sheep. Similarly, in goats, ERV-derived sequences were found in approximately 74% of protein-coding genes and 75% of lncRNA genes. Our findings lead to the conclusion that the majority of ERVs in the Caprinae genomes can be categorized as fossils, representing remnants of past retroviral infections that have become permanently integrated into the genomes. Nevertheless, the identification of the Cap_ERV_20, Cap_ERV_21, Cap_ERV_24, and Cap_ERV_25 groups indicates the presence of relatively recent and potentially active ERVs in these genomes. These particular groups may contribute to the ongoing evolution of the Caprinae genome. The identification of putatively active ERVs in the Caprinae genomes raises the possibility of harnessing them for future genetic marker development.
Collapse
Affiliation(s)
- Ali Shoaib Moawad
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Fengxu Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (F.W.); (J.H.)
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
| | - Ahmed A. Saleh
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City 11865, Egypt
| | - Jian Hou
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (F.W.); (J.H.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
| |
Collapse
|
4
|
Weiss MN, Mocci E, Zhu S, Davenport MJ, English E, Renn CL, Dorsey SG. Nociceptive and Transcriptomic Responses in a Swine Diabetic Wound Model Treated With a Topical Angiotensin 1 Receptor Antagonist. Nurs Res 2024; 73:118-125. [PMID: 37916845 PMCID: PMC10922245 DOI: 10.1097/nnr.0000000000000704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
BACKGROUND Painful, treatment-resistant wounds are prevalent among diabetic patients and significantly affect health-related quality of life (HRQOL). Topical treatments may help alleviate pain without risk of dependence or side effects. However, there is a lack of topical wound compounds targeting pain-specific receptors. One possible target is proinflammatory angiotensin 1 receptor (AT1R), which is upregulated in diabetic skin and has been implicated in nociception. OBJECTIVES We investigated the effects of topical valsartan, an AT1R antagonist, on pain (nociceptive thresholds) and gene expression changes (transcriptomics) in a swine model of diabetic wounds. METHODS Eight wounds were surgically induced in diabetic, hyperglycemic Yucatan miniature swine ( n = 4). Topical AT1R antagonist was applied to wounds on one side and vehicle on the other side. Nocifensive testing was conducted at baseline and then weekly, beginning 7 days after wound induction. Mechanical and thermal stimuli were applied to the wound margins until a nocifensive reaction was elicited or a predetermined cutoff was reached. After 7 weeks of testing, tissue from the dorsal horn, dorsal root ganglion, and wounds were sequenced and analyzed with DESeq2. Unbiased pathway analyses using Metascape were conducted on differentially expressed genes. RESULTS There was no significant difference in mechanical tolerance threshold between AT1R antagonist-treated and vehicle-treated wounds ( p = .106). Thermal tolerance was significantly higher in AT1R antagonist-treated wounds compared to vehicle-treated ( p = .015). Analysis of differentially expressed genes revealed enriched pathways of interest: interleukin-18 signaling in dorsal horn laminae IV-V and sensory perception of mechanical stimulus in wound tissue. DISCUSSION In this study, wounds modeling diabetic ulcers were created in hyperglycemic swine and treated with a topical AT1R antagonist. AT1R-antagonist-treated wounds had a higher tolerance threshold than vehicle-treated wounds for thermal hyperalgesia, but not mechanical allodynia. Pathway analyses of differentially expressed genes revealed several pathways of interest for future pain research. Although further studies are needed to confirm the findings, this study can improve nursing care by providing information about a potential future treatment that may be used to decrease pain and improve HRQOL in patients with diabetic wounds.
Collapse
|
5
|
Du H, Diao C, Zhuo Y, Zheng X, Hu Z, Lu S, Jin W, Zhou L, Liu JF. Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity. Genomics 2024; 116:110782. [PMID: 38176574 DOI: 10.1016/j.ygeno.2024.110782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/27/2023] [Accepted: 01/01/2024] [Indexed: 01/06/2024]
Abstract
There is an increasing understanding that a reference genome representing an individual cannot capture all the gene repertoire of a species. Here, we conduct a population-scale missing sequences detection of Chinese domestic pigs using whole-genome sequencing data from 534 individuals. We identify 132.41 Mb of sequences absent in the reference assembly, including eight novel genes. In particular, the breeds spread in Chinese high-altitude regions perform significantly different frequencies of new sequences in promoters than other breeds. Furthermore, we dissect the role of non-coding variants and identify a novel sequence inserted in the 3'UTR of the FMO3 gene, which may be associated with the intramuscular fat phenotype. This novel sequence could be a candidate marker for meat quality. Our study provides a comprehensive overview of the missing sequences in Chinese domestic pigs and indicates that this dataset is a valuable resource for understanding the diversity and biology of pigs.
Collapse
Affiliation(s)
- Heng Du
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Chenguang Diao
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Yue Zhuo
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xianrui Zheng
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhengzheng Hu
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shiyu Lu
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenjiao Jin
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lei Zhou
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Jian-Feng Liu
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
6
|
Miao J, Wei X, Cao C, Sun J, Xu Y, Zhang Z, Wang Q, Pan Y, Wang Z. Pig pangenome graph reveals functional features of non-reference sequences. J Anim Sci Biotechnol 2024; 15:32. [PMID: 38389084 PMCID: PMC10882747 DOI: 10.1186/s40104-023-00984-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied. RESULTS In this study, we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb. Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome. Furthermore, we observed that NRSs were rarely found within coding sequences, while NRS insertions were enriched in immune-related Gene Ontology terms. Notably, our investigation also unveiled a close association between novel genes and the immune capacity of pigs. We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs, and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X. Additionally, we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in Southern Chinese pigs. CONCLUSIONS Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.
Collapse
Affiliation(s)
- Jian Miao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xingyu Wei
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Caiyun Cao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jiabao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yuejin Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China.
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| |
Collapse
|
7
|
Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
Collapse
Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
8
|
Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023; 55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.
Collapse
Affiliation(s)
- Pengju Zhao
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| |
Collapse
|
9
|
Zhong Z, Wang Z, Xie X, Tian S, Wang F, Wang Q, Ni S, Pan Y, Xiao Q. Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations. Animals (Basel) 2023; 13:2010. [PMID: 37370521 DOI: 10.3390/ani13122010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Indigenous pig populations in Hainan Province live in tropical climate conditions and a relatively closed geographical environment, which has contributed to the formation of some excellent characteristics, such as heat tolerance, strong disease resistance and excellent meat quality. Over the past few decades, the number of these pig populations has decreased sharply, largely due to a decrease in growth rate and poor lean meat percentage. For effective conservation of these genetic resources (such as heat tolerance, meat quality and disease resistance), the whole-genome sequencing data of 78 individuals from 3 native Chinese pig populations, including Wuzhishan (WZS), Tunchang (TC) and Dingan (DA), were obtained using a 150 bp paired-end platform, and 25 individuals from two foreign breeds, including Landrace (LR) and Large White (LW), were downloaded from a public database. A total of 28,384,282 SNPs were identified, of which 27,134,233 SNPs were identified in native Chinese pig populations. Both genetic diversity statistics and linkage disequilibrium (LD) analysis indicated that indigenous pig populations displayed high genetic diversity. The result of population structure implied the uniqueness of each native Chinese pig population. The selection signatures were detected between indigenous pig populations and foreign breeds by using the population differentiation index (FST) method. A total of 359 candidate genes were identified, and some genes may affect characteristics such as immunity (IL-2, IL-21 and ZFYVE16), adaptability (APBA1), reproduction (FGF2, RNF17, ADAD1 and HIPK4), meat quality (ABCA1, ADIG, TLE4 and IRX5), and heat tolerance (VPS13A, HSPA4). Overall, the findings of this study will provide some valuable insights for the future breeding, conservation and utilization of these three Chinese indigenous pig populations.
Collapse
Affiliation(s)
- Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Ziyi Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Xinfeng Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Shuaishuai Tian
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Qishan Wang
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Shiheng Ni
- Animal Husbandry Technology Extending Stations of Hainan Province, Haikou 570203, China
| | - Yuchun Pan
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| |
Collapse
|
10
|
Piña JS, Orozco-Arias S, Tobón-Orozco N, Camargo-Forero L, Tabares-Soto R, Guyot R. G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era. Evol Bioinform Online 2023; 19:11769343221150585. [PMID: 36703866 PMCID: PMC9871978 DOI: 10.1177/11769343221150585] [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: 11/14/2022] [Accepted: 12/23/2022] [Indexed: 01/22/2023] Open
Abstract
A common task in bioinformatics is to compare DNA sequences to identify similarities between organisms at the sequence level. An approach to such comparison is the dot-plots, a 2-dimensional graphical representation to analyze DNA or protein alignments. Dot-plots alignment software existed before the sequencing revolution, and now there is an ongoing limitation when dealing with large-size sequences, resulting in very long execution times. High-Performance Computing (HPC) techniques have been successfully used in many applications to reduce computing times, but so far, very few applications for graphical sequence alignment using HPC have been reported. Here, we present G-SAIP (Graphical Sequence Alignment in Parallel), a software capable of spawning multiple distributed processes on CPUs, over a supercomputing infrastructure to speed up the execution time for dot-plot generation up to 1.68× compared with other current fastest tools, improve the efficiency for comparative structural genomic analysis, phylogenetics because the benefits of pairwise alignments for comparison between genomes, repetitive structure identification, and assembly quality checking.
Collapse
Affiliation(s)
- Johan S. Piña
- Department of Data Science, People
Contact, Manizales, Caldas, Colombia,Department of Computer Science,
Universidad Autónoma de Manizales, Manizales, Caldas, Colombia,Johan S. Piña, Department of Computer
Science, Universidad Autónoma de Manizales, Antigua estación del ferrocarril,
Manizales, Caldas 170004, Colombia.
| | - Simon Orozco-Arias
- Department of Computer Science,
Universidad Autónoma de Manizales, Manizales, Caldas, Colombia,Department of Systems and Informatics,
Universidad de Caldas, Manizales, Caldas, Colombia
| | - Nicolas Tobón-Orozco
- Department of Computer Science,
Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
| | | | - Reinel Tabares-Soto
- Department of Electronics and
Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
| | - Romain Guyot
- Department of Electronics and
Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia,Institut de Recherche pour le
Développement, CIRAD, University of Montpellier, Montpellier, France
| |
Collapse
|
11
|
Liu Y, Fu Y, Yang Y, Yi G, Lian J, Xie B, Yao Y, Chen M, Niu Y, Liu L, Wang L, Zhang Y, Fan X, Tang Y, Yuan P, Zhu M, Li Q, Zhang S, Chen Y, Wang B, He J, Lu D, Liachko I, Sullivan ST, Pang B, Chen Y, He X, Li K, Tang Z. Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs. GENETICS SELECTION EVOLUTION 2022; 54:62. [PMID: 36104777 PMCID: PMC9476355 DOI: 10.1186/s12711-022-00754-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.
Results
We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality.
Conclusions
Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.
Collapse
|
12
|
Li X, Zhang X, Luo Y, Liu R, Sun Y, Zhao S, Yu M, Cao J. Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells. Genes (Basel) 2022; 13:genes13091515. [PMID: 36140681 PMCID: PMC9498719 DOI: 10.3390/genes13091515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/25/2022] Open
Abstract
The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the CD163 had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection.
Collapse
Affiliation(s)
- Xiaolong Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yandong Luo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ru Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianhua Cao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
| |
Collapse
|
13
|
Zheng M, Guo T, Yang B, Zhang Z, Huang L. Origin, evolution, and tissue-specific functions of the porcine repetitive element 1. Genet Sel Evol 2022; 54:54. [PMID: 35896967 PMCID: PMC9327148 DOI: 10.1186/s12711-022-00745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Background The porcine repetitive element 1 (PRE1) is the most abundant short interspersed nuclear element (SINE) in the Sus scrofa genome and it has been suggested that some PRE1 can have regulatory functions. The million copies of PRE1 in the porcine genome have accumulated abundant CpG dinucleotides and unique structural variations, such as direct repeats and patterns of sequence degeneration. The aims of this study were to analyse these structural variations to trace the origin and evolutionary pattern of PRE1 and to investigate potential methylation-related functions of PRE1 based on methylation patterns of PRE1 CpG dinucleotides in different tissues. Results We investigated the evolutionary trajectory of PRE1 and found that PRE1 originated from the ancestral CHRS-S1 family through three main successive partial duplications. We found that the partial duplications and deletions of PRE1 were likely due to RNA splicing events during retrotransposition. Functionally, correlation analysis showed that the methylation levels of 103 and 261 proximal PRE1 were, respectively, negatively and positively correlated with the expression levels of neighboring genes (Spearman correlation, P < 0.01). Further epigenomic analysis revealed that, in the testis, demethylation of proximal PRE1 in the HORMAD1 and HACD3 genes had tissue-specific enhancer and promoter functions, while in the muscle, methylation of proximal PRE1 repeats in the TCEA3 gene had an enhancer function. Conclusions The characteristic sequences of PRE1 reflect unique patterns of origin and evolution and provide a structural basis for diverse regulatory functions. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00745-3.
Collapse
Affiliation(s)
- Min Zheng
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Tianfu Guo
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| |
Collapse
|
14
|
Zhang J, Xu Y, Zhang Y, Bossila EA, Shi M, Zhao Y. Bioinformatic analysis as a first step to predict the compatibility of hematopoiesis and immune system genes between humans and pigs. Xenotransplantation 2022; 29:e12764. [PMID: 35695327 DOI: 10.1111/xen.12764] [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: 02/15/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022]
Abstract
The shortage of allogeneic donor organs leaves its supply far short of clinical need. There are great expectations on xenotransplantation, especially with pigs' organs. With the genetic modification of donor pigs, the rejection and cross-species transmission issues have now been widely addressed. However, research on the compatibility of genes between humans and pigs was limited. We performed a systematic screening analysis of predicted incompatible genes between humans and pigs, judged by low protein sequence similarities or different predicted protein domain compositions. By combining with gene set enrichment analysis, we screened out several key genes of hematopoiesis and the immune system with possible incompatibilities, which might be important for establishing chimera and xenotransplantation between humans and pigs. There were seven chemokine genes, including CCL1, CCL5, CCL24, CCL25, CCL28, CXCL12, and CXCL16, that exhibited limited similarity between humans and pigs (similarity < 0.8). Among hematopoiesis process-related genes, 15 genes of adhesion molecules, Notch ligands, and cytokine receptors exhibited differences between humans and pigs. In complement and coagulation cascades, 19 genes showed low similarity and 77 genes had different domain compositions between humans and pigs. Our study provides a good reference for further genetic modification of pigs, which might be beneficial for xenotransplantation.
Collapse
Affiliation(s)
- Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingzi Zhang
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elhusseny A Bossila
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Biotechnology Department, Faculty of Agriculture Al-Azhar University, Cairo, Egypt
| | - Mingpu Shi
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
15
|
Liu L, Megens HJ, Crooijmans RP, Bosse M, Huang Q, Sonsbeek GBV, Groenen MA, Madsen O. The Visayan warty pig (Sus cebifrons) genome provides insight into chromosome evolution and sensory adaptation in pigs. Mol Biol Evol 2022; 39:6596366. [PMID: 35642310 PMCID: PMC9178973 DOI: 10.1093/molbev/msac110] [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] [Indexed: 11/13/2022] Open
Abstract
It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent post-divergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.
Collapse
Affiliation(s)
- Langqing Liu
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | | | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Qitong Huang
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | | | - Martien Am Groenen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| |
Collapse
|
16
|
Signaling Pathways Involved in Myocardial Ischemia-Reperfusion Injury and Cardioprotection: A Systematic Review of Transcriptomic Studies in Sus scrofa. J Cardiovasc Dev Dis 2022; 9:jcdd9050132. [PMID: 35621843 PMCID: PMC9145716 DOI: 10.3390/jcdd9050132] [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: 03/30/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/17/2022] Open
Abstract
Myocardial damage in acute myocardial infarctions (AMI) is primarily the result of ischemia−reperfusion injury (IRI). Recognizing the timing of transcriptional events and their modulation by cardioprotective strategies is critical to address the pathophysiology of myocardial IRI. Despite the relevance of pigs for translational studies of AMI, only a few have identified how transcriptomic changes shape cellular signaling pathways in response to injury. We systematically reviewed transcriptomic studies of myocardial IRI and cardioprotection in Sus scrofa. Gene expression datasets were analyzed for significantly enriched terms using the Enrichr analysis tool, and statistically significant results (adjusted p-values of <0.05) for Signaling Pathways, Transcription Factors, Molecular Functions, and Biological Processes were compared between eligible studies to describe how these dynamic changes transform the myocardium from an injured and inflamed tissue into a scar. Then, we address how cardioprotective interventions distinctly modulate the myocardial transcriptome and discuss the implications of uncovering gene regulatory networks for cardiovascular pathologies and translational applications.
Collapse
|
17
|
Chen J, Zhong J, He X, Li X, Ni P, Safner T, Šprem N, Han J. The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications. Anim Genet 2022; 53:281-292. [PMID: 35238061 PMCID: PMC9314987 DOI: 10.1111/age.13181] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/12/2022] [Accepted: 02/12/2022] [Indexed: 02/05/2023]
Abstract
The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long‐range information provided by 10× Linked‐Reads sequencing. We achieved a high‐quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference‐assistant scaffolding method. Using the ‘assembly‐to‐assembly’ approach, we identified intra‐chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (R2 > 0.64, p < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large‐scale inter‐chromosomal evolution, by resolving parental‐derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (p < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (p < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter‐chromosomal interaction between the sex chromosome and autosomes.
Collapse
Affiliation(s)
- Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Zhong
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuefei He
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyu Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Pan Ni
- Animal Husbandry and Veterinary Institute of Keqiao District, Shaoxing, Zhejiang, China
| | - Toni Safner
- Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, (CoE CroP-BioDiv), Zagreb, Croatia
| | - Nikica Šprem
- Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Jianlin Han
- International Livestock Research Institute, Nairobi, Kenya.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
18
|
Xu SS, Zhang XL, Liu SS, Feng ST, Xiang GM, Xu CJ, Fan ZY, Xu K, Wang N, Wang Y, Che JJ, Liu ZG, Mu YL, Li K. Multi-Omic Analysis in a Metabolic Syndrome Porcine Model Implicates Arachidonic Acid Metabolism Disorder as a Risk Factor for Atherosclerosis. Front Nutr 2022; 9:807118. [PMID: 35284467 PMCID: PMC8906569 DOI: 10.3389/fnut.2022.807118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background The diet-induced gut microbiota dysbiosis has been suggested as a major risk factor for atherothrombosis, however, the detailed mechanism linking these conditions is yet to be fully understood. Methods We established a long-term excessive-energy diet-induced metabolic syndrome (MetS) inbred Wuzhishan minipig model, which is characterized by its genetic stability, small size, and human-like physiology. The metabolic parameters, atherosclerotic lesions, gut microbiome, and host transcriptome were analyzed. Metabolomics profiling revealed a linkage between gut microbiota and atherothrombosis. Results We showed that white atheromatous plaque was clearly visible on abdominal aorta in the MetS model. Furthermore, using metagenome and metatranscriptome sequencing, we discovered that the long-term excessive energy intake altered the local intestinal microbiota composition and transcriptional profile, which was most dramatically illustrated by the reduced abundance of SCFAs-producing bacteria including Bacteroides, Lachnospiraceae, and Ruminococcaceae in the MetS model. Liver and abdominal aorta transcriptomes in the MetS model indicate that the diet-induced gut microbiota dysbiosis activated host chronic inflammatory responses and significantly upregulated the expression of genes related to arachidonic acid-dependent signaling pathways. Notably, metabolomics profiling further revealed an intimate linkage between arachidonic acid metabolism and atherothrombosis in the host-gut microbial metabolism axis. Conclusions These findings provide new insights into the relationship between atherothrombosis and regulation of gut microbiota via host metabolomes and will be of potential value for the treatment of cardiovascular diseases in MetS.
Collapse
Affiliation(s)
- Song-Song Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiu-Ling Zhang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Sha-Sha Liu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Animal Husbandry and Veterinary Department, Beijing Vocational College of Agriculture, Beijing, China
| | - Shu-Tang Feng
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang-Ming Xiang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chang-Jiang Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zi-Yao Fan
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Wang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Wang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing-Jing Che
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Guo Liu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu-Lian Mu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yu-Lian Mu
| | - Kui Li
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kui Li
| |
Collapse
|
19
|
Ma Y, Jia J, Fan R, Lu Y, Zhao X, Zhong Y, Yang J, Ma L, Wang Y, Lv M, Yang H, Mou L, Dai Y, Feng S, Zhang J. Screening and Identification of the First Non-CRISPR/Cas9-Treated Chinese Miniature Pig With Defective Porcine Endogenous Retrovirus pol Genes. Front Immunol 2022; 12:797608. [PMID: 35126361 PMCID: PMC8807647 DOI: 10.3389/fimmu.2021.797608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Pig to human xenotransplantation is considered to be a possible approach to alleviate the shortage of human allografts. Porcine endogenous retrovirus (PERV) is the most significant pathogen in xenotransplantation. We screened for pigs that consistently did not transmit human-tropic replication competent PERVs (HTRC PERVs), namely, non-transmitting pigs. Then, we conducted whole-genome resequencing and full-length transcriptome sequencing to further investigate the sequence characteristics of one non-transmitting pig. Using in vitro transmission assays, we found 5 (out of 105) pigs of the Chinese Wuzhishan minipig inbred line that did not transmit PERV to human cells, i.e., non-transmitting pigs. Whole-genome resequencing and full-length transcriptome sequencing of one non-transmitting pig showed that all of the pol genes were defective at both the genome and transcript levels. We speculate that the defective PERV pol genes in this pig might be attributable to the long-term inbreeding process. This discovery is promising for the development of a strain of highly homozygous and genetically stable pigs with defective PERV pol genes as a source animal species for xenotransplantation.
Collapse
Affiliation(s)
- Yuyuan Ma
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Junting Jia
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Rui Fan
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Ying Lu
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Xiong Zhao
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Yadi Zhong
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Jierong Yang
- Research and Development Department, Grand Life Science and Technology. Ltd., Beijing, China
| | - Limin Ma
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Yanlin Wang
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Maomin Lv
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Haiyuan Yang
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China
| | - Lisha Mou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- *Correspondence: Jingang Zhang, ; Shutang Feng, ; Yifan Dai, ; Lisha Mou,
| | - Yifan Dai
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China
- *Correspondence: Jingang Zhang, ; Shutang Feng, ; Yifan Dai, ; Lisha Mou,
| | - Shutang Feng
- Research and Development Department, Grand Life Science and Technology. Ltd., Beijing, China
- *Correspondence: Jingang Zhang, ; Shutang Feng, ; Yifan Dai, ; Lisha Mou,
| | - Jingang Zhang
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
- *Correspondence: Jingang Zhang, ; Shutang Feng, ; Yifan Dai, ; Lisha Mou,
| |
Collapse
|
20
|
Feng Z, Yang Y, Liu Z, Zhao W, Huang L, Wu T, Mu Y. Integrated analysis of DNA methylome and transcriptome reveals the differences in biological characteristics of porcine mesenchymal stem cells. BMC Genom Data 2021; 22:56. [PMID: 34922435 PMCID: PMC8684131 DOI: 10.1186/s12863-021-01016-8] [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: 07/05/2021] [Accepted: 11/19/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bone marrow (BM) and umbilical cord (UC) are the main sources of mesenchymal stem cells (MSCs). These two MSCs display significant differences in many biological characteristics, yet the underlying regulation mechanisms of these cells remain largely unknown. RESULTS BMMSCs and UCMSCs were isolated from inbred Wuzhishan miniature pigs and the first global DNA methylation and gene expression profiles of porcine MSCs were generated. The osteogenic and adipogenic differentiation ability of porcine BMMSCs is greater than that of UCMSCs. A total of 1979 genes were differentially expressed and 587 genes were differentially methylated at promoter regions in these cells. Integrative analysis revealed that 102 genes displayed differences in both gene expression and promoter methylation. Gene ontology enrichment analysis showed that these genes were associated with cell differentiation, migration, and immunogenicity. Remarkably, skeletal system development-related genes were significantly hypomethylated and upregulated, whereas cell cycle genes were opposite in UCMSCs, implying that these cells have higher cell proliferative activity and lower differentiation potential than BMMSCs. CONCLUSIONS Our results indicate that DNA methylation plays an important role in regulating the differences in biological characteristics of BMMSCs and UCMSCs. Results of this study provide a molecular theoretical basis for the application of porcine MSCs in human medicine.
Collapse
Affiliation(s)
- Zheng Feng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China
| | - Yalan Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China
| | - Zhiguo Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weimin Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tianwen Wu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yulian Mu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
21
|
Huang CP, Liu LC, Chang CC, Wu CC, Shyr CR. Intratumoral xenogeneic tissue-specific cell immunotherapy inhibits tumor growth by increasing antitumor immunity in murine triple negative breast and pancreatic tumor models. Cancer Lett 2021; 545:115478. [PMID: 35902043 DOI: 10.1016/j.canlet.2021.10.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/18/2021] [Accepted: 10/31/2021] [Indexed: 12/13/2022]
Abstract
Low immunogenicity in tumors and the immunosuppressive tumor microenvironment (TME) represent major obstacles to the full success of immunotherapy in cancer patients. A novel intratumoral xenogeneic tissue-specific cell immunotherapeutic approach could overcome the obstacles. Murine 4T1 triple negative breast cancer (TNBC) cells and Pan18 pancreatic ductal adenocarcinoma (PDAC) cells were used for establishing syngeneic graft tumor models to evaluate antitumor effect of intratumoral injection of xenogeneic tissue-specific cells. Responses to treatment were assessed by measuring tumor growth and tumor weight of the tumor-bearing mice. To investigate the mechanisms of action, tumor histology and immunohistochemistry and cytokine gene expression were measured. Splenic lymphocytes proliferation, cytokine production and cytotoxicity activities were also assessed. The findings showed that intratumoral injection of xenogeneic tissue-specific cells in monotherapy and combination with chemotherapy inhibit tumor growth. The therapeutic efficacy of intratumoral xenogeneic cells was significantly enhanced by the addition of cytotoxic chemotherapeutic agents. Mice that received combined treatment showed maximal attenuation in tumor growth rate. The antitumor immunity was explained by altered immune cell infiltration in tumors and immune cell functions. Our findings demonstrate that xenogeneic tissue-specific cells given intratumorally, provide a potent antitumor effect in murine breast and pancreatic tumor models by enhancing recruitment and activation of immune cells in tumors for local and systemic antitumor effects. Moreover, intratumoral xenogeneic cell treatment turns immunologically "cold" tumors to "hot" ones, generates systemic antitumor immunity, and synergizes with chemotherapy. Thus, the intratumoral xenogeneic tissue-specific cell immunotherapy may represent a useful therapeutic option to difficult-to-treat cancers.
Collapse
Affiliation(s)
- Chi-Ping Huang
- Department of Medicine, Department of Urology, College of Medicine, China Medical University and Hospital, Taichung, 404, Taiwan
| | - Liang-Chih Liu
- Department of Medicine, Department of Surgery, College of Medicine, China Medical University and Hospital, Taichung, 404, Taiwan
| | - Chih-Chun Chang
- Sex Hormone Research Center, Department of Medical Laboratory Science and Biotechnology, China Medical University and Hospital, Taichung, 404, Taiwan
| | - Chun-Chie Wu
- Department of Medicine, Department of Urology, College of Medicine, China Medical University and Hospital, Taichung, 404, Taiwan
| | - Chih-Rong Shyr
- Sex Hormone Research Center, Department of Medical Laboratory Science and Biotechnology, China Medical University and Hospital, Taichung, 404, Taiwan.
| |
Collapse
|
22
|
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: 7] [Impact Index Per Article: 2.3] [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
|
23
|
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
|
24
|
Zhang Y, Fan G, Liu X, Skovgaard K, Sturek M, Heegaard PM. The genome of the naturally evolved obesity-prone Ossabaw miniature pig. iScience 2021; 24:103081. [PMID: 34585119 PMCID: PMC8455653 DOI: 10.1016/j.isci.2021.103081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/08/2021] [Accepted: 08/31/2021] [Indexed: 12/03/2022] Open
Abstract
The feral pigs of Ossabaw Island (USA) have an outstanding propensity to obesity and develop complete metabolic syndrome (MetS) upon prolonged high energy dieting. We now report the first high quality genome of the Ossabaw pig with Contig N50 of ∼6.03 Mb, significantly higher than most other published pig genomes. Genomic comparison to Duroc reveals that variations including SNPs, INDELs and one ∼2 Mb inversion identified in Ossabaw pig may be related to its "thrifty" phenotype. Finally, an important positively selected gene (PSG) was found to be LEPR (leptin receptor) containing two positively selected sites which may lead to pseudogenization of this gene with possible significant effects on obesity and inflammation development. This work provides the first complete mapping of a genome representing a naturally 'feast and famine' evolved phenotype of MetS, serving as a blueprint to guide the search for new targets and new biomarkers for obesity comorbidities.
Collapse
Affiliation(s)
- Yaolei Zhang
- Translational Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Kerstin Skovgaard
- Translational Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Michael Sturek
- Department of Anatomy, Cell Biology, & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Peter M.H. Heegaard
- Translational Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Innate Immunology Group, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
25
|
Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods. Genes (Basel) 2021; 12:genes12091374. [PMID: 34573356 PMCID: PMC8467702 DOI: 10.3390/genes12091374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Adipose is an important body tissue in pigs, and fatty traits are critical in pig production. The function of long non-coding RNA (lncRNA) in fat deposition and metabolism has been found in previous studies. In this study, we collected the adipose tissue of six Landrace pigs with contrast backfat thickness (nhigh = 3, nlow = 3), after which we performed strand-specific RNA sequencing (RNA-seq) based on pooling and biological replicate methods. Biological replicate and pooling RNA-seq revealed 1870 and 1618 lncRNAs, respectively. Using edgeR, we determined that 1512 genes and 220 lncRNAs, 2240 genes and 127 lncRNAs were differentially expressed in biological replicate and pooling RNA-seq, respectively. After target gene prediction, we found that ACSL3 was cis-targeted by lncRNA TCONS-00052400 and could activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 cis-regulated gene ACACB regulated the rate-limiting enzyme in fatty acid oxidation. Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect backfat deposition in swine through regulation of their target genes. Our study explored the regulation of lncRNA and their target genes in porcine backfat deposition and provided new insights for further investigation of the biological functions of lncRNA.
Collapse
|
26
|
Zhu J, Chen F, Luo L, Wu W, Dai J, Zhong J, Lin X, Chai C, Ding P, Liang L, Wang S, Ding X, Chen Y, Wang H, Qiu J, Wang F, Sun C, Zeng Y, Fang J, Jiang X, Liu P, Tang G, Qiu X, Zhang X, Ruan Y, Jiang S, Li J, Zhu S, Xu X, Li F, Liu Z, Cao G, Chen D. Single-cell atlas of domestic pig cerebral cortex and hypothalamus. Sci Bull (Beijing) 2021; 66:1448-1461. [PMID: 36654371 DOI: 10.1016/j.scib.2021.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/07/2020] [Accepted: 03/12/2021] [Indexed: 01/20/2023]
Abstract
The brain of the domestic pig (Sus scrofa domesticus) has drawn considerable attention due to its high similarities to that of humans. However, the cellular compositions of the pig brain (PB) remain elusive. Here we investigated the single-nucleus transcriptomic profiles of five regions of the PB (frontal lobe, parietal lobe, temporal lobe, occipital lobe, and hypothalamus) and identified 21 cell subpopulations. The cross-species comparison of mouse and pig hypothalamus revealed the shared and specific gene expression patterns at the single-cell resolution. Furthermore, we identified cell types and molecular pathways closely associated with neurological disorders, bridging the gap between gene mutations and pathogenesis. We reported, to our knowledge, the first single-cell atlas of domestic pig cerebral cortex and hypothalamus combined with a comprehensive analysis across species, providing extensive resources for future research regarding neural science, evolutionary developmental biology, and regenerative medicine.
Collapse
Affiliation(s)
- Jiacheng Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen 518083, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Lihua Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Weiying Wu
- BGI-Shenzhen, Shenzhen 518083, China; Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brian Medicine, and the MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310031, China
| | - Jinxia Dai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jixing Zhong
- School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Chaochao Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Peiwen Ding
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Langchao Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Shiyou Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiangning Ding
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Yin Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Haoyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiaying Qiu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | | | - Chengcheng Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China; School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Yuying Zeng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China; College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Jian Fang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaosen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Ping Liu
- BGI-Shenzhen, Shenzhen 518083, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Gen Tang
- Shenzhen Children's Hospital, Shenzhen 518083, China
| | - Xin Qiu
- Shenzhen Children's Hospital, Shenzhen 518083, China
| | | | - Yetian Ruan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | | | | | - Shida Zhu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Zhongmin Liu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China.
| | | |
Collapse
|
27
|
Zhao R, Dong Z, Wei X, Gu X, Han P, Wu H, Yan Y, Huang L, Li H, Zhang C, Li F, Li P. Inflammatory factors are crucial for the pathogenesis of post-traumatic osteoarthritis confirmed by a novel porcine model: "Idealized" anterior cruciate ligament reconstruction" and gait analysis. Int Immunopharmacol 2021; 99:107905. [PMID: 34242997 DOI: 10.1016/j.intimp.2021.107905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To determine whether idealized anterior cruciate ligament reconstruction (IACL-R) restores normal gait features, and whether inflammatory factors are involved in the pathogenesisof post-traumatic osteoarthritis (PTOA). METHODS Fourteen mature female minipigs were allocated to a sham group (n = 7) or an IACL-R group (n = 7). Load asymmetry during gait was recorded using a pressure-sensing walkway measurement system to evaluate the gait features of the right knee joint before and after surgery. Inflammatory factors (including interleukin [IL]-1α, IL-1β, IL-2, IL-6, IL-8, IL-18, tumor necrosis factor-α, and granulocyte-macrophage colony-stimulating factor) in synovial fluid were measured using Luminex assays before and after surgery. Cartilage integrity and the subchondral bone plate of the right knee were evaluated using histology and imaging at 3 months postoperatively. RESULTS Swing time and stance time returned to their preoperative values on day 31, while maximum force, contact area, peak force ,and impulse returned to their preoperative values on day 45 after the surgery in the IACL-R group (P = 0.073, 0.053, 0.107, 0.052, 0.152, and 0.059, respectively).Thus, IACL-R restored normal gait. Compared with their preoperative concentrations, all tested inflammatory factors showed significantly increased concentrations in the synovial fluid in the IACL-R group, especially at 3, 7, and 15 days postoperatively. X-ray, computed tomography, magnetic resonance imaging, and histological data showed severe cartilage damage in the IACL-R model. CONCLUSION IACL-R restored normal gait features but caused significant cartilage damage, indicating that significantly elevated inflammatory factors maybe crucial for the pathogenesis of PTOA.
Collapse
Affiliation(s)
- Ruipeng Zhao
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| | - Zhengquan Dong
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| | - Xiaochun Wei
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| | - Xiaodong Gu
- Department of Orthopaedics, Bethune Hospital, Shanxi Medical University, Taiyuan 030032, PR China.
| | - Pengfei Han
- Department of Orthopedics, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi Province 046000, PR China.
| | - Hongru Wu
- Shanxi Institute of Sports Science, Taiyuan 030000, PR China.
| | - Yanxia Yan
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| | - Lingan Huang
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| | - Haoqian Li
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| | - Chengming Zhang
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| | - Fei Li
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| | - Pengcui Li
- Department of orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan 030001, PR China.
| |
Collapse
|
28
|
Zolfaghari Emameh R, Hosseini SN, Parkkila S. Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases. Database (Oxford) 2021; 2021:baab029. [PMID: 34003248 PMCID: PMC8130508 DOI: 10.1093/database/baab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/19/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022]
Abstract
Sus scrofa or pig was domesticated thousands of years ago. Through various indigenous breeds, different phenotypes were produced such as Chinese inbred miniature minipig or Wuzhishan pig (WZSP), which is broadly used in the life and medical sciences. The whole genome of WZSP was sequenced in 2012. Through a bioinformatics study of pig carbonic anhydrase (CA) sequences, we detected some β- and γ-class CAs among the WZSP CAs annotated in databases, while β- or γ-CAs had not previously been described in vertebrates. This finding urged us to analyze the quality of whole genome sequence of WZSP for the possible bacterial contamination. In this study, we used bioinformatics methods and web tools such as UniProt, European Bioinformatics Institute, National Center for Biotechnology Information, Ensembl Genome Browser, Ensembl Bacteria, RSCB PDB and Pseudomonas Genome Database. Our analysis defined that pig has 12 classical α-CAs and 3 CA-related proteins. Meanwhile, it was approved that the detected CAs in WZSP are categorized in the β- and γ-CA families, which belong to Pseudomonas spp. and Acinetobacter spp. The protein structure study revealed that the identified β-CA sequence from WZSP belongs to Pseudomonas aeruginosa with PDB ID: 5JJ8, and the identified γ-CA sequence from WZSP belongs to P. aeruginosa with PDB ID: 3PMO. Bioinformatics and computational methods accompanied with bacterial-specific markers, such as 16S rRNA and β- and γ-class CA sequences, can be used to identify bacterial contamination in mammalian DNA samples.
Collapse
Affiliation(s)
- Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran
| | - Seyed Nezamedin Hosseini
- Department of Recombinant Hepatitis B Vaccine, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Ltd, Tampere University Hospital, Tampere, Finland
| |
Collapse
|
29
|
Chueca LJ, Kochmann J, Schell T, Greve C, Janke A, Pfenninger M, Klimpel S. De novo Genome Assembly of the Raccoon Dog ( Nyctereutes procyonoides). Front Genet 2021; 12:658256. [PMID: 33995489 PMCID: PMC8117329 DOI: 10.3389/fgene.2021.658256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Luis J Chueca
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV-EHU), Vitoria-Gasteiz, Spain
| | - Judith Kochmann
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany
| | - Axel Janke
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Markus Pfenninger
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Sven Klimpel
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| |
Collapse
|
30
|
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
|
31
|
Abstract
Pigs represent a potentially attractive model for medical research. Similar body size and physiological patterns of kidney injury that more closely mimic those described in humans make larger animals attractive for experimentation. Using larger animals, including pigs, to investigate the pathogenesis of acute kidney injury (AKI) also serves as an experimental bridge, narrowing the gap between clinical disease and preclinical discoveries. This article compares the advantages and disadvantages of large versus small AKI animal models and provides a comprehensive overview of the development and application of porcine models of AKI induced by clinically relevant insults, including ischemia-reperfusion, sepsis, and nephrotoxin exposure. The primary focus of this review is to evaluate the use of pigs for AKI studies by current investigators, including areas where more information is needed.
Collapse
Affiliation(s)
- Jianni Huang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - George Bayliss
- Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, Rhode Island
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, Rhode Island
| |
Collapse
|
32
|
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: 15] [Impact Index Per Article: 5.0] [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
|
33
|
Zhu Q, Sang F, Withey S, Tang W, Dietmann S, Klisch D, Ramos-Ibeas P, Zhang H, Requena CE, Hajkova P, Loose M, Surani MA, Alberio R. Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage. Cell Rep 2021; 34:108735. [PMID: 33567277 PMCID: PMC7873836 DOI: 10.1016/j.celrep.2021.108735] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/17/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Investigations of the human germline and programming are challenging because of limited access to embryonic material. However, the pig as a model may provide insights into transcriptional network and epigenetic reprogramming applicable to both species. Here we show that, during the pre- and early migratory stages, pig primordial germ cells (PGCs) initiate large-scale epigenomic reprogramming, including DNA demethylation involving TET-mediated hydroxylation and, potentially, base excision repair (BER). There is also macroH2A1 depletion and increased H3K27me3 as well as X chromosome reactivation (XCR) in females. Concomitantly, there is dampening of glycolytic metabolism genes and re-expression of some pluripotency genes like those in preimplantation embryos. We identified evolutionarily young transposable elements and gene coding regions resistant to DNA demethylation in acutely hypomethylated gonadal PGCs, with potential for transgenerational epigenetic inheritance. Detailed insights into the pig germline will likely contribute significantly to advances in human germline biology, including in vitro gametogenesis.
Collapse
Affiliation(s)
- Qifan Zhu
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Fei Sang
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Sarah Withey
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Walfred Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Sabine Dietmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Doris Klisch
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Priscila Ramos-Ibeas
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Haixin Zhang
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Cristina E Requena
- MRC London Institute of Medical Sciences (LMS), London, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Petra Hajkova
- MRC London Institute of Medical Sciences (LMS), London, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Matt Loose
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK; Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
| |
Collapse
|
34
|
Liu T, Li J, Yu L, Sun HX, Li J, Dong G, Hu Y, Li Y, Shen Y, Wu J, Gu Y. Cross-species single-cell transcriptomic analysis reveals pre-gastrulation developmental differences among pigs, monkeys, and humans. Cell Discov 2021; 7:8. [PMID: 33531465 PMCID: PMC7854681 DOI: 10.1038/s41421-020-00238-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Interspecies blastocyst complementation enables organ-specific enrichment of xenogeneic pluripotent stem cell (PSC) derivatives, which raises an intriguing possibility to generate functional human tissues/organs in an animal host. However, differences in embryo development between human and host species may constitute the barrier for efficient chimera formation. Here, to understand these differences we constructed a complete single-cell landscape of early embryonic development of pig, which is considered one of the best host species for human organ generation, and systematically compared its epiblast development with that of human and monkey. Our results identified a developmental coordinate of pluripotency spectrum among pigs, humans and monkeys, and revealed species-specific differences in: (1) pluripotency progression; (2) metabolic transition; (3) epigenetic and transcriptional regulations of pluripotency; (4) cell surface proteins; and (5) trophectoderm development. These differences may prevent proper recognition and communication between donor human cells and host pig embryos, resulting in low integration and survival of human cells. These results offer new insights into evolutionary conserved and divergent processes during mammalian development and may be helpful for developing effective strategies to overcome low human-pig chimerism, thereby enabling the generation of functional human organs in pigs in the future.
Collapse
Affiliation(s)
- Tianbin Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jie Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Hai-Xi Sun
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jing Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Guoyi Dong
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yingying Hu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yong Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ying Gu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China. .,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
35
|
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
|
36
|
Wang Y, Chen X, Huang Z, Chen D, Yu B, Yu J, Chen H, He J, Luo Y, Zheng P. Dietary Ferulic Acid Supplementation Improves Antioxidant Capacity and Lipid Metabolism in Weaned Piglets. Nutrients 2020; 12:nu12123811. [PMID: 33322714 PMCID: PMC7763429 DOI: 10.3390/nu12123811] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Ferulic acid (FA) is a phenolic compound that has antioxidant, hepatoprotective, anticarcinogenic, anti-inflammatory, antiallergic, antimicrobial, antiviral, and vasodilatory effects. This study was conducted to explore the effects of dietary FA supplementation on antioxidant capacity and lipid metabolism in weaned piglets. Eighteen 21-day-old castrated male DLY (Duroc × Landrace × Yorkshire) weaned piglets were randomly divided into control, 0.05%, and 0.45% FA groups. The results showed that, in serum, CAT and T-SOD activities and content of HDL-C were increased, but the content of MDA and the activities of T-CHO and LDL-C were decreased, by FA supplementation. In liver, dietary FA supplementation increased CAT, T-SOD, and GSH-PX activities and upregulated the mRNA levels of SOD1, SOD2, CAT, GST, GPX1, GR, Nrf2, HSL, CPT1b, and PPARα but decreased the contents of MDA and TG. Furthermore, dietary FA supplementation increased the protein level of Nrf2, HO-1, and NQO-1. In longissimus dorsi muscle, dietary FA supplementation increased the activity of T-SOD and the mRNA abundance of SOD1, SOD2, CAT, GST, GPX1, GR, and Nrf2 but decreased the contents of MDA and T-CHO. Additionally, dietary FA supplementation increased the protein expressions of Nrf2, HO-1, and NQO1. Together, our data suggest that FA could improve antioxidant capacity and lipid metabolism in weaned piglets.
Collapse
Affiliation(s)
- Youxia Wang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
| | - Xiaoling Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
- Correspondence: ; Tel./Fax: +86-28-8629-0976
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
| | - Hong Chen
- College of Food Science, Sichuan Agricultural University, Yaan 625014, China;
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.C.); (D.C.); (B.Y.); (J.Y.); (J.H.); (Y.L.); (P.Z.)
| |
Collapse
|
37
|
Lamb HJ, Hayes BJ, Nguyen LT, Ross EM. The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock. Genes (Basel) 2020; 11:E1478. [PMID: 33317066 PMCID: PMC7763041 DOI: 10.3390/genes11121478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Oxford Nanopore Technologies' MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: 'crush-side genotyping' for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.
Collapse
Affiliation(s)
- Harrison J. Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4067, Australia; (B.J.H.); (L.T.N.); (E.M.R.)
| | | | | | | |
Collapse
|
38
|
The Peripherin Gene Regulates the Migration of Bone Marrow Mesenchymal Stem Cells in Wuzhishan Mini Pigs. Stem Cells Int 2020; 2020:8856388. [PMID: 33101422 PMCID: PMC7576346 DOI: 10.1155/2020/8856388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/04/2020] [Accepted: 09/05/2020] [Indexed: 11/18/2022] Open
Abstract
Increasing the migratory capacity of the implanted mesenchymal stem cells (MSCs) is a major challenge in developing successful cell transplantation therapies. Nevertheless, the regulatory factors involved in the migration of BMMSCs remain largely unknown. In this study, we studied the role of the peripherin (PRPH) gene in regulating the ability of Wuzhishan mini pig (WZSP) BMMSCs to migrate in vitro. Four different shRNA vectors directed against PRPH were designed and transfected into BMMSCs. The vector with the best interference effect was chosen to be used in the following experiments. The expression level of PRPH in BMMSCs was determined by quantitative real-time PCR and western blot analysis. The migration capacity of the BMMSCs was estimated using a scratch assay, a transwell in vitro migration model assay, and filamentous actin staining. The results showed that shRNA-mediated knockdown of the expression of the PRPH gene in BMMSCs reduced the ability of these cells to migrate. Overall, these results illustrate that the PRPH gene regulates the migration of BMMSCs in the WZSP.
Collapse
|
39
|
Wang H, Fu Y, Gu P, Zhang Y, Tu W, Chao Z, Wu H, Cao J, Zhou X, Liu B, Michal JJ, Fan C, Tan Y. Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds. Animals (Basel) 2020; 10:ani10101792. [PMID: 33023098 PMCID: PMC7600727 DOI: 10.3390/ani10101792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/15/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Simple sequence repeats (SSRs) are present at high densities in regulatory elements, suggesting that they may affect gene function and phenotypic traits. Therefore, SSRs can be exploited in marker-assisted selection. In addition, they can be widely used as molecular markers to study genetic diversity, population structure, and evolution. While SSRs have been widely studied in many mammalian species, very little research has focused on genome-wide SSRs of miniature pigs, a small but special group of pigs that express the dwarf phenotype. Based on the SSR-enriched library building and sequencing, about 30,000 novel polymorphic SSRs for four miniature pig breeds were mapped to the Duroc pig reference genome. The four miniature pig breeds had different numbers and types of SSRs and distributions of repeat units. There were 2518 polymorphic SSRs in the intron or exon regions that were common to all four breeds and functional analyses revealed 17 genes that were associated with body size and other genes that were associated with growth and development. In conclusion, the SSRs detected in the miniature pigs in this study may provide useful genetic markers for the selection of farm animals and the polymorphic SSRs provide valuable insights into the determination of mature body size, as well as the immunity, growth and development of animals. Abstract Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as FGF23, MYF6, IGF1R, and LEPROT, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development.
Collapse
Affiliation(s)
- Hongyang Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Yang Fu
- Research Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China;
| | - Peng Gu
- Institute of Comparative Medicine & Laboratory Animal Management Center, Southern Medical University, Guangzhou 510515, China;
| | - Yingying Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Weilong Tu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
| | - Huali Wu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Jianguo Cao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (B.L.)
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (X.Z.); (B.L.)
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA;
| | - Chun Fan
- Shanghai Laboratory Animal Research Center, Shanghai 201203, China;
| | - Yongsong Tan
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (H.W.); (Y.Z.); (W.T.); (H.W.); (J.C.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201302, China
- Correspondence: ; Tel.: +86-021-34505325
| |
Collapse
|
40
|
Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs. Sci Rep 2020; 10:9433. [PMID: 32523001 PMCID: PMC7286894 DOI: 10.1038/s41598-020-66061-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 05/14/2020] [Indexed: 12/05/2022] Open
Abstract
Chinese indigenous pigs exhibit considerable phenotypic diversity, but their population structure and the genetic basis of agriculturally important traits need further exploration. Here, we sequenced the whole genomes of 24 individual pigs representing 22 breeds distributed throughout China. For comparison with European and commercial breeds (one pig per breed), we included seven published pig genomes with our new genomes for analyses. Our results showed that breeds grouped together based on morphological classifications are not necessarily more genetically similar to each other than to breeds from other groups. We found that genetic material from European pigs likely introgressed into five Chinese breeds. We have identified two new subpopulations of domestic pigs that encompass morphology-based criteria in China. The Southern Chinese subpopulation comprises the classical South Chinese Type and part of the Central China Type. In contrast, the Northern Chinese subpopulation comprises the North China Type, the Lower Yangtze River Basin Type, the Southwest Type, the Plateau Type, and the remainder of the Central China Type. Eight haplotypes and two recombination sites were identified within a conserved 40.09 Mb linkage-disequilibrium (LD) block on the X chromosome. Potential candidate genes (LEPR, FANCC, COL1A1, and PCCA) influencing body size were identified. Our findings provide insights into the phylogeny of Chinese indigenous pig breeds and benefit gene mining efforts to improve major economic traits.
Collapse
|
41
|
Reimer C, Ha NT, Sharifi AR, Geibel J, Mikkelsen LF, Schlather M, Weigend S, Simianer H. Assessing breed integrity of Göttingen Minipigs. BMC Genomics 2020; 21:308. [PMID: 32299342 PMCID: PMC7161115 DOI: 10.1186/s12864-020-6590-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Göttingen Minipigs (GMP) is the smallest commercially available minipig breed under a controlled breeding scheme and is globally bred in five isolated colonies. The genetic isolation harbors the risk of stratification which might compromise the identity of the breed and its usability as an animal model for biomedical and human disease. We conducted whole genome re-sequencing of two DNA-pools per colony to assess genomic differentiation within and between colonies. We added publicly available samples from 13 various pig breeds and discovered overall about 32 M loci, ~ 16 M. thereof variable in GMPs. Individual samples were virtually pooled breed-wise. FST between virtual and DNA pools, a phylogenetic tree, principal component analysis (PCA) and evaluation of functional SNP classes were conducted. An F-test was performed to reveal significantly differentiated allele frequencies between colonies. Variation within a colony was quantified as expected heterozygosity. RESULTS Phylogeny and PCA showed that the GMP is easily discriminable from all other breads, but that there is also differentiation between the GMP colonies. Dependent on the contrast between GMP colonies, 4 to 8% of all loci had significantly different allele frequencies. Functional annotation revealed that functionally non-neutral loci are less prone to differentiation. Annotation of highly differentiated loci revealed a couple of deleterious mutations in genes with putative effects in the GMPs . CONCLUSION Differentiation and annotation results suggest that the underlying mechanisms are rather drift events than directed selection and limited to neutral genome regions. Animal exchange seems not yet necessary. The Relliehausen colony appears to be the genetically most unique GMP sub-population and could be a valuable resource if animal exchange is required to maintain uniformity of the GMP.
Collapse
Affiliation(s)
- Christian Reimer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| | - Ngoc-Thuy Ha
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| | - Ahmad Reza Sharifi
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| | - Johannes Geibel
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| | | | - Martin Schlather
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
- Institute of Mathematics, University of Mannheim, B6 26, 68131 Mannheim, Germany
| | - Steffen Weigend
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
- Institute of Farm Animal Genetics of the Friedrich-Loeffler-Institut, Höltystraße 10, 31535 Neustadt, Germany
| | - Henner Simianer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Göttingen, Albrecht-Thaer-Weg 3, 37017 Göttingen, Germany
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
| |
Collapse
|
42
|
Ex vivo diffusion-weighted MRI tractography of the Göttingen minipig limbic system. Brain Struct Funct 2020; 225:1055-1071. [DOI: 10.1007/s00429-020-02058-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/18/2020] [Indexed: 10/24/2022]
|
43
|
Jeličová M, Lierová A, Šinkorová Z, Pejchal J. CHANGES IN BLOOD COUNT AND LYMPHOCYTE MICRONUCLEI IN PIGLETS AFTER WHOLE-BODY IRRADIATION. RADIATION PROTECTION DOSIMETRY 2019; 186:176-180. [PMID: 31711213 DOI: 10.1093/rpd/ncz198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/19/2019] [Accepted: 04/15/2019] [Indexed: 06/10/2023]
Abstract
Biodosimetry is focused on effects of ionizing radiation at cellular and molecular levels of living organisms so that a qualified retrospective estimate of radiation load can be made. Two biodosimetry methods were evaluated in irradiated piglets: complete blood count analysis and quantification of chromosomal aberrations in lymphocytes using a micronucleus test. Animals were whole-body irradiated with gamma radiation at doses of 0-10 Gy. The analysis of complete blood count was performed at intervals ranging from 0 to 48 hours. Micronuclei were measured at 4 hours after irradiation. Changes in lymphocyte counts and increased levels of micronuclei reflected received dose of ionizing radiation.
Collapse
Affiliation(s)
- Marcela Jeličová
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defence, Hradec Králové, Czech Republic
| | - Anna Lierová
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defence, Hradec Králové, Czech Republic
| | - Zuzana Šinkorová
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defence, Hradec Králové, Czech Republic
| | - Jaroslav Pejchal
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Hradec Králové, Czech Republic
| |
Collapse
|
44
|
Son DH, Hwang NH, Chung WH, Seong HS, Lim H, Cho ES, Choi JW, Kang KS, Kim YM. Whole-genome resequencing analysis of 20 Micro-pigs. Genes Genomics 2019; 42:263-272. [PMID: 31833050 DOI: 10.1007/s13258-019-00891-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Miniature pigs have been increasingly used as mammalian model animals for biomedical research because of their similarity to human beings in terms of their metabolic features and proportional organ sizes. However, despite their importance, there is a severe lack of genome-wide studies on miniature pigs. OBJECTIVE In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics. RESULTS Approximately 595 gigabase pairs (Gb) of sequence reads were generated to be mapped to the swine reference genome assembly (Sus scrofa 10.2); on average, the sequence reads covered 99.15% of the reference genome at an average of 9.6-fold coverage. We detected a total of 19,518,548 SNPs, of which 8.7% were found to be novel. With further annotation of all of the SNPs, we retrieved 144,507 nonsynonymous SNPs (nsSNPs); of these, 5968 were found in all 20 individuals used in this study. SIFT prediction for these SNPs identified that 812 nsSNPs in 402 genes were deleterious. Among these 402 genes, we identified some genes that could potentially affect traits of interest in Micro-pigs, such as RHEB and FRAS1. Furthermore, we performed runs of homozygosity analysis to locate potential selection signatures in the genome, detecting several loci that might be involved in phenotypic characteristics in Micro-pigs, such as MSTN, GDF5, and GDF11. CONCLUSION In this study, we identified numerous nsSNPs that could be used as candidate genetic markers with involvement in traits of interest. Furthermore, we detected putative selection footprints that might be associated with recent selection applied to miniature pigs.
Collapse
Affiliation(s)
- Da-Hye Son
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Nam-Hyun Hwang
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Won-Hyong Chung
- Research Division of Food Functionality, Research Group of Healthcare, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Ha-Seung Seong
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Hyungbum Lim
- Medikinetics Co., Ltd, 4 Hansan-gil, Cheongbuk-eup, Pyeongtaek-si, Gyeonggi-do, 17792, Republic of Korea
| | - Eun-Seok Cho
- Division of Swine Science, National Institute of Animal Science, RDA, Cheonan, 31000, Republic of Korea
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Kyung-Soo Kang
- Medikinetics Co., Ltd, 4 Hansan-gil, Cheongbuk-eup, Pyeongtaek-si, Gyeonggi-do, 17792, Republic of Korea.
| | - Yong-Min Kim
- Division of Swine Science, National Institute of Animal Science, RDA, Cheonan, 31000, Republic of Korea.
| |
Collapse
|
45
|
Effects of Dietary Apple Polyphenols Supplementation on Hepatic Fat Deposition and Antioxidant Capacity in Finishing Pigs. Animals (Basel) 2019; 9:ani9110937. [PMID: 31717391 PMCID: PMC6912552 DOI: 10.3390/ani9110937] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Excessive fat deposition (5–10%) in the liver could lead to liver damage and nonalcohol fatty liver disease (NAFLD). However, there is no satisfactory safe and effective measure of preventive and therapeutic treatments so far. Thus, the prevention of excessive fat deposition through diet modification might be a better strategy to protect humans from metabolic diseases. Due to the anatomical and physiological similarities between humans and pigs, the present study took the finishing pig as an animal model to investigate the effects of apple polyphenols on hepatic fat deposition and antioxidant capacity and their mechanisms. The present study indicated that apple polyphenols might be an effective dietary supplementation for decreasing the excessive fat deposition in liver tissue, improving lipid profiles and increasing the antioxidant capacity of finishing pigs. This study provides a better preventive strategy to protect humans from excessive fat deposition in the liver. Abstract Excessive fat deposition in the liver could lead to fatty liver and an increased risk of many metabolic diseases. Apple polyphenols (APPs), the major antioxidants in apples, possess wide-ranging beneficial biological functions. The present study aimed to investigate the effects of APPs on hepatic fat deposition and antioxidant capacity in finishing pigs, and their mechanisms. Results showed that APPs improved lipid profiles, increased antioxidant enzyme activities and reduced the fat deposition in the liver. In the liver, SOD1, CAT, GPX1, GST, NF-E2-related nuclear factor 2 (Nrf2), hormone sensitive lipase (HSL), carnitine palmitoyl transferase-1b (CPT1b), peroxisome proliferator-activated receptor α (PPARα), cholesterol 7α-hydroxylase (CYP7A1) and low-density lipoprotein receptor (LDL-R) mRNA levels were increased by APPs, while Kelch-like ECH-associated protein 1 (Keap1) mRNA level, C16:0 and C20:4n-6 proportions and Δ9-18 dehydrogenase activity were decreased. In conclusion, this study indicated that APPs might be an effective dietary supplementation for improving lipid profiles, increasing antioxidant capacities and decreasing fat deposition in the liver.
Collapse
|
46
|
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: 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: 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
|
47
|
Dynamic mRNA Expression Analysis of the Secondary Palatal Morphogenesis in Miniature Pigs. Int J Mol Sci 2019; 20:ijms20174284. [PMID: 31480549 PMCID: PMC6747431 DOI: 10.3390/ijms20174284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 08/30/2019] [Indexed: 12/12/2022] Open
Abstract
Normal mammalian palatogenesis is a complex process that requires the occurrence of a tightly regulated series of specific and sequentially regulated cellular events. Cleft lip/palate (CLP), the most frequent craniofacial malformation birth defects, may occur if any of these events undergo abnormal interference. Such defects not only affect the patients, but also pose a financial risk for the families. In our recent study, the miniature pig was shown to be a valuable alternative large animal model for exploring human palate development by histology. However, few reports exist in the literature to document gene expression and function during swine palatogenesis. To better understand the genetic regulation of palate development, an mRNA expression profiling analysis was performed on miniature pigs, Sus scrofa. Five key developmental stages of miniature pigs from embryonic days (E) 30–50 were selected for transcriptome sequencing. Gene expression profiles in different palate development stages of miniature pigs were identified. Nine hundred twenty significant differentially expressed genes were identified, and the functional characteristics of these genes were determined by gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Some of these genes were associated with HH (hedgehog), WNT (wingless-type mouse mammary tumor virus integration site family), and MAPK (mitogen-activated protein kinase) signaling, etc., which were shown in the literature to affect palate development, while some genes, such as HIP (hedgehog interacting protein), WNT16, MAPK10, and LAMC2 (laminin subunit gamma 2), were additions to the current understanding of palate development. The present study provided a comprehensive analysis for understanding the dynamic gene regulation during palate development and provided potential ideas and resources to further study normal palate development and the etiology of cleft palate.
Collapse
|
48
|
Liang Y, Wang Y, Ma L, Zhong Z, Yang X, Tao X, Chen X, He Z, Yang Y, Zeng K, Kang R, Gong J, Ying S, Lei Y, Pang J, Lv X, Gu Y. Comparison of microRNAs in adipose and muscle tissue from seven indigenous Chinese breeds and Yorkshire pigs. Anim Genet 2019; 50:439-448. [PMID: 31328299 DOI: 10.1111/age.12826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 01/29/2023]
Abstract
Elucidation of the pig microRNAome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits. Here, we extracted small RNAs from skeletal muscle and adipose tissue, and we compared their expression levels between one Western breed (Yorkshire) and seven indigenous Chinese breeds. We detected the expression of 172 known porcine microRNAs (miRNAs) and 181 novel miRNAs. Differential expression analysis found 92 and 12 differentially expressed miRNAs in adipose and muscle tissue respectively. We found that different Chinese breeds shared common directional miRNA expression changes compared to Yorkshire pigs. Some miRNAs differentially expressed across multiple Chinese breeds, including ssc-miR-129-5p, ssc-miR-30 and ssc-miR-150, are involved in adipose tissue function. Functional enrichment analysis revealed that the target genes of the differentially expressed miRNAs are associated mainly with signaling pathways rather than metabolic and biosynthetic processes. The miRNA-target gene and miRNA-phenotypic traits networks identified many hub miRNAs that regulate a large number of target genes or phenotypic traits. Specifically, we found that intramuscular fat content is regulated by the greatest number of miRNAs in muscle tissue. This study provides valuable new candidate miRNAs that will aid in the improvement of meat quality and production.
Collapse
Affiliation(s)
- Y Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - L Ma
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, 610052, Sichuan Province China
| | - Z Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Z He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - K Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - R Kang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - J Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - S Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - J Pang
- Chengdu Biotechservice Institute, Chengdu, 610041, Sichuan Province China
| | - X Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| |
Collapse
|
49
|
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: 33] [Impact Index Per Article: 6.6] [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
|
50
|
Xu X, Chen X, Huang Z, Chen D, Yu B, Chen H, He J, Luo Y, Zheng P, Yu J, Luo J. Dietary apple polyphenols supplementation enhances antioxidant capacity and improves lipid metabolism in weaned piglets. J Anim Physiol Anim Nutr (Berl) 2019; 103:1512-1520. [PMID: 31268198 DOI: 10.1111/jpn.13152] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/27/2019] [Accepted: 06/08/2019] [Indexed: 01/10/2023]
Abstract
Apple polyphenols (APPs) are biologically active flavonoids that have antioxidant, anti-inflammatory, improving insulin sensitivity, hypocholesterolaemic effect and antiviral properties. This study was conducted to explore effects of dietary APPs supplementation on antioxidant activities and lipid metabolism in weaned piglets. Fifty-four weaned piglets (half male and female) were randomly divided into three groups with six replicates in each group and three piglets in each repetition. Piglets were fed control diet (basal diet) or a control diet supplemented with 400 mg/kg or 800 mg/kg APPs for 6 weeks. Blood and liver samples were collected to determine biochemical, antioxidant and lipid metabolism parameters. Here we showed that dietary APPs supplementation increased HDL-C and decreased T-CHO, TG and LDL-C concentrations. Dietary APPs supplementation increased antioxidative capacity in serum and CAT activity in liver, and significantly increased the mRNA expressions of CAT, GST and SOD1 in liver. ACC mRNA level and LPL activity were tended to decrease by APPs. HMG-CoAR, CTP7A1, CD36 and FATP1 mRNA levels were decreased by APPs, while LDL-R, PGC-1α, Sirt1 and CPT1b mRNA levels were increased by 400 mg/kg APPs. No alterations in growth performance were found in all treatments. This study firstly provided the evidence that dietary APPs supplementation could enhance systemic antioxidant capacity and improve lipid metabolism in weaned piglets. The mechanism by which APPs improve lipid metabolism might be through regulating hepatic cholesterol metabolism and increasing fatty acid oxidation, and decreasing fatty acid uptake and de novo synthesis.
Collapse
Affiliation(s)
- Xiaojiao Xu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoling Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hong Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| |
Collapse
|