1
|
Comparative Transcriptomics of Gonads Reveals the Molecular Mechanisms Underlying Gonadal Development in Giant Freshwater Prawns (Macrobrachium rosenbergii). JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The giant freshwater prawn, Macrobrachium rosenbergii, is a prawn that has economic significance throughout the world. It exhibits sex-related growth dimorphism, whereby the males grow significantly more rapidly than the females. Therefore, a study on the molecular regulatory mechanism, which underlies the sexual differentiation of M. rosenbergii, is of both scientific and commercial importance. However, a scarcity of genomic and transcriptomic resources severely limits our knowledge of the sexual differentiation mechanisms in M. rosenbergii. Here, transcriptome sequencing of several gonadic samples of males and females in M. rosenbergii was performed to investigate the molecular basis underlying gonadal development. Our results showed that 2149 unigenes presented as differentially expressed genes (DEGs) in the ovaries of females compared to the testes of males, which contained 484 down-regulated and 1665 up-regulated genes. Enrichment analysis of DEGs revealed many of these genes to be related to sexual differentiation and gonadal development. From our transcriptome analyses, and as confirmed by quantitative real-time PCR, male-related genes (Mrr, MRPINK, IR, IAGBP, TESK1, and dsx) in the testes were significantly up-regulated, and female-related genes (ERR, Sxl3, cyclinB, Dmrt99B, PPP2A, and ADCY9) in the ovaries were also significantly up-regulated. This indicates the potential role these genes play in the gonadal development of M. rosenbergii. Furthermore, multiple signal transduction pathways relating to gonadal maturation and spermatogenesis, including MAPK, were identified herein. Our data also supports previous ideas that IAG and IAGBP-IR signaling schemes could help in the regulation of testis’ development in M. rosenbergii and the ERR gene could regulate ovarian development by affecting the expression of cyclinB, PPP2A, and ADCY9. The data from this study provides incredibly usefully genomic resources for future research on the sexual differentiation and practical aquaculture of M. rosenbergii.
Collapse
|
2
|
Habimana R, Ngeno K, Okeno TO, Hirwa CDA, Keambou Tiambo C, Yao NK. Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda. Front Genet 2021; 12:723980. [PMID: 34745207 PMCID: PMC8570395 DOI: 10.3389/fgene.2021.723980] [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: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
A chicken genome has several regions with quantitative trait loci (QTLs). However, replication and confirmation of QTL effects are required particularly in African chicken populations. This study identified single nucleotide polymorphisms (SNPs) and putative genes responsible for body weight (BW) and antibody response (AbR) to Newcastle disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and 10% for significant and suggestive thresholds, respectively. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) significantly (p ≤ 7.6E-5) associated with BW were identified on chromosomes (CHRs) 8, 11, and 19. In the vicinity of these SNPs, four genes such as pre-B-cell leukaemia homeobox 1 (PBX1), GPATCH1, MPHOSPH6, and MRM1 were identified. Four other significant SNPs (rs314787954, rs13623466, rs13910430, and rs737507850) all located on chromosome 1 were strongly (p ≤ 7.6E-5) associated with chicken antibody response to ND. The closest genes to these four SNPs were cell division cycle 16 (CDC16), zinc finger, BED-type containing 1 (ZBED1), myxovirus (influenza virus) resistance 1 (MX1), and growth factor receptor bound protein 2 (GRB2) related adaptor protein 2 (GRAP2). Besides, other SNPs and genes suggestively (p ≤ 1.5E-5) associated with BW and antibody response to ND were reported. This work offers a useful entry point for the discovery of causative genes accountable for essential QTLs regulating BW and antibody response to ND traits. Results provide auspicious genes and SNP-based markers that can be used in the improvement of growth performance and ND resistance in IC populations based on gene-based and/or marker-assisted breeding selection.
Collapse
Affiliation(s)
- Richard Habimana
- College of Agriculture, Animal Science and Veterinary Medicine, University of Rwanda, Kigali, Rwanda.,Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Kiplangat Ngeno
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Tobias Otieno Okeno
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | | | - Christian Keambou Tiambo
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Nairobi, Kenya
| | - Nasser Kouadio Yao
- Biosciences Eastern and Central Africa - International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| |
Collapse
|
3
|
Feng P, Zeng T, Yang H, Chen G, Du J, Chen L, Shen J, Tao Z, Wang P, Yang L, Lu L. Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China. BMC Genomics 2021; 22:401. [PMID: 34058976 PMCID: PMC8165772 DOI: 10.1186/s12864-021-07710-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/12/2021] [Indexed: 01/03/2023] Open
Abstract
Background Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. Results Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks. Conclusion Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07710-2.
Collapse
Affiliation(s)
- Peishi Feng
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China.,Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Yang
- Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Science, Wuhan, China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junda Shen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenrong Tao
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ping Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China.
| | - Lin Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| |
Collapse
|
4
|
Xiong Y, Zheng X, Ke W, Gong G, Wang Y, Dan C, Huang P, Wu J, Guo W, Mei J. Function and association analysis of Cyclophilin A gene with resistance to Edwardsiella ictaluri in yellow catfish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 113:103783. [PMID: 32735962 DOI: 10.1016/j.dci.2020.103783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/08/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Edwardsiella ictaluri (E. ictaluri) is one of the main bacterial pathogens in catfish which has caused serious economic loss to yellow catfish (Pelteobagrus fulvidraco) in China. In our previous work, we demonstrated that CypA was up-regulated at the early stage of E. ictaluri infection in yellow catfish and displayed strong chemotactic activity for leukocytes in vitro. However, the effect of CypA on E. ictaluri is unknown in vivo. Therefore, two homozygous transgenic zebrafish lines expressing yellow catfish CypA (TG-CypA-1 and TG-CypA-2) were generated. After challenged with E. ictaluri at a dose of 1.0 × 104 CFU per adult fish, both two transgenic lines exhibited a higher resistance to bacterial infection than the wildtype zebrafish. Herein, CypA gene in E. ictaluri-challenged yellow catfish was screened for presence of polymorphisms by sequencing and six single nucleotide polymorphisms (SNPs) were identified. SNP association analysis revealed that 528T/C SNP in the first intron was significantly different in disease-susceptible and -resistant groups, which was confirmed in two independent populations of yellow catfish. Moreover, the relative expression of CypA in the resistant group (CC genotype in 528T/C SNP) was significantly higher than that in the susceptible group (TT genotype in 528T/C SNP) in different immune organs of yellow catfish including spleen, head kidney, body kidney and liver. Our results reveal the potential function of CypA in host defense to bacterial infection and suggest the SNP marker in CypA gene associated with the resistance to E. ictaluri may facilitate the selective breeding of disease-resistant yellow catfish in the future.
Collapse
Affiliation(s)
- Yang Xiong
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaozhen Zheng
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wensi Ke
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gaorui Gong
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhong Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Peipei Huang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiankai Wu
- Kangyu Fisheries Technology Co. Ltd. of Sheyang County, Sheyang, 224300, China
| | - Wenjie Guo
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
5
|
Dorajoo R, Chang X, Gurung RL, Li Z, Wang L, Wang R, Beckman KB, Adams-Haduch J, M Y, Liu S, Meah WY, Sim KS, Lim SC, Friedlander Y, Liu J, van Dam RM, Yuan JM, Koh WP, Khor CC, Heng CK. Loci for human leukocyte telomere length in the Singaporean Chinese population and trans-ethnic genetic studies. Nat Commun 2019; 10:2491. [PMID: 31171785 PMCID: PMC6554354 DOI: 10.1038/s41467-019-10443-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/09/2019] [Indexed: 01/02/2023] Open
Abstract
Genetic factors underlying leukocyte telomere length (LTL) may provide insights into telomere homeostasis, with direct links to disease susceptibility. Genetic evaluation of 23,096 Singaporean Chinese samples identifies 10 genome-wide loci (P < 5 × 10-8). Several of these contain candidate genes (TINF2, PARP1, TERF1, ATM and POT1) with potential roles in telomere biology and DNA repair mechanisms. Meta-analyses with additional 37,505 European individuals reveals six more genome-wide loci, including associations at MPHOSPH6, NKX2-3 and TYMS. We demonstrate that longer LTL associates with protection against respiratory disease mortality [HR = 0.854(0.804-0.906), P = 1.88 × 10-7] in the Singaporean Chinese samples. We further show that the LTL reducing SNP rs7253490 associates with respiratory infections (P = 7.44 × 10-4) although this effect may not be strongly mediated through LTL. Our data expands on the genetic basis of LTL and may indicate on a potential role of LTL in immune competence.
Collapse
Affiliation(s)
- Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, 119074, Singapore
| | - Resham Lal Gurung
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
| | - Zheng Li
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Ling Wang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Kenneth B Beckman
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jennifer Adams-Haduch
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Yiamunaa M
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
| | - Sylvia Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
| | - Wee Yang Meah
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Kar Seng Sim
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
- Diabetes Centre, Khoo Teck Puat Hospital, Singapore, 768828, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
| | - Yechiel Friedlander
- School of Public Health and Community Medicine, Hebrew University of Jerusalem, Jerusalem, 12272, Israel
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
- Health Systems and Services Research, Duke-NUS Medical School Singapore, Singapore, 169857, Singapore
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore.
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore.
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, 119074, Singapore.
| |
Collapse
|
6
|
Zhang Y, Wang S, Wen X, Zhang S, Yang Y. Association of ACYP2 and MPHOSPH6 genetic polymorphisms with the risk of hepatocellular carcinoma in chronic hepatitis B virus carriers. Oncotarget 2017; 8:86011-86019. [PMID: 29156773 PMCID: PMC5689663 DOI: 10.18632/oncotarget.20846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/02/2017] [Indexed: 12/02/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the dominant histologic type of primary liver cancer, and hepatitis B virus (HBV) infection is one of the major causes of HCC in the chronic HBV. Our study was investigated the association between the polymorphisms of ACYP2 and MPHOSPH6 genes and the risk of HCC induced by HBV infection. A total of 490 subjects were divided into two groups: 248 HBV patients with HCC (Case group), and 242 HBV patients without HCC (Control group). Unconditional logistic regression analysis was used to evaluate the association. The genetic association analysis revealed variant of rs12621038 in ACYP2 gene had a significant association with increasing the risk of HBV-induced HCC based on the genotype, dominant and additive model (P<0.05). Moreover, our results also showed that minor allele “C” of rs3751862 was prevalent in cases than controls (P<0.05), and rs3751862 significantly increased the risk of HCC in chronic HBV carriers under genotype and dominant model (P<0.05). In addition, the haplotype “T-G-G” in MPHOSPH6 showed a harmful factor for the HBV-induced HCC (P<0.05). The results suggested that ACYP2 and MPHOSPH6 as the plausible candidate genes may predict the risk of HCC after chronic HBV infection in Chinese Han population, and further investigations in studies with a larger sample size and other races are needed to validate our findings. These data provide a theoretical foundation for future studies of this correlation between the polymorphisms of ACYP2 and MPHOSPH6 genes and the HCC in chronic HBV carriers.
Collapse
Affiliation(s)
- Yingai Zhang
- Central Laboratory, Haikou People's Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou 570208, Hainan, China
| | - Shunlan Wang
- Central Laboratory, Haikou People's Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou 570208, Hainan, China
| | - Xiaohong Wen
- Central Laboratory, Haikou People's Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou 570208, Hainan, China
| | - Shufang Zhang
- Central Laboratory, Haikou People's Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou 570208, Hainan, China
| | - Yijun Yang
- Department of Hepatobiliary Surgery, Haikou People's Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou 570208, Hainan, China
| |
Collapse
|
7
|
Yang X, Zhang Y, Li W, Su Y, Niu D, Wang Y, Huang H, Han H, Zhang D, Xie M, Su H, Xu W, Wei J. Association between MPHOSPH6 gene polymorphisms and IgA nephropathy risk in a Chinese Han population. Oncotarget 2017; 8:72375-72380. [PMID: 29069794 PMCID: PMC5641137 DOI: 10.18632/oncotarget.19758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/03/2017] [Indexed: 11/25/2022] Open
Abstract
Multiple genetic and environmental factors together contribute to the risk of IgA nephropathy (IgAN). MPHOSPH6 play an important role in the recruitment of the exosome to the pre-rRNA. However, to date, little information is found about the association between MPHOSPH6 polymorphisms and the IgAN risk. In this case-control study, we genotyped five single nucleotide polymorphisms (SNPs) in MPHOSPH6 gene in 416 IgAN cases and 495 controls using Sequenom Mass-ARRAY technology and evaluated their association with IgAN using the χ2 and genetic model analysis. In the allelic model analysis, we determined rs1056654 was associated with a 0.774-fold decrease in the risk of IgAN (95%CI= 0.630-0.952; p = 0.015). In the genetic model analysis, we found that the “C/C” genotype of rs1056675 was associated with an increased risk of IgAN based on the codominant model (OR =1.48; 95% CI=1.03-2.13; p=0.033) and recessive model (OR =1.52; 95% CI=1.11-2.09; p=0.0095). The “G/A-A/A” genotype of rs1056654 was associated with a decreased risk of IgAN based on the dominant model (OR =0.75; 95% CI=0.58-0.98; p=0.032) and log-additvie model (OR =0.78; 95% CI=0.64-0.96; p=0.0188). Our data suggested that gene polymorphisms in the MPHOSPH6 may exert influences IgAN susceptibility in a Chinese Han population.
Collapse
Affiliation(s)
- Xiaohong Yang
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Yin Zhang
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Wenning Li
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Yan Su
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Dan Niu
- Department of Nephrology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yanni Wang
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Haiyang Huang
- Central Laboratory, Hainan General Hospital, Haikou Hainan 570311, China
| | - Hui Han
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Daofa Zhang
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Maowei Xie
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Huiluan Su
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Wentan Xu
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| | - Jiali Wei
- Department of Nephrology, Hainan General Hospital, Haikou Hainan 570311, China
| |
Collapse
|
8
|
Song Y, Yan M, Li J, Li J, Jin T, Chen C. Association between TNIP1, MPHOSPH6 and ZNF208 genetic polymorphisms and the coronary artery disease risk in Chinese Han population. Oncotarget 2017; 8:77233-77240. [PMID: 29100383 PMCID: PMC5652776 DOI: 10.18632/oncotarget.20432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/24/2017] [Indexed: 11/27/2022] Open
Abstract
Introduction Coronary artery disease (CAD) is a common disease and among the leading cause of death in the general population. Inherited factors are involved in the pathogenesis of CAD. Aims Our study examined whether SNPs in TNIP1, MPHOSPH6, ZNF208 to be associated with CAD risk in a Chinese Han population. We recruited 596 CAD patients, 603 controls and genotyping fifteen SNPs using Sequenom MassARRAY. For association analysis between TNIP1, MPHOSPH6 and ZNF208 and CAD was determined by Odds ratios (ORs) with 95% confidence intervals (CIs) using Logistic Regression. Results The results indicated in allel model, the rs960709 in TNIP1 was associated with CAD risk (OR = 0.78, 95%CI = 0.65-0.94, P=0.010). The genetic model results showed that the rs960709 (A/G) polymorphism was associated with the risk of developing CAD in codominant, Dominant and Log-additive. The rs1056654 A/A allele and CAD patients compared to the healthy controls in recessive model (OR = 0.55, 95%CI = 0.34-0.90; P = 0.018). We also found that three SNPS in ZNF208 associated with CAD, respectively, rs2188971, rs8103163 and rs7248488. Linkage disequilibrium (LD) and haplotype analyses of the SNPs found that the CTA haplotype (rs1056675, rs1056654, rs11859599) and rs2188972A/rs2188971T/rs8103163A/rs7248488A (ATAA) were associated with CAD. Conclusion In conclusion, the present study provided evidence that SNPs in the TNIP1, ZNF208 and MPHOSPH6 were associated with CAD in Chinese Han population. It is possible that these SNPs are CAD risk factors and these data can provide.
Collapse
Affiliation(s)
- Yanbin Song
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, Shaanxi 710069, China.,School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,Department of Cardiovascular, Yanan University Affiliated Hospital, Yanan, Shaanxi 716000, China
| | - Mengdan Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, Shaanxi 710069, China.,School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, Shaanxi 710069, China.,School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jingjie Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, Shaanxi 710069, China.,School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, Shaanxi 710069, China.,School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Chao Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, Shaanxi 710069, China.,School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| |
Collapse
|
9
|
Jung H, Yoon BH, Kim WJ, Kim DW, Hurwood DA, Lyons RE, Salin KR, Kim HS, Baek I, Chand V, Mather PB. Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction. Int J Mol Sci 2016; 17:ijms17050690. [PMID: 27164098 PMCID: PMC4881516 DOI: 10.3390/ijms17050690] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 11/29/2022] Open
Abstract
The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.
Collapse
Affiliation(s)
- Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia.
| | - Byung-Ha Yoon
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305806, Korea.
- Department of Bioinformatics, University of Science and Technology, Daejeon 305333, Korea.
| | - Woo-Jin Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea.
| | - Dong-Wook Kim
- All Bio Technology Co., LTD, Internet Business Incubation Center, Mokweon University, Daejeon 302729, Korea.
| | - David A Hurwood
- Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia.
| | - Russell E Lyons
- School of Veterinary Science, University of Queensland, Queensland 4067, Australia.
| | - Krishna R Salin
- School of Environment, Resources and Development, Asian Institute of Technology, Pathumthani 12120, Thailand.
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609735, Korea.
| | - Ilseon Baek
- Division of Marine Technology, Chonnam National University, Yeosu 550250, Korea.
| | - Vincent Chand
- Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia.
| | - Peter B Mather
- Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia.
| |
Collapse
|
10
|
Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2015; 16:1006. [PMID: 26607692 PMCID: PMC4659196 DOI: 10.1186/s12864-015-2219-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/16/2015] [Indexed: 01/15/2023] Open
Abstract
Background The Pacific white shrimp (Litopenaeus vannamei) is the world’s most prevalent cultured crustacean species. However, the supply of high-quality broodstocks is limited and baseline information related to its reproductive activity and molecular issues related to gonad development are scarce. In this study, we performed transcriptome sequencing on the gonads of adult male and female L. vannamei to identify sex-related genes. Results A total of 25.16 gigabases (Gb) of sequences were generated from four L. vannamei gonadal tissue libraries. After quality control, 24.11 Gb of clean reads were selected from the gonadal libraries. De-novo assembly of all the clean reads generated a total of 65,218 unigenes with a mean size of 1021 bp and a N50 of 2000 bp. A search of all-unigene against Nr, SwissProt, KEGG, COG and NT databases resulted in 26,482, 23,062, 20,659, 11,935 and 14,626 annotations, respectively, providing a total of 30,304 annotated unigenes. Among annotated unigenes, 12,320 unigenes were assigned to gene ontology categories and 20,659 unigenes were mapped to 258 KEGG pathways. By comparing the ovary and testis libraries, 19,279 testicular up-regulated and 3,529 ovarian up-regulated unigenes were identified. Enrichment analysis of differentially expressed unigenes resulted in 1060 significantly enriched GO terms and 34 significantly enriched KEGG pathways. Nine ovary-specific, 6 testis-specific, 45 testicular up-regulated and 39 ovarian up-regulated unigenes were then confirmed by semi-quantitative PCR and quantitative real-time PCR. In addition, using all-unigenes as a reference, a total of 13,233 simple sequence repeats (SSRs) were identified in 10,411 unigene sequences. Conclusions The present study depicts the first large-scale RNA sequencing of shrimp gonads. We have identified many important sex-related functional genes, GO terms and pathways, all of which will facilitate future research into the reproductive biology of shrimp. We expect that the SSRs detected in this study can then be used as genetic markers for germplasm evaluation of breeding and imported populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2219-4) contains supplementary material, which is available to authorized users.
Collapse
|