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Kwon D, Ahn J, Kim H, Kim H, Kim J, Wy S, Ko Y, Kim J. Convergent dwarfism consequences of minipigs under independent artificial selections. BMC Genomics 2024; 25:761. [PMID: 39107730 PMCID: PMC11301983 DOI: 10.1186/s12864-024-10677-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Currently, diverse minipigs have acquired a common dwarfism phenotype through independent artificial selections. Characterizing the population and genetic diversity in minipigs is important to unveil genetic mechanisms regulating their body sizes and effects of independent artificial selections on those genetic mechanisms. However, full understanding for the genetic mechanisms and phenotypic consequences in minipigs still lag behind. RESULTS Here, using whole genome sequencing data of 41 pig breeds, including eight minipigs, we identified a large genomic diversity in a minipig population compared to other pig populations in terms of population structure, demographic signatures, and selective signatures. Selective signatures reveal diverse biological mechanisms related to body size in minipigs. We also found evidence for neural development mechanism as a minipig-specific body size regulator. Interestingly, selection signatures within those mechanisms containing neural development are also highly different among minipig breeds. Despite those large genetic variances, PLAG1, CHM, and ESR1 are candidate key genes regulating body size which experience different differentiation directions in different pig populations. CONCLUSIONS These findings present large variances of genetic structures, demographic signatures, and selective signatures in the minipig population. They also highlight how different artificial selections with large genomic diversity have shaped the convergent dwarfism.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jiyeong Ahn
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyeonji Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Junyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin, Gyeonggi-Do, 17035, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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2
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Wy S, Kwon D, Park W, Chai HH, Cho IC, Kim J. A chromosome-level genome assembly of the Korean minipig (Sus scrofa). Sci Data 2024; 11:840. [PMID: 39097649 PMCID: PMC11297928 DOI: 10.1038/s41597-024-03680-8] [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: 05/08/2024] [Accepted: 07/25/2024] [Indexed: 08/05/2024] Open
Abstract
Recent advancements in sequencing and genome assembly technologies have led to rapid generation of high-quality genome assemblies for various species and breeds. Despite the importance as minipigs an animal model in biomedical research, the construction of high-quality genome assemblies of minipigs still lags behind other pig breeds. To address this problem, we constructed a high-quality chromosome-level genome assembly of the Korean minipig (KMP) utilizing multiple different types of sequencing reads and reference genomes. The KMP assembly included 19 chromosome-level sequences with a total length of 2.52 Gb and N50 of 137 Mb. Comparative analyses with the pig reference genome (Sscrofa11.1) demonstrated comparable contiguity and completeness of the KMP assembly. Additionally, genome annotation analyses identified 22,666 protein-coding genes and repetitive elements occupying 40.10% of the genome. The KMP assembly and genome annotation provide valuable resources that can contribute to various future research on minipig and other pig breeds.
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Affiliation(s)
- Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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3
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Deng D, Lei H, Cao Z, Zhang C, Du R, Gao X, Wei J, Lu Y, Zhou X, Zhang L. Microbiome-gut-brain axis contributes to patients and Bama miniature pigs with acute large ischemic stroke. Front Neurosci 2024; 18:1378844. [PMID: 39071180 PMCID: PMC11272540 DOI: 10.3389/fnins.2024.1378844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
Acute large hemispheric infarction (ALHI) is an overwhelming emergency with a great challenge of gastrointestinal dysfunction clinically. Here, we initially proposed delayed bowel movements as the clinical phenotype of strike to gut-brain axis (GBA) in ALHI patients by epidemiological analysis of 499 acute ischemic stroke (AIS) patients. 1H NMR-based metabolomics revealed that AIS markedly altered plasma global metabolic profiling of patients compared with healthy controls. Risk factors of strike on GBA were the National Institutes of Health Stroke Scale (NIHSS) score ≥ 5 and stroke onset time ≤ 24 h. As a result, first defecating time after admission to the hospital ≥2 days could be considered as a potential risk factor for strike on GBA. Subsequently, the ALHI Bama miniature (BM) pig model with acute symptomatic seizure was successfully established by ligation of the left ascending pharyngeal artery combined with local air injection. Clinical phenotypes of brain necrosis such as hemiplegia were examined with brain diffusion-weighted imaging (DWI) and pathological diagnosis. In addition to global brain injury and inflammation, we also found that ALHI induced marked alterations of intestinal barrier integrity, the gut microbial community, and microbiota-derived metabolites including serotonin and neurotransmitters in both plasma and multiple brain tissues of BM pigs. These findings revealed that microbiota-gut-brain axis highly contributed to the occurrence and development of ALHI.
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Affiliation(s)
- Dazhi Deng
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- Department of Emergency, The People's Hospital of Guangxi Zhuang Autonomous Region and Guangxi Academy of Medical Sciences, Nanning, China
| | - Hehua Lei
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, National Centre for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Cao
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, National Centre for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cui Zhang
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, National Centre for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruichen Du
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, National Centre for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Gao
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, National Centre for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjie Wei
- Department of Neurology, The People's Hospital of Guangxi Zhuang Autonomous Region and Guangxi Academy of Medical Sciences, Nanning, China
| | - Yibo Lu
- Department of Radiology, Nanning Fourth People's Hospital and Guangxi AIDS Clinical Treatment Center, Nanning, China
| | - Xiangzhen Zhou
- Department of Pathology, The People's Hospital of Guangxi Zhuang Autonomous Region and Guangxi Academy of Medical Sciences, Nanning, China
| | - Limin Zhang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, National Centre for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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4
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Meyerholz DK, Burrough ER, Kirchhof N, Anderson DJ, Helke KL. Swine models in translational research and medicine. Vet Pathol 2024; 61:512-523. [PMID: 38197394 DOI: 10.1177/03009858231222235] [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] [Indexed: 01/11/2024]
Abstract
Swine are increasingly studied as animal models of human disease. The anatomy, size, longevity, physiology, immune system, and metabolism of swine are more like humans than traditional rodent models. In addition, the size of swine is preferred for surgical placement and testing of medical devices destined for humans. These features make swine useful for biomedical, pharmacological, and toxicological research. With recent advances in gene-editing technologies, genetic modifications can readily and efficiently be made in swine to study genetic disorders. In addition, gene-edited swine tissues are necessary for studies testing and validating xenotransplantation into humans to meet the critical shortfall of viable organs versus need. Underlying all of these biomedical applications, the knowledge of husbandry, background diseases and lesions, and biosecurity needs are important for productive, efficient, and reproducible research when using swine as a human disease model for basic research, preclinical testing, and translational studies.
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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.
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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
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Wu Y, Mo J, Liang J, Pu X, Dong Y, Zhu X, Zhao H, Qiu H, Wu S, Lu T. Multiomic study of the protective mechanism of Persicaria capitata (Buch.-Ham. ex D.Don) H.Gross against streptozotocin-induced diabetic nephropathy in Guizhou miniature pigs. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155499. [PMID: 38492367 DOI: 10.1016/j.phymed.2024.155499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Persicaria capitata (Buch.-Ham. ex D.Don) H.Gross (P. capitata, PCB), a traditional drug of the Miao people in China, is potential traditional drug used for the treatment of diabetic nephropathy (DN). PURPOSE The purpose of this study is to investigate the function of P. capitata and clarify its protective mechanism against DN. METHODS We induced DN in the Guizhou miniature pig with injections of streptozotocin, and P. capitata was added to the pigs' diet to treat DN. In week 16, all the animals were slaughtered, samples were collected, and the relative DN indices were measured. 16S rRNA sequencing, metagenomics, metabolomics, RNA sequencing, and proteomics were used to explore the protective mechanism of P. capitata against DN. RESULTS Dietary supplementation with P. capitata significantly reduced the extent of the disease, not only in term of the relative disease indices but also in hematoxylin-eosin-stained tissues. A multiomic analysis showed that two microbes (Clostridium baratii and Escherichia coli), five metabolites (oleic acid, linoleic acid, 4-phenylbutyric acid, 18-β-glycyrrhetinic acid, and ergosterol peroxide), four proteins (ENTPD5, EPHX1, ARVCF and TREH), four important mRNAs (encoding ENTPD5, EPHX1, ARVCF, and TREH), six lncRNAs (TCONS_00024194, TCONS_00085825, TCONS_00006937, TCONS_00070981, TCONS_00074099, and TCONS_00097913), and two circRNAs (novel_circ_0001514 and novel_circ_0017507) are all involved in the protective mechanism of P. capitata against DN. CONCLUSIONS Our results provide multidimensional theoretical support for the study and application of P. capitata.
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Affiliation(s)
- Yanjun Wu
- Guizhou University of Traditional Chinese Medicine, Dongqing road, Guiyang, Guizhou 550025, China
| | - Jiayuan Mo
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Xiang Pu
- Guizhou University of Traditional Chinese Medicine, Dongqing road, Guiyang, Guizhou 550025, China
| | - Yuanqiu Dong
- Guizhou University of Traditional Chinese Medicine, Dongqing road, Guiyang, Guizhou 550025, China
| | - Xiang Zhu
- Guizhou University of Traditional Chinese Medicine, Dongqing road, Guiyang, Guizhou 550025, China
| | - Hai Zhao
- Guizhou University of Traditional Chinese Medicine, Dongqing road, Guiyang, Guizhou 550025, China
| | - Huaming Qiu
- Guizhou University of Traditional Chinese Medicine, Dongqing road, Guiyang, Guizhou 550025, China
| | - Shuguang Wu
- Guizhou University of Traditional Chinese Medicine, Dongqing road, Guiyang, Guizhou 550025, China
| | - Taofeng Lu
- Guizhou University of Traditional Chinese Medicine, Dongqing road, Guiyang, Guizhou 550025, China.
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7
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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.
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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.
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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.
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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.
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Qi W, Zhu S, Feng L, Liang J, Guo X, Cheng F, Guo Y, Lan G, Liang J. Integrated Analysis of the Transcriptome and Microbial Diversity in the Intestine of Miniature Pig Obesity Model. Microorganisms 2024; 12:369. [PMID: 38399773 PMCID: PMC10891586 DOI: 10.3390/microorganisms12020369] [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: 01/14/2024] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Obesity, a key contributor to metabolic disorders, necessitates an in-depth understanding of its pathogenesis and prerequisites for prevention. Guangxi Bama miniature pig (GBM) offers an apt model for obesity-related studies. In this research, we used transcriptomics and 16S rRNA gene sequencing to discern the differentially expressed genes (DEGs) within intestinal (jejunum, ileum, and colon) tissues and variations in microbial communities in intestinal contents of GBM subjected to normal diets (ND) and high-fat, high-carbohydrate diets (HFHCD). After a feeding duration of 26 weeks, the HFHCD-fed experimental group demonstrated notable increases in backfat thickness, BMI, abnormal blood glucose metabolism, and blood lipid levels alongside the escalated serum expression of pro-inflammatory factors and a marked decline in intestinal health status when compared to the ND group. Transcriptomic analysis revealed a total of 1669 DEGs, of which 27 had similar differences in three intestinal segments across different groups, including five immune related genes: COL6A6, CYP1A1, EIF2AK2, NMI, and LGALS3B. Further, we found significant changes in the microbiota composition, with a significant decrease in beneficial bacterial populations within the HFHCD group. Finally, the results of integrated analysis of microbial diversity with transcriptomics show a positive link between certain microbial abundance (Solibacillus, norank_f__Saccharimonadaceae, Candidatus_Saccharimonas, and unclassified_f__Butyricicoccaceae) and changes in gene expression (COL6A6 and NMI). Overall, HFHCD appears to co-contribute to the initiation and progression of obesity in GBM by aggravating inflammatory responses, disrupting immune homeostasis, and creating imbalances in intestinal flora.
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Affiliation(s)
- Wenjing Qi
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (W.Q.); (G.L.)
| | - Siran Zhu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (W.Q.); (G.L.)
| | - Lingli Feng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (W.Q.); (G.L.)
| | - Jinning Liang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China
| | - Xiaoping Guo
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China
| | - Feng Cheng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (W.Q.); (G.L.)
| | - Yafen Guo
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (W.Q.); (G.L.)
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (W.Q.); (G.L.)
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (W.Q.); (G.L.)
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10
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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.
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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.
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11
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Jiang YF, Wang S, Wang CL, Xu RH, Wang WW, Jiang Y, Wang MS, Jiang L, Dai LH, Wang JR, Chu XH, Zeng YQ, Fang LZ, Wu DD, Zhang Q, Ding XD. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 2023; 26:106119. [PMID: 36852268 PMCID: PMC9958381 DOI: 10.1016/j.isci.2023.106119] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
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Affiliation(s)
- Yi-Fan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chong-Long Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ru-Hai Xu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wen-Wen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Li-He Dai
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jie-Ru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiao-Hong Chu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yong-Qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Ling-Zhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Xiang-Dong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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12
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Li Y, Wang H, Chen H, Liao Y, Gou S, Yan Q, Zhuang Z, Li H, Wang J, Suo Y, Lan T, Liu Y, Zhao Y, Zou Q, Nie T, Hui X, Lai L, Wu D, Fan N. Generation of a genetically modified pig model with CREBRF R457Q variant. FASEB J 2022; 36:e22611. [PMID: 36250915 DOI: 10.1096/fj.202201117] [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: 07/13/2022] [Accepted: 10/03/2022] [Indexed: 11/11/2022]
Abstract
Obesity is among the strongest risk factors for type 2 diabetes (T2D). The CREBRF missense allele rs373863828 (p. Arg457Gln, p. R457Q) is associated with increased body mass index but reduced risk of T2D in people of Pacific ancestry. To investigate the functional consequences of the CREBRF variant, we introduced the corresponding human mutation R457Q into the porcine genome. The CREBRFR457Q pigs displayed dramatically increased fat deposition, which was mainly distributed in subcutaneous adipose tissue other than visceral adipose tissue. The CREBRFR457Q variant promoted preadipocyte differentiation. The increased differentiation capacity of precursor adipocytes conferred pigs the unique histological phenotype that adipocytes had a smaller size but a greater number in subcutaneous adipose tissue (SAT) of CREBRFR457Q variant pigs. In addition, in SAT of CREBRFR457Q pigs, the contents of the peroxidative metabolites 4-hydroxy-nonenal and malondialdehyde were significantly decreased, while the activity of antioxidant enzymes, such as glutathione peroxidase, superoxide dismutase, and catalase, was increased, which was in accordance with the declined level of the reactive oxygen species (ROS) in CREBRFR457Q pigs. Together, these data supported a causal role of the CREBRFR457Q variant in the pathogenesis of obesity, partly via adipocyte hyperplasia, and further suggested that reduced oxidative stress in adipose tissue may mediate the relative metabolic protection afforded by this variant despite the related obesity.
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Affiliation(s)
- Yingying Li
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Hai Wang
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Huangyao Chen
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yuan Liao
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Shixue Gou
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Quanmei Yan
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhenpeng Zhuang
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Hao Li
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Jiaowei Wang
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yangyang Suo
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Ting Lan
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yang Liu
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yu Zhao
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Tao Nie
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyan Hui
- School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong SAR
| | - Liangxue Lai
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, China
| | - Donghai Wu
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Nana Fan
- CAS Key Laboratory of Regenerative Biology, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
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13
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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.
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14
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Resveratrol Inhibits Proliferation and Differentiation of Porcine Preadipocytes by a Novel LincRNA-ROFM/miR-133b/AdipoQ Pathway. Foods 2022; 11:foods11172690. [PMID: 36076875 PMCID: PMC9455634 DOI: 10.3390/foods11172690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Resveratrol (RES) has a wide range of biological and pharmacological activities with various health benefits for humans as a food additive. In animal production, RES has been considered a potential functional feed additive for producing high-quality pork. Long noncoding RNAs (lncRNAs) have emerged as essential regulators of fat metabolism, and phytochemicals can regulate fat metabolism through lncRNA. However, it is unclear whether RES can improve back-fat thickness by regulating lncRNA. In this study, we identified a novel lncRNA, which was named a long intergenic non-protein coding RNA, a regulator of fat metabolism (LincRNA-ROFM), from our previous lncRNA sequencing data. LincRNA-ROFM can inhibit adipocyte proliferation and differentiation. In-depth analyses showed that LincRNA-ROFM acts as a molecular sponge for miR-133b, and adiponectin (AdipoQ) is a direct target of miR-133b in porcine preadipocytes. In addition, the expression of LincRNA-ROFM was positively correlated with AdipoQ. RES can promote the expression of LincRNA-ROFM by PPARα and C/EBPα. Altogether, our research showed that LincRNA-ROFM acts as a ceRNA to sequester miR-133b and is upregulated by RES, leading to heightened AdipoQ expression, and thus decreased adipocyte proliferation and differentiation, which reduces back-fat thickness of pigs. Taken together, the RES/LincRNA-ROFM/miR-133b/AdipoQ regulatory network preliminarily explains the mechanism of action of RES in inhibiting fat deposition, which provides new insight into the downstream mechanism of RES inhibition of fat deposits by regulating the lncRNA.
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15
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Mo J, Lu Y, GangYan, Wang Y, Zhang K, Zhang S, Wang M, Chen X, Lan G, Liang J. Identifying selection signatures for litter size in Guangxi Bama Xiang pigs. Reprod Domest Anim 2022; 57:1536-1543. [PMID: 35989556 DOI: 10.1111/rda.14230] [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: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022]
Abstract
Litter size is an important economic trait in pig production. However, the genetic mechanisms underlying varying litter size in Guangxi Bama Xiang pigs remain unknown. To identify selection signatures for litter size in Guangxi Bama Xiang pigs, we obtained 297 Illumina PorcineSNP50 BeadChip array data and the average born number (ABN) from parity one to nine in Guangxi Bama Xiang pigs. Fixation index (Fst) methods were used to identify the selection signature of the litter size, and three phenotypic gradient differential population pairs (according to the ABN) in individuals were used to reduce the false positives of signature selections. Single nucleotide polymorphisms (SNPs) were identified in the VEGFA promoter and exons. The general linear model was used to analyse the differences in distinct genotypes after they were typed using three-round multiplex PCR technology. Finally, the transcriptome factor and CpG island in the VEGFA promoter were predicted. A total of 328, 328 and 317 significant loci were identified in the 1st, 2nd and 3rd population pairs, respectively. After removing the false positives, 25 SNPs were defined as the selection signatures in relation to litter size. Ten (VEGFA, USP49, USP25, SRPK1, SLC26A8, RPL10A, PPARD, MAPK14, HMGA1 and CHRDL2) out of 52 genes in the selection regions were annotated as the candidate genes of litter size, respectively, VEGFA. There were no SNPs in the VEGFA exon region, but we obtained three SNPs (rs786889605, rs343769603 and rs323942424) in the VEGFA promoter regions. The ABN in CC was significantly higher than that in TT in rs786889605, and the ABN in TT was significantly lower than that in GG in rs323942424. Meanwhile, the mutation of the VEGFA promoter result in the loss of Sp1 and NF-1 and the formation of Oct-1. In summary, we obtained ten candidate genes, and two mutations in the VEGFA promoter that could be important potential molecular biomarkers for litter size in Bama Xiang pigs.
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Affiliation(s)
- Jiayuan Mo
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Yujie Lu
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - GangYan
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Yubing Wang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Kun Zhang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Shuai Zhang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Mengying Wang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Xingfa Chen
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning, China
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16
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Mo J, Lu Y, Xing T, Xu D, Zhang K, Zhang S, Wang Y, Yan G, Lan G, Liang J. Blood metabolic and physiological profiles of Bama miniature pigs at different growth stages. Porcine Health Manag 2022; 8:35. [PMID: 35941611 PMCID: PMC9358802 DOI: 10.1186/s40813-022-00278-7] [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: 04/27/2022] [Accepted: 07/30/2022] [Indexed: 11/15/2022] Open
Abstract
Background Bama miniature pigs aged between six (6 M) and twelve months (12 M) are usually used in human medical research as laboratory pigs. However, the difference in serum metabolic profiles from 6 to 12 M-old pigs remains unclear. This study aimed to identify the metabolic and physiological profiles present in the blood to further explain changes in Bama miniature pig growth. We collected blood samples from 6 M-, eight-month- (8 M-), ten-month- (10 M-), and 12 M-old healthy Guangxi Bama miniature pigs. A total of 20 blood physiological indices (BPIs) were measured: seven for white blood cells, eight for red blood cells, and five for platelet indices. Liquid chromatography and mass spectrometry-based non-targeted metabolomic approaches were used to analyze the difference in metabolites. The associations between the differences were calculated using Spearman correlations with Benjamini–Hochberg adjustment. The 100 most abundant differential metabolites were selected for analysis of their metabolic profiles. Results There were no significant differences in BPIs at different ages, but the mid cell ratio and red blood cell number increased with age. Seven BPIs in Bama miniature pigs were closer to human BPIs than to mouse BPIs. A total of 14 and 25 significant differential metabolites were identified in 6 M vs. 12 M and 8 M vs. 12 M, respectively. In total, 9 and 18 amino acids and their derivatives showed significantly lower concentrations in 6 M- and 8 M-old pigs than in 12 M-old pigs. They were identified as the core significantly different metabolites between the age groups 6 M vs. 12 M and 8 M vs. 12 M. Half of the enriched pathways were the amino acids metabolism pathways. The concentration of six amino acids (dl-tryptophan, phenylacetylglycine, muramic acid, N-acetylornithine, l(−)-pipecolinic acid, and creatine) and their derivatives increased with age. A total of 61 of the top 100 most abundant metabolites were annotated. The metabolic profiles contained 14 amino acids and derivatives, six bile acids and derivatives, 19 fatty acids and derivatives, and 22 others. The concentrations of fatty acids and derivatives were found to be inversely proportional to those of amino acids and derivatives. Conclusion These findings suggest high levels of MID cell ratio, red blood count, and amino acids in 12 M-old pigs as indicators for improved body function over time in Bama miniature pigs, similar to those in human development. This makes the pig a more suitable medical model organism than the mouse. The results of this study are limited to the characteristics of blood metabolism in the inbred Bama miniature pigs, and the effects of impacting factors such as breed, age, sex, health status and nutritional level should be considered when studying other pig populations. Supplementary Information The online version contains supplementary material available at 10.1186/s40813-022-00278-7.
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Affiliation(s)
- Jiayuan Mo
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Yujie Lu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Tianqi Xing
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Di Xu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Kun Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Shuai Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Yubin Wang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Gang Yan
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China.
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17
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Identification of Body Size Determination Related Candidate Genes in Domestic Pig Using Genome-Wide Selection Signal Analysis. Animals (Basel) 2022; 12:ani12141839. [PMID: 35883386 PMCID: PMC9312078 DOI: 10.3390/ani12141839] [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: 06/16/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 01/03/2023] Open
Abstract
This study aimed to identify the genes related to the body size of pigs by conducting genome-wide selection analysis (GWSA). We performed a GWSA scan on 50 pigs belonging to four small-bodied pig populations (Diannan small-eared pig, Bama Xiang pig, Wuzhishan pig, and Jeju black pig from South Korea) and 124 large-bodied pigs. We used the genetic parameters of the pairwise fixation index (FST) and π ratio (case/control) to screen candidate genome regions and genes related to body size. The results revealed 47,339,509 high-quality SNPs obtained from 174 individuals, while 280 interacting candidate regions were obtained from the top 1% signal windows of both parameters, along with 187 genes (e.g., ADCK4, AMDHD2, ASPN, ASS1, and ATP6V0C). The results of the candidate gene (CG) annotation showed that a series of CGs (e.g., MSTN, LTBP4, PDPK1, PKMYT1, ASS1, and STAT6) was enriched into the gene ontology terms. Moreover, molecular pathways, such as the PI3K-Akt, HIF-1, and AMPK signaling pathways, were verified to be related to body development. Overall, we identified a series of key genes that may be closely related to the body size of pigs, further elucidating the heredity basis of body shape determination in pigs and providing a theoretical reference for molecular breeding.
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18
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Mo J, Lu Y, Zhu S, Feng L, Qi W, Chen X, Xie B, Chen B, Lan G, Liang J. Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs. Front Vet Sci 2022; 9:892815. [PMID: 35711794 PMCID: PMC9195146 DOI: 10.3389/fvets.2022.892815] [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: 03/09/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Litter size and teat number are economically important traits in the porcine industry. However, the genetic mechanisms influencing these traits remain unknown. In this study, we analyzed the genetic basis of litter size and teat number in Bama Xiang pigs and evaluated the genomic inbreeding coefficients of this breed. We conducted a genome-wide association study to identify runs of homozygosity (ROH), and copy number variation (CNV) using the novel Illumina PorcineSNP50 BeadChip array in Bama Xiang pigs and annotated the related genes in significant single nucleotide polymorphisms and common copy number variation region (CCNVR). We calculated the ROH-based genomic inbreeding coefficients (FROH) and the Spearman coefficient between FROH and reproduction traits. We completed a mixed linear model association analysis to identify the effect of high-frequency copy number variation (HCNVR; over 5%) on Bama Xiang pig reproductive traits using TASSEL software. Across eight chromosomes, we identified 29 significant single nucleotide polymorphisms, and 12 genes were considered important candidates for litter-size traits based on their vital roles in sperm structure, spermatogenesis, sperm function, ovarian or follicular function, and male/female infertility. We identified 9,322 ROHs; the litter-size traits had a significant negative correlation to FROH. A total of 3,317 CNVs, 24 CCNVR, and 50 HCNVR were identified using cnvPartition and PennCNV. Eleven genes related to reproduction were identified in CCNVRs, including seven genes related to the testis and sperm function in CCNVR1 (chr1 from 311585283 to 315307620). Two candidate genes (NEURL1 and SH3PXD2A) related to reproduction traits were identified in HCNVR34. The result suggests that these genes may improve the litter size of Bama Xiang by marker-assisted selection. However, attention should be paid to deter inbreeding in Bama Xiang pigs to conserve their genetic diversity.
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Affiliation(s)
- Jiayuan Mo
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Yujie Lu
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Siran Zhu
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Lingli Feng
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Wenjing Qi
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Xingfa Chen
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Bingkun Xie
- College of Animal Science & Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi Institute of Animal Science, Nanning, China
| | - Baojian Chen
- Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi Institute of Animal Science, Nanning, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning, China
- *Correspondence: Jing Liang
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19
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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: 6] [Impact Index Per Article: 3.0] [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.
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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
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20
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Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB, Arif M, Li X, Lin L, Yu J, Ma T, Xu F, Han P, Jiang H, Mardinoglu A, Zhang C, von Feilitzen K, Xu X, Wang J, Yang H, Bolund L, Zhong W, Fagerberg L, Lindskog C, Pontén F, Mulder J, Luo Y, Uhlen M. Genome-wide annotation of protein-coding genes in pig. BMC Biol 2022; 20:25. [PMID: 35073880 PMCID: PMC8788080 DOI: 10.1186/s12915-022-01229-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/07/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND There is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here, a new annotation strategy is introduced based on dimensionality reduction and density-based clustering of whole-body co-expression patterns. This strategy has been used to explore the gene expression landscape in pig, and we present a whole-body map of all protein-coding genes in all major pig tissues and organs. RESULTS An open-access pig expression map ( www.rnaatlas.org ) is presented based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups. A new UMAP-based classification scheme is introduced, in which all protein-coding genes are stratified into tissue expression clusters based on body-wide expression profiles. The distribution and tissue specificity of all 22,342 protein-coding pig genes are presented. CONCLUSIONS Here, we present a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering. A genome-wide resource of the transcriptome map across all major tissues and organs in pig is presented, and the data is available as an open-access resource ( www.rnaatlas.org ), including a comparison to the expression of human orthologs.
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Affiliation(s)
- Max Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Per Oksvold
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jinrong Huang
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - María Bueno Álvez
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xiangyu Li
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jiaying Yu
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Tao Ma
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | | | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Lars Bolund
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Wen Zhong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Mathias Uhlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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21
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Measurement and Destruction of Porcine Endogenous Retrovirus in the Chinese Bama Minipig. Transplant Proc 2022; 54:516-521. [PMID: 35039157 DOI: 10.1016/j.transproceed.2021.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023]
Abstract
Porcine hepatocytes are widely used in bioartificial liver (BAL) systems for the treatment of liver failure, and Chinese Bama minipigs (BMPs) are extensively used for animal experiments in the field of medicine in China. The genome of porcine endogenous retroviruses (PERVs) has not yet been accurately quantified, posing a threat to their clinical application because they act as a source of cells. In this study, we used genome sequence data from BMPs to predict PERV copies and their distribution. We validated and quantified the identified PERV copies and subtypes across different BMP individuals and tissues using quantitative real-time polymerase chain reaction and droplet digital polymerase chain reaction, respectively, and found that the BMP genome contains only 11 to 21 PERV copies. Notably, they lack the C subtype, which is a relatively safe cell source. Moreover, we applied CRISPR/Cas9 technology to knock out the pol fragment of PERVs in primary renal fibroblasts (PRFs) from BMPs and obtain PERV-destructed cells. Overall, our results lay a foundation for obtaining PERV-destructed BMPs as a safe source of hepatocytes for BALs for future applications.
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22
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Ma H, Jiang J, He J, Liu H, Han L, Gong Y, Li B, Yu Z, Tang S, Zhang Y, Duan Y, Yin Y, Zeng Q, Yi J, He X, Zeng Y, Kim KS, Xu K, Liang F, He J. Long-read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds. Mol Ecol Resour 2021; 22:1508-1520. [PMID: 34758184 DOI: 10.1111/1755-0998.13550] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]
Abstract
Advances in long-read sequencing technology and genome assembly provide an opportunity to improve the pig genome and reveal the full range of structural variations (SVs) between local Chinese and European pigs. To date, little is known about the genomes of some unique Chinese indigenous breeds, such as the Ningxiang pig. Here, we report the sequencing and assembly of a highly contiguous Ningxiang pig genome (NX) via an integration of PacBio single-molecule real-time sequencing, Illumina next-generation sequencing, BioNano optical mapping and Hi-C (chromosome conformation capture) approaches. The assembled genome comprises 2.44 Gb with a contig N50 of 26.1 Mb and 418 contigs in total. These contigs are organized into 121 scaffolds with a scaffold N50 of 139.0 Mb. More than 99.1% of the assembled sequence could be localized to 19 pseudochromosomes and is annotated with 20,914 protein-coding genes and 34.04% repetitive sequences. Comparisons between the NX and European Duroc assemblies revealed many SVs in genes involved in the immune system, nervous system, lipid metabolism and environmental adaptation. The genetic variants include 47 Chinese domestic pig-specific SVs and the associated 74 genes may contribute to the differences in domestic traits compared to European pigs. Moreover, single nucleotide polymorphisms (SNPs) identified from whole genome resequencing data of 73 Chinese pigs, representing 17 geographically isolated breeds, showed their specific genetic variations, population structure and evolutionary patterns. Finally, we explore transcriptional regulation in the first intron of the MYL4 gene, as the genomic SV (281-bp deletion) in Ningxiang pig promotes its subcutaneous fat compared to European pig breeds. This work identifies a set of Asian-specific SVs and SNPs, which will be important resources for modern pig breeding and genetic conservation.
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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
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23
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Huo JL, Zhang LQ, Zhang X, Wu XW, Ye XH, Sun YH, Cheng WM, Yang K, Pan WR, Zeng YZ. Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line. Anim Genet 2021; 53:146-151. [PMID: 34658041 DOI: 10.1111/age.13149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 01/28/2023]
Abstract
Inbred pigs are promising animal models for biomedical research and xenotransplantation. Established in 1980, the Banna minipig inbred (BMI) line originated from a sow and its own male offspring. It was selected from a small backcountry minority Lahu village, where records show that no other pig breed has ever been introduced. During the inbreeding process, we perfomed extreme inbreeding over 23 consecutive generations using full-sibling or parent-offspring mating. In order to investigate the inbreeding effects in BMI pigs across generations over the past 40 years, in this study we conducted a genome-wide SNP genotyping of the last 10 generations, representing generations 14-23. In total, we genotyped 57,746 SNPs, corresponding to an average decrease in heterozygosity rate of 0.0078 per generation. Furthermore, we were only able to identify 18,216 polymorphic loci with a MAF larger than 0.05, which is substantially lower than the values in previous reports on other pig breeds. In addition, we sequenced the genome of the first pig in the twenty-third generation (inbreeding coefficient 99.28%) to an average coverage of 12.4× to evaluate at the genome level the impact of advanced inbreeding. ROH analysis indicates that BMI pigs have longer ROHs than Wuzhishan and Duroc pigs. Those long ROH regions in BMI pigs are enriched for distinct functions compared with the highly polymorphic regions. Our study reveals a genome-wide allele diversity loss during the progress of inbreeding in BMI pigs and characterizes ROH and polymorphic regions as a result of inbreeding. Overall, our results indicate the successful establishment of the BMI line, which paves the way for further in-depth studies.
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Affiliation(s)
- J L Huo
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China.,Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - L Q Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - X Zhang
- College of Life Science, Lvliang University, Lvliang, 033001, China
| | - X W Wu
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - X H Ye
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Y H Sun
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - W M Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - K Yang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - W R Pan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Y Z Zeng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
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24
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Gene cloning, prokaryotic expression and antiviral activities of interferon-αω from Chinese Bama miniature pigs. Vet Res Commun 2021; 46:59-66. [PMID: 34581981 DOI: 10.1007/s11259-021-09829-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/07/2021] [Indexed: 01/30/2023]
Abstract
Porcine interferon (PoIFN) complex represents an ideal model for studying IFN evolution that resulted from viral pressure during domestication. IFN-αω is an emergent subtype of type I IFNs which has been primarily characterized in domestic pigs. In this study, the PoIFN-αω cDNA was cloned from Chinese Bama miniature pigs by RT-PCR, and its tissue expression profile was analyzed by real-time RT-PCR. The cDNA was expressed in Escherichia coli as a His-tagged protein and purified by nickel affinity chromatography. The antiviral activities of recombinant PoIFN-αω (rPoIFN-αω) against four different pig viruses were measured using cytopathic effect (CPE) inhibition assay. Although the PoIFN-αω sequence of Bama miniature pigs was identical to that of domestic pigs, the tissue expression profiles differed significantly between the two pig species. The rPoIFN-αω showed dose-dependent pre-infection antiviral activities against porcine pseudorabies virus, vesicular stomatitis virus and porcine reproductive and respiratory syndrome virus, but not against porcine circovirus type 2. When used as treatment post infection with the three viruses, rPoIFN-αω showed the efficacy in decreasing CPE in the infected cells in a time-dependent manner. Therefore, the expressed rPoIFN-αω could be used as an antiviral agent against pig virus infections.
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25
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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.
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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
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26
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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.
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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
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Zeng S, Zhou R, Bao S, Li X, Deng Z, Hou D, Weng S, He J, Huang Z. Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing. Front Genet 2020; 11:71. [PMID: 32133029 PMCID: PMC7040362 DOI: 10.3389/fgene.2020.00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 01/22/2020] [Indexed: 12/23/2022] Open
Abstract
The pacific white shrimp, Litopenaeus vannamei, with the largest shrimp industry production in the world, is currently threatened by a severe disease, white feces syndrome (WFS), which cause devastating losses globally, while its causal agents remain largely unknown. Herein, compared to the Control shrimp by metagenomic analysis, we firstly investigated that the altered functions of intestinal microbial community in WFS shrimp were the enrichment of bacterial chemotaxis and flagellar assembly pathways, hinting at a potential role of pathogenic bacteria for growth and development, which might be related to WFS occurrence. Single-molecule real-time (SMRT) sequencing was to further identify the gene structure and gene regulation for more clues in WFS aetiology. Totally 50,049 high quality transcripts were obtained, capturing 39,995 previously mapped and 10,054 newly detected transcripts, which were annotated to 30,554 genes. A total of 158 differentially expressed genes (DEGs) were characterized in WFS shrimp. These DEGs were strongly associated with various immune related genes that regulated the expression of multiple antimicrobial peptides (e.g., antilipopolysaccharide factors, penaeidins, and crustin), which were further experimentally validated using quantitative PCR on transcript level. Collectively, multigene biomarkers were identified to be closely associated with WFS, especially those functional alterations in microbial community and the upregulated immune related gene with antibacterial activities. Our finding not only inspired our cogitation on WFS aetiology from both microbial and host immune response perspectives with combined metagenomic and full-length transcriptome sequencing, but also provided valuable information for enhancing shrimp aquaculture.
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Affiliation(s)
- Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center, Sun Yat-sen University, Guangzhou, China
| | - Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shicheng Bao
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuanting Li
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhixuan Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center, Sun Yat-sen University, Guangzhou, China
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center, Sun Yat-sen University, Guangzhou, China
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28
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Porcine models for studying complications and organ crosstalk in diabetes mellitus. Cell Tissue Res 2020; 380:341-378. [PMID: 31932949 DOI: 10.1007/s00441-019-03158-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/28/2019] [Indexed: 02/06/2023]
Abstract
The worldwide prevalence of diabetes mellitus and obesity is rapidly increasing not only in adults but also in children and adolescents. Diabetes is associated with macrovascular complications increasing the risk for cardiovascular disease and stroke, as well as microvascular complications leading to diabetic nephropathy, retinopathy and neuropathy. Animal models are essential for studying disease mechanisms and for developing and testing diagnostic procedures and therapeutic strategies. Rodent models are most widely used but have limitations in translational research. Porcine models have the potential to bridge the gap between basic studies and clinical trials in human patients. This article provides an overview of concepts for the development of porcine models for diabetes and obesity research, with a focus on genetically engineered models. Diabetes-associated ocular, cardiovascular and renal alterations observed in diabetic pig models are summarized and their similarities with complications in diabetic patients are discussed. Systematic multi-organ biobanking of porcine models of diabetes and obesity and molecular profiling of representative tissue samples on different levels, e.g., on the transcriptome, proteome, or metabolome level, is proposed as a strategy for discovering tissue-specific pathomechanisms and their molecular key drivers using systems biology tools. This is exemplified by a recent study providing multi-omics insights into functional changes of the liver in a transgenic pig model for insulin-deficient diabetes mellitus. Collectively, these approaches will provide a better understanding of organ crosstalk in diabetes mellitus and eventually reveal new molecular targets for the prevention, early diagnosis and treatment of diabetes mellitus and its associated complications.
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