1
|
Xu Y, Yu F, Feng W, Wei J, Su S, Li J, Hua G, Li W, Tang Y. Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases. Brief Funct Genomics 2024:elae030. [PMID: 38984674 DOI: 10.1093/bfgp/elae030] [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: 04/11/2024] [Revised: 06/02/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
At present, public databases house an extensive repository of transcriptome data, with the volume continuing to grow at an accelerated pace. Utilizing these data effectively is a shared interest within the scientific community. In this study, we introduced a novel strategy that harnesses SNPs and InDels identified from transcriptome data, combined with sample metadata from databases, to effectively screen for molecular markers correlated with traits. We utilized 228 transcriptome datasets of Eriocheir sinensis from the NCBI database and employed the Genome Analysis Toolkit software to identify 96 388 SNPs and 20 645 InDels. Employing the genome-wide association study analysis, in conjunction with the gender information from databases, we identified 3456 sex-biased SNPs and 639 sex-biased InDels. The KOG and KEGG annotations of the sex-biased SNPs and InDels revealed that these genes were primarily involved in the metabolic processes of E. sinensis. Combined with SnpEff annotation and PCR experimental validation, a highly sex-biased SNP located in the Kelch domain containing 4 (Klhdc4) gene, CHR67-6415071, was found to alter the splicing sites of Klhdc4, generating two splice variants, Klhdc4_a and Klhdc4_b. Additionally, Klhdc4 exhibited robust expression across the ovaries, testes, and accessory glands. The sex-biased SNPs and InDels identified in this study are conducive to the development of unisexual cultivation methods for E. sinensis, and the alternative splicing event caused by the sex-biased SNP in Klhdc4 may serve as a potential mechanism for sex regulation in E. sinensis. The analysis strategy employed in this study represents a new direction for the rational exploitation and utilization of transcriptome data in public databases.
Collapse
Affiliation(s)
- Yuanfeng Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Fan Yu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wenrong Feng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jia Wei
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jianlin Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Guoan Hua
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou 225309, China
| | - Wenjing Li
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou 225309, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| |
Collapse
|
2
|
Zhao S, Hu Q, Jiang H, Zhao Y, Wang Y, Feng C, Li X. Multi-omics analysis of oxidative stress and apoptosis in hepatopancreas cells induced by Polyascus gregaria parasitizing the Eriocheir sinensis. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109180. [PMID: 37863124 DOI: 10.1016/j.fsi.2023.109180] [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: 08/11/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023]
Abstract
Polyascus gregaria, a parasitic barnacle, poses a significant threat to Eriocheir sinensis farms by inhibiting crab growth. However, the molecular and pathological mechanisms behind P. gregaria infection in the hepatopancreas of E. sinensis remain unclear. In this study, we investigated the impact and underlying mechanisms of P. gregaria infection on E. sinensis through analyzing the infected hepatopancreatic tissues by tandem mass tag technology and RNA-Seq high-throughput sequencing. Among the identified 10,693 differentially expressed genes, 294 genes were significantly altered following P. gregaria infection, including 92 upregulated and 202 downregulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses further revealed the involvement of these genes in oxidative decomposition, lipid metabolism, inflammation, and hepatopancreas metabolism. Meanwhile, the identified 253 differentially expressed proteins, including 143 upregulated and 110 downregulated proteins, are mainly related to cellular and metabolic processes, catalytic activity, and cell components. The pathway analysis indicated their enrichment in glycolysis/gluconeogenesis, oxidative phosphorylation, endoplasmic reticulum protein processing, and actin cytoskeleton regulation. The involvement of these differentially expressed genes and proteins in the peroxisome proliferator-activated receptors pathway during host immune responses against P. gregaria infection has been highlighted. Furthermore, pathological examinations and biochemical indicators jointly demonstrated the hepatopancreatic damage and increased oxidative stress and apoptosis in the infected E. sinensis. Collectively, our study provides crucial insights into the mechanisms underlying the E. sinensis-P. gregaria interactions, and may contribute to the development of novel strategies for parasite control and reducing economic losses in aquaculture.
Collapse
Affiliation(s)
- Shiwei Zhao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qingbiao Hu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hongbo Jiang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingying Zhao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yanping Wang
- Linong Testing (Binzhou) Co., Ltd., Binzhou Bohai Advanced Technology Research Institute, Binzhou, 256600, China
| | - Chengcheng Feng
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Xiaodong Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| |
Collapse
|
3
|
Ye Z, Bishop T, Wang Y, Shahriari R, Lynch M. Evolution of sex determination in crustaceans. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:1-11. [PMID: 37073332 PMCID: PMC10077267 DOI: 10.1007/s42995-023-00163-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/28/2022] [Indexed: 05/03/2023]
Abstract
Sex determination (SD) involves mechanisms that determine whether an individual will develop into a male, female, or in rare cases, hermaphrodite. Crustaceans harbor extremely diverse SD systems, including hermaphroditism, environmental sex determination (ESD), genetic sex determination (GSD), and cytoplasmic sex determination (e.g., Wolbachia controlled SD systems). Such diversity lays the groundwork for researching the evolution of SD in crustaceans, i.e., transitions among different SD systems. However, most previous research has focused on understanding the mechanism of SD within a single lineage or species, overlooking the transition across different SD systems. To help bridge this gap, we summarize the understanding of SD in various clades of crustaceans, and discuss how different SD systems might evolve from one another. Furthermore, we review the genetic basis for transitions between different SD systems (i.e., Dmrt genes) and propose the microcrustacean Daphnia (clade Branchiopoda) as a model to study the transition from ESD to GSD.
Collapse
Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287 USA
| | - Trent Bishop
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287 USA
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Ryan Shahriari
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287 USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287 USA
| |
Collapse
|
4
|
Guo C, Zhang X, Li Y, Xie J, Gao P, Hao P, Han L, Zhang J, Wang W, Liu P, Ding J, Chang Y. Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus. BMC Genomics 2023; 24:25. [PMID: 36647018 PMCID: PMC9843871 DOI: 10.1186/s12864-023-09113-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Apostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. japonicus, mainly harvested in the Vladivostok region, exhibits significant phenotypic differentiation, including in many economically important traits, compared with Chinese A. japonicus owing to differences in their habitat. However, both the genetic basis for the phenotypic divergence and the population genetic structure of Russian and Chinese A. japonicus are unknown. RESULT In this study, 210 individuals from seven Russian and Chinese A. japonicus populations were sampled for whole-genome resequencing. The genetic structure analysis differentiated the Russian and Chinese A. japonicus into two groups. Population genetic analyses indicated that the Russian population showed a high degree of allelic linkage and had undergone stronger positive selection compared with the Chinese populations. Gene ontology terms enriched among candidate genes with group selection analysis were mainly involved in immunity, such as inflammatory response, antimicrobial peptides, humoral immunity, and apoptosis. Genome-wide association analysis yielded eight single-nucleotide polymorphism loci significantly associated with parapodium number, and these loci are located in regions with a high degree of genomic differentiation between the Chinese and Russia populations. These SNPs were associated with five genes. Gene expression validation revealed that three of these genes were significantly differentially expressed in individuals differing in parapodium number. AJAP08772 and AJAP08773 may directly affect parapodium production by promoting endothelial cell proliferation and metabolism, whereas AJAP07248 indirectly affects parapodium production by participating in immune responses. CONCLUSIONS This study, we performed population genetic structure and GWAS analysis on Chinese and Russian A. japonicus, and found three candidate genes related to the number of parapodium. The results provide an in-depth understanding of the differences in the genetic structure of A. japonicus populations in China and Russia, and provide important information for subsequent genetic analysis and breeding of this species.
Collapse
Affiliation(s)
- Chao Guo
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Xianglei Zhang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Yuanxin Li
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Jiahui Xie
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Pingping Gao
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Pengfei Hao
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Lingshu Han
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China ,grid.203507.30000 0000 8950 5267Ningbo University, Ningbo, Zhejiang 315211 People’s Republic of China
| | - Jinyuan Zhang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Wenpei Wang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Peng Liu
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Jun Ding
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Yaqing Chang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| |
Collapse
|
5
|
The Sex-Specific Splicing of Doublesex in Brine Shrimp Artemia franciscana. Genes (Basel) 2022; 13:genes13111997. [PMID: 36360234 PMCID: PMC9690683 DOI: 10.3390/genes13111997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/18/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
The understanding of sex determination and differentiation in animals has recently made remarkable strides through the use of advanced research tools. At the gene level, the Mab-3-related transcription factor (Dmrt) gene family, which encodes for the typical DNA-binding doublesex/Mab-3 (DM) domain in their protein, is known for its contribution to sex determination and differentiation in insects. In this study, DNA-binding DM domain screening has identified eight transcripts from Artemia franciscana transcriptomic that encode proteins containing one conserved DNA-binding DM domain. The genome mapping confirmed that these eight transcripts are transcribed from six different loci on the A. franciscana genome assembly. One of those loci, the Af.dsx-4 locus, is closely related to Doublesex, a gene belonging to the Dmrt gene family. This locus could be transcribed into three alternative transcripts, namely Af.dsx4, Af.dsxF and Af.dsxM. While Af.dsx4 and Af.dsxF could putatively be translated to form an identical Af.dsxF protein of 186 aa long, Af.dsxM translates for an Af.dsxM protein of 289 aa long but shares a DNA-binding DM domain. Interestingly, Af.dsxF and Af.dsxM are confirmed as sex-specific transcripts, Af.dsxF is only present in females, and Af.dsxM is only present in male individuals. The results suggest that the sex-specific splicing mechanism of the doublesex described in insects is also present in A. franciscana. Af.dxs-4 locus can be used in further studies to clarify the sex determination pathways in A. fracnciscana.
Collapse
|
6
|
Wang Q, Liu Y, Wang Y, Jiang S, Zhang C, Li B. GWAS Reveal Novel Sex-Related Markers and Candidate Genes in Sea Urchin Mesocentrotus nudus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:32-39. [PMID: 34812992 DOI: 10.1007/s10126-021-10084-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Mesocentrotus nudus is an economically important mariculture species. Identification of sex-related markers and candidate genes has potential implications for sex-control breeding of Mesocentrotus nudus. The aim of this study was to identify the molecular markers and genes associated with the sex of M. nudus. Initial GWAS analysis based on 80 individuals genotyped by using GBS identified 22 sex-related SNPs located on 9 GBS tags. Further targeted sequencing in another population of 124 individuals confirmed that 7 SNPs located on 7 GBS tags displayed complete associations with sex, suggesting a ZW/ZZ sex-determination system in M. nudus. Besides, genome and transcriptome annotations presented that the heat shock protein 75 kDa, mitochondrial (trap1), and protein furry homolog-like (fryl) may be important candidate genes involved in sex determination and differentiation in M. nudus. However, further studies are needed to elucidate the functions of these genes. Overall, the current results not only provide molecular markers that may contribute to the sex-control breeding for M. nudus, but also provide new insights to understand the regulatory mechanism of sea urchin sex.
Collapse
Affiliation(s)
- Quanchao Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ying Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaoyu Jiang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanxin Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Baoquan Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| |
Collapse
|
7
|
Development of 84 single nucleotide polymorphism (SNP) markers for the three-spot swimming crab (Portunus sanguinolentus) by using RAD approach. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01236-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Cui Z, Liu Y, Yuan J, Zhang X, Ventura T, Ma KY, Sun S, Song C, Zhan D, Yang Y, Liu H, Fan G, Cai Q, Du J, Qin J, Shi C, Hao S, Fitzgibbon QP, Smith GG, Xiang J, Chan TY, Hui M, Bao C, Li F, Chu KH. The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation. Nat Commun 2021; 12:2395. [PMID: 33888695 PMCID: PMC8062507 DOI: 10.1038/s41467-021-22604-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/19/2021] [Indexed: 02/02/2023] Open
Abstract
The infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. Here we report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crab Eriocheir sinensis, a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. We show the expansion of specific gene families in the crab, including F-ATPase, which enhances our knowledge on the adaptive plasticity of this successful invasive species. Our analysis of spatio-temporal transcriptomes and the genome of E. sinensis and other decapods shows that brachyurization development is associated with down-regulation of Hox genes at the megalopa stage when tail shortening occurs. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics. These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general.
Collapse
Affiliation(s)
- Zhaoxia Cui
- School of Marine Sciences, Ningbo University, Ningbo, China.
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yuan Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jianbo Yuan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Tomer Ventura
- School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Ka Yan Ma
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Chengwen Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Yanan Yang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Hourong Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | | | - Jing Du
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jing Qin
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | | | - Shijie Hao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Quinn P Fitzgibbon
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Gregory G Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Min Hui
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chenchang Bao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| |
Collapse
|
9
|
Lv J, Lu X, Ti X, Liu P, Li J, Li J. QTL mapping and marker identification for sex determination in the ridgetail white prawn, Exopalaemon carinicauda. Genomics 2020; 112:5240-5247. [PMID: 32956845 DOI: 10.1016/j.ygeno.2020.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/25/2022]
Abstract
Sex determination is an important and intriguing research topic in the field of evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex is helpful in clarifying the sex determination system of species. In this study, a second high-resolution genetic linkage map was constructed for the ridgetail white prawn, Exopalaemon carinicauda, which included 9280 markers, covering 99.98% of the complete genome. Based on the linkage map, a highly significant sex-related QTL was first mapped to a single linkage group (LG3, LOD > 55.6). Fifty-two markers in the QTL region were significantly associated with sex (p ≤ 10-40), of which heterogametic genotypes in females supported the ZW sex determination mechanism. Six markers were verified to be significantly associated with sex in the wild population. Some sex-related genes were identified, including phospholipase D, protein kinase shaggy, and longitudinals lacking protein. These results inform our understanding of the mechanisms of sex determination in E. carinicauda.
Collapse
Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xuan Lu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xingbin Ti
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jitao Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| |
Collapse
|
10
|
Sui J, Luan S, Dai P, Fu Q, Meng X, Luo K, Cao B, Kong J. High accuracy of pooled DNA genotyping by 2b-RAD sequencing in the Pacific white shrimp, Litopenaeus vannamei. PLoS One 2020; 15:e0236343. [PMID: 32730349 PMCID: PMC7392308 DOI: 10.1371/journal.pone.0236343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 07/04/2020] [Indexed: 11/18/2022] Open
Abstract
Using pooled DNA genotyping to estimate the proportional contributions from multiple families in a pooled sample is of particular interest for selective breeding in aquaculture. We compared different pooled libraries with separate 2b-RAD sequencing of Litopenaeus vannamei individuals to assess the effect of different population structures (different numbers of individuals and families) on pooled DNA sequencing, the accuracy of parent sequencing of the DNA pools and the effect of SNP numbers on pooled DNA sequencing. We demonstrated that small pooled DNA genotyping of up to 53 individuals by 2b-RAD sequencing could provide a highly accurate assessment of population allele frequencies. The accuracy increased as the number of individuals and families increased. The allele frequencies of the parents from each pool were highly correlated with those of the pools or the corresponding individuals in the pool. We chose 500-28,000 SNPs to test the effect of SNP number on the accuracy of pooled sequencing, and no linear relationship was found between them. When the SNP number was fixed, increasing the number of individuals in the mixed pool resulted in higher accuracy of each pooled genotyping. Our data confirmed that pooled DNA genotyping by 2b-RAD sequencing could achieve higher accuracy than that of individual-based genotyping. The results will provide important information for shrimp breeding programs.
Collapse
Affiliation(s)
- Juan Sui
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Sheng Luan
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping Dai
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qiang Fu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xianhong Meng
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kun Luo
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Baoxiang Cao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Kong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
| |
Collapse
|
11
|
Wang Y, Yu Y, Li S, Zhang X, Xiang J, Li F. Sex-Specific Transcriptome Sequencing of Zoea I Larvae and Identification of Sex-Linked Genes Using Bulked Segregant Analysis in Pacific White Shrimp Litopenaeus vannamei. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:423-432. [PMID: 32281012 DOI: 10.1007/s10126-020-09962-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
In order to learn the sex determination and differentiation process in shrimp, we performed sex-specific transcriptome sequencing of the Zoea I larvae in Litopenaeus vannamei (L. vannamei) using a DNA/RNA co-extraction method. The sex-specific genes and the sex-linked SNPs were identified. De novo assembly of all the clean reads generated 41,270 unigenes with an average length of 1026 bp and an N50 of 1922 bp. A total of 60 differentially expressed genes (DEGs) between females and males at Zoea I stage were obtained, in which 41 unigenes had annotations. DEGs that might be related to sex development in L. vannamei were analyzed. Besides, paralogous genes of some known sex-related genes in model organisms such as sex-lethal (Sxl) showed no sex-biased difference, which indicated they may not play roles in sex development at Zoea I stage. Candidate sex-linked SNPs were validated in six populations of L. vannamei, and SNPs in Unigene0020898 and Unigene0020336 were fully linked to genders, suggesting the two genes located in the sex-determining region of L. vannamei. Our report provided the sex-specific gene expression in early developmental stage of L. vannamei, and found some sex-biased genes that may participate in the sex development process. We also detected two sex-linked genes which may be located in the sex determination region of L. vannamei through bulked segregant analysis, and the SNPs on these genes also provided a method for genetic sex identification at transcriptional level. Our findings will facilitate further researches on molecular mechanism of sex determination and differentiation in shrimps.
Collapse
Affiliation(s)
- Yue Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.
| |
Collapse
|
12
|
Accurate Sex Identification of Ancient Elephant and Other Animal Remains Using Low-Coverage DNA Shotgun Sequencing Data. G3-GENES GENOMES GENETICS 2020; 10:1427-1432. [PMID: 32107273 PMCID: PMC7144076 DOI: 10.1534/g3.119.400833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g., osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics have not yet developed, or where organisms do not exhibit sex-associated phenotypic dimorphisms. Here we adapt a method developed for human sex determination so that it can be used to identify the sex of ancient and modern animal taxa. The method identifies sex by calculating the ratio of DNA reads aligning to the X chromosome to DNA reads aligning to autosomes (termed the Rx ratio). We tested the accuracy of this method using low coverage genomes from 15 modern elephants (Loxodonta africana) for which sex was known. We then applied this method to ancient elephant ivory samples for which sex was unknown, and describe how this method can be further adapted to the genomes of other taxa. This method may be especially useful when only low-coverage genomic data are obtainable. Furthermore, because this method relies on only the X and not the Y chromosome, it can be used to determine the sex of organisms for which a reference genome was obtained from a female or for which only the X chromosome is reported. Such taxa include the domestic cat, sheep, goat, and horse; and non-domesticated animals such as the Sumatran orangutan, western lowland gorilla and meerkat.
Collapse
|
13
|
Zhou Y, Liu H, Wang X, Fu B, Yu X, Tong J. QTL Fine Mapping for Sex Determination Region in Bighead Carp (Hypophthalmichthys nobilis) and Comparison with Silver Carp (Hypophthalmichthys molitrix). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:41-53. [PMID: 31776800 DOI: 10.1007/s10126-019-09929-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix) are genetically close aquaculture fish in the Cyprinidae, which have been confirmed to hold XX/XY sex determination. However, genomic locations of potential sex-related loci in these two fishes are still unknown. In this study, a high-resolution genetic linkage map was constructed by using 2976 SNP and 924 microsatellite markers in a F1 full-sib family of bighead carp, the length of which spanned 2022.34 cM with an average inter-marker distance of 0.52 cM. Comparative genomics revealed a high level of genomic synteny between bighead carp and zebrafish as well as grass carp. QTL fine mapping for sex trait was performed based on this linkage map of bighead carp and an unpublished linkage map of silver carp. A map distance of 3.863 cM (69.787-73.650 cM) on LG19 of bighead carp and 4.705 cM (79.096-83.801 cM) on LG21 of silver carp was significantly associated with sex phenotypes, and these two LGs are homologous between two fish species. Fourteen markers harboring in these regions were in strong linkage disequilibrium with the sex phenotype variance explained (PVE) varying from 89 to 100%. Two common markers were mapped on the QTL regions of bighead carp and silver carp, suggesting that these two carp species may have similar genetic bases for sex determination. Eleven potentially sex-related genes were identified within or near the sex QTL markers in two species. This study provided insights into elucidating mechanisms and evolution of sex determination in cyprinid fishes.
Collapse
Affiliation(s)
- Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xinhua Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
| |
Collapse
|
14
|
Wang J, Li M, Qin Z, Li J, Li J. Validation of growth-related quantitative trait loci markers in different Exopalaemon carinicauda families for marker-assisted selection. Anim Genet 2020; 51:324-329. [PMID: 31981462 DOI: 10.1111/age.12914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 01/08/2023]
Abstract
We detected growth-related QTL and associated markers from the backcross population of Exopalaemon carinicauda in the previous study. Based on our previous study, the 47 SNP markers associated with candidate growth trait QTL were selected to analyze the association between these markers and body weight (BW), body length and abdominal segment length traits in four different populations including wild population, a full-sib family, a half-sib family and a backcross population for evaluating their potential application of marker-assisted selection in E. carinicauda. The general linear model (GLM) and mixed linear model were applied and the associations between SNP loci and three growth-related traits verified. The results showed that the Marker79268 and Marker100644 were significantly associated with the BW trait in more than three populations by the GLM method. The Marker100644 was significantly associated with BW in the full-sib family, half-sib family and backcross populations by the GLM and mixed linear model methods. Our findings will provide useful SNP markers to go forward to improve growth performance through more refined marker-assisted selection in E. carinicauda.
Collapse
Affiliation(s)
- J Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - M Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,College of Fishery and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Z Qin
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - J Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - J Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| |
Collapse
|
15
|
Lv J, Sun D, Yan D, Ti X, Liu P, Li J. Quantitative Trait Loci Mapping and Marker Identification for Low Salinity Tolerance Trait in the Swimming Crab ( Portunus trituberculatus). Front Genet 2019; 10:1193. [PMID: 31850064 PMCID: PMC6900548 DOI: 10.3389/fgene.2019.01193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/28/2019] [Indexed: 01/17/2023] Open
Abstract
Low salinity is one of the most important abiotic factors that directly affect the abundance of the swimming crab, Portunus trituberculatus. Quantitative trait loci (QTL) mapping could be helpful in identifying the markers and genes involved in low salinity tolerance. In this study, two QTLs of low salt tolerance were mapped on linkage group 17 (LG17, 2.6-5.2 cM) based on a high-density linkage map. Ninety-five markers related to low salinity tolerance were identified via association analysis, and seventy-nine low salt-related candidate genes (including ammonium transport, aldehyde dehydrogenase, and glucosyltransferase) were screened from draft genome of the species via these markers. This represents the first report of QTL mapping for low salinity tolerance in the swimming crab, which may be useful to elucidate salinity adaptation mechanisms.
Collapse
Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dongfang Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Deping Yan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xingbin Ti
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
16
|
Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba). Polar Biol 2019. [DOI: 10.1007/s00300-019-02592-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Abstract
Antarctic krill (Euphausia superba) is a highly abundant keystone species of the Southern Ocean ecosystem, directly connecting primary producers to high-trophic level predators. Sex ratios of krill vary remarkably between swarms and this phenomenon is poorly understood, as identification of krill sex relies on external morphological differences that appear late during development. Sex determination mechanisms in krill are unknown, but could include genetic, environmental or parasitic mechanisms. Similarly, virtually nothing is known about molecular sex differentiation. The krill genome has to date not been sequenced, and due to its enormous size and large amount of repetitive elements, it is currently not feasible to develop sex-specific DNA markers. To produce a reliable molecular marker for sex in krill and to investigate molecular sex differentiation we therefore focused on identifying sex-specific transcriptomic differences. Through transcriptomic analysis, we found large gene expression differences between testes and ovaries and identified three genes exclusively expressed in female whole krill from early juvenile stages onwards. The sex-specific expression of these three genes persisted through sexual regression, although our regressed samples originated from a krill aquarium and may differ from wild-regressed krill. Two slightly male-biased genes did not display sufficient expression differences to clearly differentiate sexes. Based on the expression of the three female-specific genes we developed a molecular test that for the first time allows the unambiguous sex determination of krill samples lacking external sex-specific features from juvenile stages onwards, including the sexually regressed krill we examined.
Collapse
|
17
|
Molecular Characterization and Functional Study of Insulin-Like Androgenic Gland Hormone Gene in the Red Swamp Crayfish, Procambarus clarkii. Genes (Basel) 2019; 10:genes10090645. [PMID: 31455039 PMCID: PMC6770367 DOI: 10.3390/genes10090645] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/07/2019] [Accepted: 08/21/2019] [Indexed: 12/13/2022] Open
Abstract
The androgenic gland (AG) is a male-specific endocrine organ that controls the primary and secondary sexual characteristics in male crustaceans. More evidence indicates that the insulin-like androgenic gland hormone gene (IAG) is the key male sexual differentiation factor, particularly the application of RNA interference (RNAi) technology on IAG. In this study, the full-length cDNA of IAG (termed PcIAG) was isolated from the red swamp crayfish, Procambarusclarkii. Tissue distribution analysis showed that in addition to its expression in the AG of male P. clarkii, PcIAG was widely expressed in female tissues and other male tissues. The PcIAG protein was detected in the reproductive and nervous systems of adult male P. clarkii. Additionally, RNAi results showed that the PcIAG expression could be silenced efficiently, and the male sperm maturation and release possibly present a transient adverse interference at lower doses (0.1 μg/g and 1 μg/g) of PcIAG–dsRNA (PcIAG double-stranded RNA). Dramatically, the expression level of PcIAG increased sharply shortly after the injection of higher doses (5 μg/g and 10 μg/g) of PcIAG–dsRNA, which might accelerate the maturation and release of sperm. Moreover, the expression of PcSxl (P. clarkii Sex-lethal) was detected by Quantitative Real-Time PCR (qPCR) after the injection of PcIAG–dsRNA to explore whether the PcIAG gene regulates the PcSxl gene, and we found that the PcIAG did not directly regulate PcSxl in P. clarkii. The study could help accelerate the progress of PcIAG functional research and provide a useful reference for the single-sex selective breeding of P. clarkii.
Collapse
|
18
|
Li J, Lv J, Liu P, Chen P, Wang J, Li J. Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits. BMC Genomics 2019; 20:598. [PMID: 31331278 PMCID: PMC6647322 DOI: 10.1186/s12864-019-5981-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species. RESULTS In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8-15.7% of the total growth-traits variation. CONCLUSIONS The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.
Collapse
Affiliation(s)
- Jitao Li
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jianjian Lv
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Ping Liu
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Ping Chen
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jiajia Wang
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China
| | - Jian Li
- Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao, 266071, China. .,Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao, 266071, China.
| |
Collapse
|
19
|
Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome. Genome Biol Evol 2019; 11:1033-1044. [PMID: 30865260 PMCID: PMC6456005 DOI: 10.1093/gbe/evz053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/25/2022] Open
Abstract
Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.
Collapse
Affiliation(s)
| | - Melissa A Toups
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| |
Collapse
|
20
|
Waiho K, Shi X, Fazhan H, Li S, Zhang Y, Zheng H, Liu W, Fang S, Ikhwanuddin M, Ma H. High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab ( Scylla paramamosain). Front Genet 2019; 10:298. [PMID: 31024620 PMCID: PMC6459939 DOI: 10.3389/fgene.2019.00298] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
Mud crab, Scylla paramamosain is one of the most important crustacean species in global aquaculture. To determine the genetic basis of sex and growth-related traits in S. paramamosain, a high-density genetic linkage map with 16,701 single nucleotide polymorphisms (SNPs) was constructed using SLAF-seq and a full-sib family. The consensus map has 49 linkage groups, spanning 5,996.66 cM with an average marker-interval of 0.81 cM. A total of 516 SNP markers, including 8 female-specific SNPs segregated in two quantitative trait loci (QTLs) for phenotypic sex were located on LG32. The presence of female-specific SNP markers only on female linkage map, their segregation patterns and lower female: male recombination rate strongly suggest the conformation of a ZW/ZZ sex determination system in S. paramamosain. The QTLs of most (90%) growth-related traits were found within a small interval (25.18–33.74 cM) on LG46, highlighting the potential involvement of LG46 in growth. Four markers on LG46 were significantly associated with 10–16 growth-related traits. BW was only associated with marker 3846. Based on the annotation of transcriptome data, 11 and 2 candidate genes were identified within the QTL regions of sex and growth-related traits, respectively. The newly constructed high-density genetic linkage map with sex-specific SNPs, and the identified QTLs of sex- and growth-related traits serve as a valuable genetic resource and solid foundation for marker-assisted selection and genetic improvement of crustaceans.
Collapse
Affiliation(s)
- Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| |
Collapse
|
21
|
Ma KY, Yu SH, Du YX, Feng SQ, Qiu LJ, Ke DY, Luo MZ, Qiu GF. Construction of a Genomic Bacterial Artificial Chromosome (BAC) Library for the Prawn Macrobrachium rosenbergii and Initial Analysis of ZW Chromosome-Derived BAC Inserts. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:206-216. [PMID: 30632018 DOI: 10.1007/s10126-018-09873-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 12/27/2018] [Indexed: 06/09/2023]
Abstract
Knowledge on sex determination has proven valuable for commercial production of the prawn Macrobrachium rosenbergii due to sex dimorphism of the male and female individuals. Previous studies indicated that prawn sex is determined by a ZW-ZZ chromosomal system, but no genomic information is available for the sex chromosome. Herein, we constructed a genomic bacterial artificial chromosome (BAC) library and identified the ZW-derived BAC clones for initial analysis of the sex chromosomal DNA sequence. The arrayed BAC library contains 200,448 clones with average insert size of 115.4 kb, corresponding to ∼ 4× coverage of the estimated 5.38 Gb genome. Based on a short female-specific marker, a Z- and a W-fragment were retrieved with the genomic walking method. Screening the BAC library using a ZW-specific marker as probe resulted in 12 positive clones. From these, a Z-derived (P331M17) and a W-derived (P122G2) BAC clones were randomly selected and sequenced by PacBio method. We report the construction of a large insert, deep-coverage, and high-quality BAC library for M. rosenbergii that provides a useful resource for positional cloning of target genes, genomic organization, and comparative genomics analysis. Our study not only confirmed the ZW/ZZ system but also discovered sex-linked genes on ZW chromosomes for the first time, contributing to a comprehensive understanding of the genomic structure of sex chromosomes in M. rosenbergii.
Collapse
Affiliation(s)
- Ke-Yi Ma
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Shu-Hui Yu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Yu-Xin Du
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Shi-Qing Feng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Liang-Jie Qiu
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Dai-Yi Ke
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Mei-Zhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Gao-Feng Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China.
- College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong New Area, 201306, Shanghai, People's Republic of China.
| |
Collapse
|
22
|
Zhang S, Zhang X, Chen X, Xu T, Wang M, Qin Q, Zhong L, Jiang H, Zhu X, Liu H, Shao J, Zhu Z, Shi Q, Bian W, You X. Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish ( Ictalurus punctatus). Front Genet 2019; 10:251. [PMID: 30984241 PMCID: PMC6448050 DOI: 10.3389/fgene.2019.00251] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/06/2019] [Indexed: 12/11/2022] Open
Abstract
A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F1 family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.
Collapse
Affiliation(s)
- Shiyong Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Qin Qin
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Hucheng Jiang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xiaohua Zhu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Hongyan Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Junjie Shao
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Zhifei Zhu
- BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Wenji Bian
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| |
Collapse
|
23
|
Affiliation(s)
- Christine Ewers-Saucedo
- Zoological Institute and Museum, Zoological Museum of the Christian-Albrechts University, Kiel, Germany
| |
Collapse
|
24
|
Fang S, Zhang Y, Shi X, Zheng H, Li S, Zhang Y, Fazhan H, Waiho K, Tan H, Ikhwanuddin M, Ma H. Identification of male-specific SNP markers and development of PCR-based genetic sex identification technique in crucifix crab (Charybdis feriatus) with implication of an XX/XY sex determination system. Genomics 2019; 112:404-411. [PMID: 30851358 DOI: 10.1016/j.ygeno.2019.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/24/2019] [Accepted: 03/05/2019] [Indexed: 12/21/2022]
Abstract
In this study, we first identified male-specific SNP markers using restriction site-associated DNA sequencing, and further developed a PCR-based sex identification technique for Charybdis feriatus. A total of 296.96 million clean reads were obtained, with 114.95 and 182.01 million from females and males. After assembly and alignment, 10 SNP markers were identified being heterozygous in males but homozygous in females. Five markers were further confirmed to be male-specific in a large number of individuals. Moreover, two male-specific sense primers and a common antisense primer were designed, using which, a PCR-based genetic sex identification method was successfully developed and used to identify the sex of 103 individuals, with a result of 49 females and 54 males. The presence of male-specific SNP markers suggests an XX/XY sex determination system for C. feriatus. These findings should be helpful for better understanding sex determination mechanism, and drafting artificial breeding program in crustaceans.
Collapse
Affiliation(s)
- Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Huaqiang Tan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| |
Collapse
|
25
|
Zhao M, Wang W, Chen W, Ma C, Zhang F, Jiang K, Liu J, Diao L, Qian H, Zhao J, Wang T, Ma L. Genome survey, high-resolution genetic linkage map construction, growth-related quantitative trait locus (QTL) identification and gene location in Scylla paramamosain. Sci Rep 2019; 9:2910. [PMID: 30814536 PMCID: PMC6393678 DOI: 10.1038/s41598-019-39070-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 01/11/2019] [Indexed: 11/09/2022] Open
Abstract
Scylla paramamosain is one of the most economically important crabs in China. In this study, the first genome survey sequencing of this crab was performed, and the results revealed that the estimated genome size was 1.21 Gb with high heterozygosity (1.3%). Then, RAD technology was used to construct a high-resolution linkage map for this species. A total of 24,444 single nucleotide polymorphism (SNP) makers were grouped into 47 linkage groups. The total length of the linkage groups was 3087.53 cM with a markers interval of 0.92 cM. With the aid of transcriptome and genome scaffold data, 4,271 markers were linked to genes, including several important growth-related genes such as transforming growth factor-beta regulator I, immune related-gene C-type lectin and ecdysone pathway gene broad-complex-like protein. Further, 442 markers, representing 279 QTLs, associated with 24 traits were identified, and of these markers, 78 were linked to genes. Some interesting genes, such as dedicator of cytokinesis protein 3, tenascin-X and DNA helicase MCM8, were believed to have important relationship with specific traits and merit further exploration. The results of this study will accelerate the genetic improvement and genome sequencing analysis of the mud crab.
Collapse
Affiliation(s)
- Ming Zhao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Wei Wang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Wei Chen
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Chunyan Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Fengying Zhang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Keji Jiang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Junguo Liu
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Le Diao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Heng Qian
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Junxia Zhao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Tian Wang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Lingbo Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China.
| |
Collapse
|
26
|
Shi X, Waiho K, Li X, Ikhwanuddin M, Miao G, Lin F, Zhang Y, Li S, Zheng H, Liu W, Aweya JJ, Azmie G, Baylon JC, Quinitio ET, Ma H. Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification. BMC Genomics 2018; 19:981. [PMID: 30594128 PMCID: PMC6311006 DOI: 10.1186/s12864-018-5380-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 12/16/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Mud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is extremely essential in aquaculture. However, the sex determination mechanism is still unclear. Development of sex-specific genetic markers based on next-generation sequencing proved to be an effective tool for discovering sex determination system in various animals. RESULTS Restriction-site associated DNA sequencing (RAD-seq) was employed to isolate sex-specific SNP markers for S. paramamosain. A total of 335.6 million raw reads were obtained from 20 individuals, of which 204.7 million were from 10 females and 130.9 million from 10 males. After sequence assembly and female-male comparison, 20 SNP markers were identified to be sex-specific. Furthermore, ten SNPs in a short sequence (285 bp) were confirmed heterozygous in females and homozygous in males in a large population by PCR amplification and sequencing. Subsequently, a female-specific primer was successfully designed according to the female-specific nucleotide which could amplify an expected band from females but not from males. Thus, a rapid and effective method for molecular sexing in S. paramamosain was developed, meanwhile, this method could successfully identify the sex of S. tranquebarica and S. serrata. Finally, nine and four female-specific SNP markers were detected in S. tranquebarica and S. serrata, respectively. CONCLUSIONS Sex-specific SNP markers were firstly identified in crab species and showed female heterogamety and male homogamety, which provided strong genetic evidence for a WZ/ZZ sex determination system in mud crabs S. paramamosain, S. tranquebarica and S. serrata. These findings will lay a solid foundation for the study of sex determination mechanism, sex chromosome evolution, and the development of mono-sex population in crustaceans.
Collapse
Affiliation(s)
- Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
| | - Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
| | - Xincang Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090 China
| | - Mhd Ikhwanuddin
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Malaysia
| | - Guidong Miao
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Fan Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Jude Juventus Aweya
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Ghazali Azmie
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Malaysia
| | - Juliana C. Baylon
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines, Visayas, 5023 Miagao, Philippines
| | - Emilia T. Quinitio
- Aquaculture Department, Southeast Asian Fisheries Development Center, 5021 Tigbauan, Philippines
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
| |
Collapse
|
27
|
Xu LY, Wang LY, Wei K, Tan LQ, Su JJ, Cheng H. High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing. BMC Genomics 2018; 19:955. [PMID: 30577813 PMCID: PMC6304016 DOI: 10.1186/s12864-018-5291-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 11/20/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map. RESULTS A total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation. CONCLUSIONS To our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.
Collapse
Affiliation(s)
- Li-Yi Xu
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li-Yuan Wang
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Kang Wei
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Li-Qiang Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jing-Jing Su
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Hao Cheng
- National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| |
Collapse
|
28
|
Danzmann RG, Norman JD, Rondeau EB, Messmer AM, Kent MP, Lien S, Igboeli O, Fast MD, Koop BF. A genetic linkage map for the salmon louse (Lepeophtheirus salmonis): evidence for high male:female and inter-familial recombination rate differences. Mol Genet Genomics 2018; 294:343-363. [PMID: 30460550 DOI: 10.1007/s00438-018-1513-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/15/2018] [Indexed: 01/28/2023]
Abstract
A salmon louse (Lepeophtheirus salmonis salmonis) genetic linkage map was constructed to serve as a genomic resource for future investigations into the biology of this important marine parasitic copepod species, and to provide insights into the inheritance patterns of genetic markers in this species. SNP genotyping of 8 families confirmed the presence of 15 linkage groups based upon the assignment of 93,773 markers. Progeny sample size weight adjusted map sizes in males (with the exception of SL12 and SL15) ranged in size from 96.50 cM (SL11) to 134.61 cM (SL06), and total combined map steps or bins ranged from 143 (SL09) to 203 (SL13). The SL12 male map was the smallest linkage group with a weight-averaged size of 3.05 cM with 6 recombination bins. Male:female specific recombination rate differences are 10.49:1 and represent one of the largest reported sex-specific differences for any animal species. Recombination ratio differences (M:F) ranged from 1.0 (SL12) to 29:1 (SL15). The number of markers exhibiting normal Mendelian segregation within the sex linkage group SL15 was extremely low (N = 80) in comparison to other linkage groups genotyped [range: 1459 (SL12)-10206 markers (SL05)]. Re-evaluation of Mendelian inheritance patterns of markers unassigned to any mapping parent according to hemizygous segregation patterns (models presented) identified matches for many of these markers to hemizygous patterns. The greatest proportion of these markers assigned to SL15 (N increased to 574). Inclusion of the hemizygous markers revised SL15 sex-specific recombination rate differences to 28:1. Recombination hot- and coldspots were identified across all linkage groups with all linkage groups possessing multiple peaks. Nine of 13 linkage groups evaluated possessed adjacent domains with hot-coldspot transitional zones. The most common pattern was for one end of the linkage to show elevated recombination in addition to internal regions. For SL01 and SL06, however, a terminal region with high recombination was not evident while a central domain possessing extremely high-recombination levels was present. High levels of recombination were weakly coupled to higher levels of SNP variation within domains, but this association was very strong for the central domains of SL01 and SL06. From the pooled paternal half-sib lots (several virgin females placed with 1 male), only 1 or two surviving family lots were obtained. Surviving families possessed parents where both the male and female possessed either inherently low or high recombination rates. This study provides insight into the organization of the sea louse genome, and describes large differences in recombination rate that exist among individuals of the same sex, and between the sexes. These differences in recombination rate may be coupled to the capabilities of this species to adapt to environmental and pharmaceutical treatments, given that family survivorship appears to be enhanced when parents have similar recombination levels.
Collapse
Affiliation(s)
- Roy G Danzmann
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Joseph D Norman
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Amber M Messmer
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Matthew P Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Okechukwu Igboeli
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| |
Collapse
|
29
|
Furman BLS, Evans BJ. Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems. Genome Biol Evol 2018; 10:742-755. [PMID: 29608717 PMCID: PMC5841384 DOI: 10.1093/gbe/evy045] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 02/02/2023] Open
Abstract
There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions.
Collapse
Affiliation(s)
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
30
|
Lv J, Sun D, Huan P, Song L, Liu P, Li J. QTL Mapping and Marker Identification for Sex-Determining: Indicating XY Sex Determination System in the Swimming Crab ( Portunus trituberculatus). Front Genet 2018; 9:337. [PMID: 30210528 PMCID: PMC6119780 DOI: 10.3389/fgene.2018.00337] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/07/2018] [Indexed: 12/23/2022] Open
Abstract
Sex determination is an important area of research, which has always had an intriguing aspect in evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex will be helpful in clarifying the sex determination system. In this study, the sex QTL mapping of the swimming crab (Portunus trituberculatus) was performed based on a high-density linkage map, and a highly significant QTL specifically mapped on a single linkage group (LG) was firstly identified (LG24, LOD > 14). Twenty markers in the QTL region showed significant associations with sex by association analysis, of which heterogametic genotypes in males supported the XY sex determination mechanism. Two sex-specific markers at the family level were identified via segregation distortion analysis, which were known to be the most closely linked to the sex of P. trituberculatus. Based on sex marker sequences (Marker3840, Marker20320, and Marker10494), three potential sex-related genes were identified, and the quantitative real-time PCR results suggested that these genes were important in spermatogenesis or sex characteristics in males. Our results will contribute to the fine-mapping of sex-determining genes and clarify the sex determination mechanism of P. trituberculatus.
Collapse
Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dongfang Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Pengpeng Huan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Liu Song
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
31
|
Feng X, Yu X, Fu B, Wang X, Liu H, Pang M, Tong J. A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus). BMC Genomics 2018; 19:230. [PMID: 29609551 PMCID: PMC5879560 DOI: 10.1186/s12864-018-4613-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/20/2018] [Indexed: 01/08/2023] Open
Abstract
Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. Results A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin. Conclusions We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp. Electronic supplementary material The online version of this article (10.1186/s12864-018-4613-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiu Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xinhua Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| |
Collapse
|
32
|
Identification and characterization of a doublesex gene which regulates the expression of insulin-like androgenic gland hormone in Fenneropenaeus chinensis. Gene 2018; 649:1-7. [DOI: 10.1016/j.gene.2018.01.043] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 12/27/2017] [Accepted: 01/11/2018] [Indexed: 11/21/2022]
|
33
|
Torrecilla Z, Martínez-Lage A, Perina A, González-Ortegón E, González-Tizón AM. Comparative cytogenetic analysis of marine Palaemon species reveals a X 1X 1X 2X 2/X 1X 2Y sex chromosome system in Palaemon elegans. Front Zool 2017; 14:47. [PMID: 29046707 PMCID: PMC5639736 DOI: 10.1186/s12983-017-0233-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/02/2017] [Indexed: 12/01/2022] Open
Abstract
Background The maintenance of species and the promotion of speciation are closely related to chromosomal rearrangements throughout evolution. Decapoda represents the most species-rich order among crustaceans and, despite its ecological and economic importance, little is known about decapod karyology. We aim at cytogenetically characterizing two sympatric prawn species. Results Analysis of mitotic metaphases and meiotic diakinesis of the common prawn Palaemon serratus and the rockpool prawn P. elegans, revealed considerable differences between their karyotypes including chromosome numbers and sex determination systems. The cytogenetic data for P. serratus showed a diploid number of 56 and the putative absence of heteromorphic sex chromosomes. However, the diploid chromosome number in P. elegans was 90 for females and 89 for males. The karyotype of the females consisted of the three largest acrocentric pairs and 42 submetacentric and metacentric pairs, while the karyotype of the males comprised a clearly identifiable large metacentric chromosome and two acrocentric pairs as well as the smaller 42 pairs. These results highlight the presence of the X1X1X2X2/X1X2Y multiple sex chromosome system in P. elegans, which constitute the only sexual system for Decapoda reported cytogenetically using modern techniques. The origin of this sex chromosome system is discussed. We hypothesize that the chromosome evolution within the genus could involve several fusion events giving rise to a reduction on the chromosome number in P. serratus. In both species, the major ribosomal genes were located in two chromosome pairs and hybridization signals of the telomeric sequences (TTAGGG)n were visualized at the telomeres of all chromosomes. C-banding revealed that, when present, constitutive heterochromatin had a predominantly telomeric distribution and no centromeric constitutive heterochromatin was observed. Conclusions Although more comparative cytogenetic analyses are needed to clarify our hypotheses, the findings of this work indicate that the prawns of the genus Palaemon represent a promising model among Decapoda representatives to investigate the karyotype evolution and the patterns of sex chromosome differentiation.
Collapse
Affiliation(s)
- Zeltia Torrecilla
- Grupo de Investigación en Biología Evolutiva (GIBE), Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira, 15071 A Coruña, Spain
| | - Andrés Martínez-Lage
- Grupo de Investigación en Biología Evolutiva (GIBE), Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira, 15071 A Coruña, Spain
| | - Alejandra Perina
- Grupo de Investigación en Biología Evolutiva (GIBE), Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira, 15071 A Coruña, Spain
| | - Enrique González-Ortegón
- Instituto de Ciencias Marinas de Andalucía (ICMAN, CSIC), Campus Universitario Río San Pedro, 11510 Puerto Real, Cádiz, Spain.,International Campus of Excellence of the Sea (CEI-MAR), Edificio Hospital Real, 11003 Cádiz, Spain
| | - Ana M González-Tizón
- Grupo de Investigación en Biología Evolutiva (GIBE), Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira, 15071 A Coruña, Spain
| |
Collapse
|
34
|
Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth-related QTL and gene identification. Sci Rep 2017; 7:7874. [PMID: 28801606 PMCID: PMC5554138 DOI: 10.1038/s41598-017-08256-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/06/2017] [Indexed: 11/09/2022] Open
Abstract
A high-resolution genetic linkage map is an essential tool for decoding genetics and genomics in non-model organisms. In this study, a linkage map was constructed for the swimming crab (Portunus trituberculatus) with 10,963 markers; as far as we know, this number of markers has never been achieved in any other crustacean. The linkage map covered 98.85% of the whole genome with a mean marker interval of 0.51 cM. The de novo assembly based on genome and transcriptome sequencing data enabled 2,378 explicit annotated markers to be anchored to the map. Quantitative trait locus (QTL) mapping revealed 10 growth-related QTLs with a phenotypic variance explained (PVE) range of 12.0-35.9. Eight genes identified from the growth-related QTL regions, in particular, RE1-silencing transcription factor and RNA-directed DNA polymerase genes with nonsynonymous substitutions, were considered important growth-related candidate genes. We have demonstrated that linkage mapping aided by de novo assembly of genome and transcriptome sequencing could serve as an important platform for QTL mapping and the identification of trait-related genes.
Collapse
|
35
|
A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp ( Carassius auratus) Using 2b-RAD Sequencing. G3-GENES GENOMES GENETICS 2017; 7:2473-2487. [PMID: 28600439 PMCID: PMC5555455 DOI: 10.1534/g3.117.041376] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A high-resolution genetic linkage map is essential for a wide range of genetics and genomics studies such as comparative genomics analysis and QTL fine mapping. Crucian carp (Carassius auratus) is widely distributed in Eurasia, and is an important aquaculture fish worldwide. In this study, a high-density genetic linkage map was constructed for crucian carp using 2b-RAD technology. The consensus map contains 8487 SNP markers, assigning to 50 linkage groups (LGs) and spanning 3762.88 cM, with an average marker interval of 0.44 cM and genome coverage of 98.8%. The female map had 4410 SNPs, and spanned 3500.42 cM (0.79 cM/marker), while the male map had 4625 SNPs and spanned 3346.33 cM (0.72 cM/marker). The average recombination ratio of female to male was 2.13:1, and significant male-biased recombination suppressions were observed in LG47 and LG49. Comparative genomics analysis revealed a clear 2:1 syntenic relationship between crucian carp LGs and chromosomes of zebrafish and grass carp, and a 1:1 correspondence, but extensive chromosomal rearrangement, between crucian carp and common carp, providing evidence that crucian carp has experienced a fourth round of whole genome duplication (4R-WGD). Eight chromosome-wide QTL for body weight at 2 months after hatch were detected on five LGs, explaining 10.1-13.2% of the phenotypic variations. Potential candidate growth-related genes, such as an EGF-like domain and TGF-β, were identified within the QTL intervals. This high-density genetic map and QTL analysis supplies a basis for genome evolutionary studies in cyprinid fishes, genome assembly, and QTL fine mapping for complex traits in crucian carp.
Collapse
|
36
|
Li P, Liu Y, Luo D, Song C, Cui Z. Two spliced isoforms of the sex-determination gene fruitless in the Chinese mitten crab Eriocheir sinensis. Comp Biochem Physiol B Biochem Mol Biol 2017; 208-209:75-83. [PMID: 28438684 DOI: 10.1016/j.cbpb.2017.04.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/11/2017] [Accepted: 04/17/2017] [Indexed: 01/06/2023]
Abstract
The fruitless (fru) gene plays an important role in the sex determination pathway and courtship behavior of Drosophila melanogaster. In the present study, two fru isoforms (Esfru1 and Esfru2) were identified from the Chinese mitten crab Eriocheir sinensis. Sequence analysis showed that Esfru1 and Esfru2 were encoded by the same genomic locus and generated by alternative splicing of pre-mRNA. Esfru1 had all introns completely spliced out, while Esfru2 had a longer exon1 with an additional 78bp sequence. They both contained a conserved BTB domain which was also found in D. melanogaster Fru isoforms. Analysis on temporal expression profiles of Esfru1-2 (a common region of Esfru1 and Esfru2) and Esfru2 (a specific region of Esfru2) showed that they expressed in similar patterns during embryonic development but in different patterns during larval development. The expression of Esfru1-2 decreased gradually from zoea III stage, however, Esfru2 increased from zoea IV stage and reached the peak at megalopa stage. Expression distribution in tissues and in situ hybridization analysis revealed that they showed sexually dimorphic expression in gonads, hepatopancreas and brains. Esfru1-2 showed significantly higher expression in female gonads and hepatopancreas than in males, but highly expressed in male brains than that in females. Interestingly, Esfru2 was displayed in a male-specific manner in each tissue, especially in gonads and hepatopancreas. Our results indicate that Esfru1 might be involved in both sexual brain neuronal structure development and related to female-specific character development. Esfru2 may participate in male-specific character development. This is the first report that characterizes two spliced variants of fru in crustaceans and provides basic information for further functional studies of the crab sex-determination mechanism.
Collapse
Affiliation(s)
- Peiyao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Danli Luo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chengwen Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhaoxia Cui
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| |
Collapse
|
37
|
Isolation and characterization of 91 single nucleotide polymorphism (SNP) markers for the blue swimming crab (Portunus pelagicus). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0720-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
38
|
A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis. Sci Rep 2017; 7:39826. [PMID: 28045132 PMCID: PMC5206627 DOI: 10.1038/srep39826] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/28/2016] [Indexed: 02/03/2023] Open
Abstract
The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs.
Collapse
|
39
|
Serial sequencing of isolength RAD tags for cost-efficient genome-wide profiling of genetic and epigenetic variations. Nat Protoc 2016; 11:2189-2200. [PMID: 27711051 DOI: 10.1038/nprot.2016.133] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Isolength restriction site-associated DNA (isoRAD) sequencing is a very simple but powerful approach that was originally developed for genome-wide genotyping at minimal labor and cost, and it has recently extended its applicability to allow quantification of DNA methylation levels. The isoRAD method is distinct from other genotyping-by-sequencing (GBS) methods because of its use of special restriction enzymes to produce isolength tags (32-36 bp), and sequencing of these uniform tags can bring many benefits. However, the relatively short tags produced by the original protocol are mostly suited to single-end (SE) sequencing (36-50 bp), and therefore they cannot efficiently match the gradually increased sequencing capacity of next-generation sequencing (NGS) platforms. To address this issue, we describe an advanced protocol that allows the preparation of five concatenated isoRAD tags for Illumina paired-end (PE) sequencing (100-150 bp). The configuration of the five concatenated tags is highly flexible, and can be defined by users to work with a desired combination of samples and/or restriction enzymes to suit specific research purposes. In comparison with the original protocol, the advanced protocol has an additional digestion and ligation step, and library preparation can be completed in ∼8 h.
Collapse
|
40
|
Wang S, Lv J, Zhang L, Dou J, Sun Y, Li X, Fu X, Dou H, Mao J, Hu X, Bao Z. MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes. Open Biol 2016; 5:rsob.150130. [PMID: 26581575 PMCID: PMC4680569 DOI: 10.1098/rsob.150130] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Characterization of dynamic DNA methylomes in diverse phylogenetic groups has attracted growing interest for a better understanding of the evolution of DNA methylation as well as its function and biological significance in eukaryotes. Sequencing-based methods are promising in fulfilling this task. However, none of the currently available methods offers the 'perfect solution', and they have limitations that prevent their application in the less studied phylogenetic groups. The recently discovered Mrr-like enzymes are appealing for new method development, owing to their ability to collect 32-bp methylated DNA fragments from the whole genome for high-throughput sequencing. Here, we have developed a simple and scalable DNA methylation profiling method (called MethylRAD) using Mrr-like enzymes. MethylRAD allows for de novo (reference-free) methylation analysis, extremely low DNA input (e.g. 1 ng) and adjustment of tag density, all of which are still unattainable for most widely used methylation profiling methods such as RRBS and MeDIP. We performed extensive analyses to validate the power and accuracy of our method in both model (plant Arabidopsis thaliana) and non-model (scallop Patinopecten yessoensis) species. We further demonstrated its great utility in identification of a gene (LPCAT1) that is potentially crucial for carotenoid accumulation in scallop adductor muscle. MethylRAD has several advantages over existing tools and fills a void in the current epigenomic toolkit by providing a universal tool that can be used for diverse research applications, e.g. from model to non-model species, from ordinary to precious samples and from small to large genomes, but at an affordable cost.
Collapse
Affiliation(s)
- Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Jia Lv
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China
| | - Lingling Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China
| | - Jinzhuang Dou
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China
| | - Yan Sun
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China
| | - Xue Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China
| | - Xiaoteng Fu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China
| | - Huaiqian Dou
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China
| | - Junxia Mao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China
| | - Xiaoli Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| |
Collapse
|
41
|
Chandler JC, Aizen J, Fitzgibbon QP, Elizur A, Ventura T. Applying the Power of Transcriptomics: Understanding Male Sexual Development in Decapod Crustacea. Integr Comp Biol 2016; 56:1144-1156. [PMID: 27252217 DOI: 10.1093/icb/icw007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The decapod Crustacea are the most species-rich order of the Crustacea and include some of the most charismatic and highly valued commercial species. Thus the decapods draw a significant research interest in relation to aquaculture, as well as gaining a broader understanding of these species' biology. However, the diverse physiology of the group considered with the lack of a model species have presented an obstacle for comparative analyses. In reflection of this, the recent integration of comparative transcriptomics has rapidly advanced our understanding of key regulatory pathways and developmental phenomena, an example being our understanding of sexual development. We discuss our work in the Eastern spiny lobster, Sagmariasus verreauxi, in the context of what is currently known about male sexual development in the decapods, highlighting the importance of transcriptomic techniques in achieving our recent advancements. We describe the progression made in our understanding of male sexual differentiation and maturation, as mediated by the insulin-like androgenic gland hormone (IAG), integrating the role of regulatory binding proteins (IGFBPs), a tyrosine kinase insulin receptor (TKIR), as well as the upstream effect of neuroendocrine hormones (GIH and MIH). We then consider the less well understood mechanism of male sex determination, with an emphasis on what we believe to be the key regulatory factors, the Dsx- and mab-3-related transcription factors (Dmrts). Finally, we discuss the function of the antennal gland (AnG) in sexual development, relating to the emergence of male-biased upregulation in the AnG in later sexual maturation and the sexually dimorphic expression of two key genes Sv-TKIR and Sv-Dmrt1 We then present the AnG as a case study to illustrate how comparative transcriptomic techniques can be applied to guide preliminary analyses, like the hypothesis that the AnG may function in pheromone biosynthesis. In summary, we describe the power of transcriptomics in facilitating the progress made in our understanding of male sexual development, as illustrated by the commercial decapod species, S. verreauxi Considering future directions, we suggest that the integration of multiple omics-based techniques offers the most powerful tool to ensure we continue to piece together the biology of the important group of decapod Crustacea.
Collapse
Affiliation(s)
- Jennifer C Chandler
- *Faculty of Science, Health, Education and Engineering, GeneCology Research Centre, University of the Sunshine Coast (USC), 4 Locked Bag, Maroochydore, Queensland 4558, Australia
| | - Joseph Aizen
- *Faculty of Science, Health, Education and Engineering, GeneCology Research Centre, University of the Sunshine Coast (USC), 4 Locked Bag, Maroochydore, Queensland 4558, Australia
| | - Quinn P Fitzgibbon
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Private Bag 49, Hobart, Tasmania 7001, Australia
| | - Abigail Elizur
- *Faculty of Science, Health, Education and Engineering, GeneCology Research Centre, University of the Sunshine Coast (USC), 4 Locked Bag, Maroochydore, Queensland 4558, Australia
| | - Tomer Ventura
- *Faculty of Science, Health, Education and Engineering, GeneCology Research Centre, University of the Sunshine Coast (USC), 4 Locked Bag, Maroochydore, Queensland 4558, Australia
| |
Collapse
|
42
|
Veenstra JA. Similarities between decapod and insect neuropeptidomes. PeerJ 2016; 4:e2043. [PMID: 27257538 PMCID: PMC4888303 DOI: 10.7717/peerj.2043] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives, and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases, the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified: elongated PDH (pigment dispersing hormone), a variation on PDH that has a two-amino-acid insertion in its core sequence. Hyrg is another peptide that is ubiquitously present in decapods and is likely a novel neuropeptide precursor. Discussion. Many insect species have lost one or more neuropeptide genes, but apart from elongated PDH and hyrg all other decapod neuropeptides are present in at least some insect species, and allatotropin is the only insect neuropeptide missing from decapods. This strong similarity between insect and decapod neuropeptidomes makes it possible to predict the receptors for decapod neuropeptides that have been deorphanized in insects. This includes the androgenic insulin-like peptide that seems to be homologous to drosophila insulin-like peptide 8.
Collapse
Affiliation(s)
- Jan A Veenstra
- Institut de Neurosciences Cognitives et Intégratives d'Aquitaine (CNRS UMR5287), University of Bordeaux , Pessac , France
| |
Collapse
|
43
|
Dou J, Li X, Fu Q, Jiao W, Li Y, Li T, Wang Y, Hu X, Wang S, Bao Z. Evaluation of the 2b-RAD method for genomic selection in scallop breeding. Sci Rep 2016; 6:19244. [PMID: 26754638 PMCID: PMC4709697 DOI: 10.1038/srep19244] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 12/10/2015] [Indexed: 01/05/2023] Open
Abstract
The recently developed 2b-restriction site-associated DNA (2b-RAD) sequencing method provides a cost-effective and flexible genotyping platform for aquaculture species lacking sufficient genomic resources. Here, we evaluated the performance of this method in the genomic selection (GS) of Yesso scallop (Patinopecten yessoensis) through simulation and real data analyses using six statistical models. Our simulation analysis revealed that the prediction accuracies obtained using the 2b-RAD markers were slightly lower than those obtained using all polymorphic loci in the genome. Furthermore, a small subset of markers obtained from a reduced tag representation (RTR) library presented comparable performance to that obtained using all markers, making RTR be an attractive approach for GS purpose. Six GS models exhibited variable performance in prediction accuracy depending on the scenarios (e.g., heritability, sample size, population structure), but Bayes-alphabet and BLUP-based models generally outperformed other models. Finally, we performed the evaluation using an empirical dataset composed of 349 Yesso scallops that were derived from five families. The prediction accuracy for this empirical dataset could reach 0.4 based on optimal GS models. In summary, the genotyping flexibility and cost-effectiveness make 2b-RAD be an ideal genotyping platform for genomic selection in aquaculture breeding programs.
Collapse
Affiliation(s)
- Jinzhuang Dou
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.,Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Xue Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China
| | - Qiang Fu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China
| | - Wenqian Jiao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China
| | - Yangping Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China
| | - Tianqi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China
| | - Yangfan Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China
| | - Xiaoli Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, China
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, China
| |
Collapse
|
44
|
Shan T, Pang S, Li J, Li X, Su L. Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Genomics 2015; 16:902. [PMID: 26541547 PMCID: PMC4635539 DOI: 10.1186/s12864-015-2184-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida. RESULTS A total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region. CONCLUSIONS A high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.
Collapse
Affiliation(s)
- Tifeng Shan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Shaojun Pang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Jing Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| | - Xia Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| | - Li Su
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| |
Collapse
|
45
|
Tian M, Li Y, Jing J, Mu C, Du H, Dou J, Mao J, Li X, Jiao W, Wang Y, Hu X, Wang S, Wang R, Bao Z. Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus. Sci Rep 2015; 5:14852. [PMID: 26439740 PMCID: PMC4594301 DOI: 10.1038/srep14852] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/28/2015] [Indexed: 11/09/2022] Open
Abstract
Genetic linkage maps are critical and indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density and high-resolution linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as echinoderms. In this study, high-density, high-resolution genetic map was constructed for a sea cucumber species, Apostichopus japonicus, utilizing the 2b-restriction site-associated DNA (2b-RAD) method. A total of 7839 markers were anchored to the linkage map with the map coverage of 99.57%, to our knowledge, this is the highest marker density among echinoderm species. QTL mapping and association analysis consistently captured one growth-related QTL located in a 5 cM region of linkage group (LG) 5. An annotated candidate gene, retinoblastoma-binding protein 5 (RbBP5), which has been reported to be an important regulator of cell proliferation, was recognized in the QTL region. This linkage map represents a powerful tool for research involving both fine-scale QTL mapping and marker assisted selection (MAS), and will facilitate chromosome assignment and improve the whole-genome assembly of sea cucumber in the future.
Collapse
Affiliation(s)
- Meilin Tian
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yangping Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jing Jing
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Chuang Mu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Huixia Du
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jinzhuang Dou
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Junxia Mao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xue Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Wenqian Jiao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yangfan Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiaoli Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Ruijia Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| |
Collapse
|
46
|
Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis. Sci Rep 2015; 5:14015. [PMID: 26369734 PMCID: PMC4570184 DOI: 10.1038/srep14015] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 08/13/2015] [Indexed: 12/19/2022] Open
Abstract
Molting is a critical developmental process for crustaceans, yet the underlying molecular mechanism is unknown. In this study, we used RNA-Seq to investigate transcriptomic profiles of the hepatopancreas and identified differentially expressed genes at four molting stages of Chinese mitten crab (Eriocheir sinensis). A total of 97,398 transcripts were assembled, with 31,900 transcripts annotated. Transcriptomic comparison revealed 1,189 genes differentially expressed amongst different molting stages. We observed a pattern associated with energy metabolism and physiological responses during a molting cycle. In specific, differentially expressed genes enriched in postmolt were linked to energy consumption whereas genes enriched in intermolt were related to carbohydrates, lipids metabolic and biosynthetic processes. In premolt, a preparation stage for upcoming molting and energy consumption, highly expressed genes were enriched in response to steroid hormone stimulus and immune system development. The expression profiles of twelve functional genes detected via RNA-Seq were corroborated through real-time RT-PCR assay. Together, our results, including assembled transcriptomes, annotated functional elements and enriched differentially expressed genes amongst different molting stages, provide novel insights into the functions of the hepatopancreas in energy metabolism and biological processes pertaining to molting in crustaceans.
Collapse
|
47
|
Liu Y, Hui M, Cui Z, Luo D, Song C, Li Y, Liu L. Comparative Transcriptome Analysis Reveals Sex-Biased Gene Expression in Juvenile Chinese Mitten Crab Eriocheir sinensis. PLoS One 2015; 10:e0133068. [PMID: 26193085 PMCID: PMC4507985 DOI: 10.1371/journal.pone.0133068] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 06/23/2015] [Indexed: 11/23/2022] Open
Abstract
Sex-biased genes are considered to account for most of phenotypic differences between males and females. In order to explore the sex-biased gene expression in crab, we performed the whole-body transcriptome analysis in male and female juveniles of the Chinese mitten crab Eriocheir sinensis using next-generation sequencing technology. Of the 23,349 annotated unigenes, 148 were identified as sex-related genes. A total of 29 candidate genes involved in primary sex determination pathways were detected, indicating the sex determination cascade of the mitten crab might be more complex than previously supposed. Differential expression analysis showed 448 differentially expressed genes (DEGs) between the two transcriptomes. Most of DEGs were involved in processes such as metabolism and immunity, and not associated with obvious sexual function. The pathway predominantly enriched for DEGs were related to lysosome, which might reflect the differences in metabolism between males and females. Of the immune DGEs, 18 up-regulated genes in females were humoral immune factors, and eight up-regulated genes in males were pattern recognition receptors, suggesting sex differences of immune defense might exist in the mitten crab. In addition, two reproduction-related genes, vitellogenin and insulin-like androgenic gland factor, were identified to express in both sexes but with significantly higher level in males. Our research provides the first whole-body RNA sequencing of sex-specific transcriptomes for juvenile E. sinensis and will facilitate further studies on molecular mechanisms of crab sexual dimorphism.
Collapse
Affiliation(s)
- Yuan Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Min Hui
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhaoxia Cui
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China
- * E-mail:
| | - Danli Luo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengwen Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingdong Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lei Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|
48
|
Molecular characterization and expression profile of three Fem-1 genes in Eriocheir sinensis provide a new insight into crab sex-determining mechanism. Comp Biochem Physiol B Biochem Mol Biol 2015; 189:6-14. [PMID: 26188322 DOI: 10.1016/j.cbpb.2015.07.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 06/25/2015] [Accepted: 07/07/2015] [Indexed: 02/02/2023]
Abstract
The FEM-1 protein of Caenorhabditis elegans plays a crucial role in the nematode sex-determination pathway. Here, we reported the characterization of three members of Fem-1 gene family in Eriocheir sinensis (designated EsFem-1a, EsFem-1b, and EsFem-1c), which were homologs of the nematode FEM-1 protein. The amino acid sequences of EsFem-1a, EsFem-1b, and EsFem-1c contained eight, nine, and eight ankyrin repeats, respectively. None of the ankyrin repeats had its own specific signature, and the evolution of ankyrin repeat was not completely independent. The predicted three-dimensional structure of EsFem-1 proteins exhibited highly similar superhelical conformation, especially the N-terminal six contiguous ankyrin repeats, which provided a binding surface for the protein-protein interaction. Phylogenetic tree based on the amino acid sequences revealed that EsFem-1a, EsFem-1b, and EsFem-1c were divided into three obvious separated clades. EsFem-1 genes were highly expressed in fertilized egg, 2-4 cell and blastula stage comparing with larval stage (P<0.01), which suggested they might be maternal genes. They also showed a certain degree of sexually dimorphic expression in some tissues. Notably, the highest expression of EsFem-1a was in the hepatopancreas, with EsFem-1b in testes and EsFem-1c in muscle (P<0.05), which indicated their potential role in a broad array of tissues. In addition, the genes initially involved in sex differentiation were not limited to those specifically expressed in the developing gonad. Taken together, these results suggested that EsFem-1 might function in crab early sex determination and late gonad development. The identification of Fem-1 gene family in E. sinensis provides a new insight into crab sex-determination mechanism.
Collapse
|