1
|
Breeding Asian seabass to increase survival against big belly disease and growth. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
2
|
Domingos JA, Shen X, Terence C, Senapin S, Dong HT, Tan MR, Gibson-Kueh S, Jerry DR. Scale Drop Disease Virus (SDDV) and Lates calcarifer Herpes Virus (LCHV) Coinfection Downregulate Immune-Relevant Pathways and Cause Splenic and Kidney Necrosis in Barramundi Under Commercial Farming Conditions. Front Genet 2021; 12:666897. [PMID: 34220943 PMCID: PMC8249934 DOI: 10.3389/fgene.2021.666897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/19/2021] [Indexed: 01/31/2023] Open
Abstract
Marine farming of barramundi (Lates calcarifer) in Southeast Asia is currently severely affected by viral diseases. To better understand the biological implications and gene expression response of barramundi in commercial farming conditions during a disease outbreak, the presence of pathogens, comparative RNAseq, and histopathology targeting multiple organs of clinically “sick” and “healthy” juveniles were investigated. Coinfection of scale drop disease virus (SDDV) and L. calcarifer herpes virus (LCHV) were detected in all sampled fish, with higher SDDV viral loads in sick than in healthy fish. Histopathology showed that livers in sick fish often had moderate to severe abnormal fat accumulation (hepatic lipidosis), whereas the predominant pathology in the kidneys shows moderate to severe inflammation and glomerular necrosis. The spleen was the most severely affected organ, with sick fish presenting severe multifocal and coalescing necrosis. Principal component analysis (PC1 and PC2) explained 70.3% of the observed variance and strongly associated the above histopathological findings with SDDV loads and with the sick phenotypes, supporting a primary diagnosis of the fish being impacted by scale drop disease (SDD). Extracted RNA from kidney and spleen of the sick fish were also severely degraded likely due to severe inflammation and tissue necrosis, indicating failure of these organs in advanced stages of SDD. RNAseq of sick vs. healthy barramundi identified 2,810 and 556 differentially expressed genes (DEGs) in the liver and muscle, respectively. Eleven significantly enriched pathways (e.g., phagosome, cytokine-cytokine-receptor interaction, ECM-receptor interaction, neuroactive ligand-receptor interaction, calcium signaling, MAPK, CAMs, etc.) and gene families (e.g., tool-like receptor, TNF, lectin, complement, interleukin, chemokine, MHC, B and T cells, CD molecules, etc.) relevant to homeostasis and innate and adaptive immunity were mostly downregulated in sick fish. These DEGs and pathways, also previously identified in L. calcarifer as general immune responses to other pathogens and environmental stressors, suggest a failure of the clinically sick fish to cope and overcome the systemic inflammatory responses and tissue degeneration caused by SDD.
Collapse
Affiliation(s)
- Jose A Domingos
- Tropical Futures Institute, James Cook University, Singapore, Singapore.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Xueyan Shen
- Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Celestine Terence
- Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Saengchan Senapin
- Faculty of Science, Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Bangkok, Thailand.,National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Ha Thanh Dong
- Faculty of Science, Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Bangkok, Thailand.,Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, Thailand
| | - Marie R Tan
- School of Applied Science (SAS), Republic Polytechnic, Singapore, Singapore
| | - Susan Gibson-Kueh
- Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Dean R Jerry
- Tropical Futures Institute, James Cook University, Singapore, Singapore.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| |
Collapse
|
3
|
Orbán L, Shen X, Phua N, Varga L. Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals? Front Genet 2021; 12:506754. [PMID: 33968125 PMCID: PMC8097054 DOI: 10.3389/fgene.2021.506754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer, Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls.
Collapse
Affiliation(s)
- László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary
| | - Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Norman Phua
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - László Varga
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllõ, Hungary.,Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllõ, Hungary
| |
Collapse
|
4
|
Lu X, Wen H, Li Q, Wang G, Li P, Chen J, Sun Y, Yang C, Wu F. Comparative analysis of growth performance and liver transcriptome response of juvenile Ancherythroculter nigrocauda fed diets with different protein levels. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100592. [PMID: 31200228 DOI: 10.1016/j.cbd.2019.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/27/2019] [Accepted: 05/01/2019] [Indexed: 01/16/2023]
Abstract
This study aimed at investigating the effects of dietary protein levels on the growth and liver transcriptome in juvenile Ancherythroculter nigrocauda. Six semi-purified diets were formulated containing 25 (control), 30, 35, 40, 45, and 50% protein. Each diet was fed to three groups of 35 fish (mean initial weight: 5.86 ± 0.10 g) for 56 days. The rate of weight gain and specific growth rate increased with dietary protein levels from 25% to 40%, but remained unchanged when fed with 45 or 50% dietary protein. The feed conversion ratio was significantly influenced by the dietary protein levels, being the lowest in fish fed 40% protein. Illumina RNA-seq analysis was performed to investigate liver gene expression changes under different dietary protein treatments. A total of 367.78 million clean reads were obtained from the six libraries. Compared with 25% protein treatment library, there were 734, 1946, 1755, 2726, and 1523 upregulated genes, and 407, 1882, 1865, 2216 and 1624 downregulated genes in the 30, 35, 40, 45, and 50% protein treatment libraries, respectively. Trend analysis of these differentially expressed genes (DEGs) identified six statistically significant trends. A series of DEGs that related to protein metabolism, growth and development, lipid metabolism and immune and stress response were identified. Moreover, gene ontology enrichment analysis of the DEGs demonstrated that cellular process, single-organism process, metabolic process and biological regulation were the most highly overrepresented biological processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that protein processing in endoplasmic reticulum, PPAR signaling pathway, complement and coagulation cascades, and cytochrome P450 (CYP450s) were significantly enriched in the dietary protein treatment groups. Furthermore, qPCR results showed excellent agreement on those of RNA-seq for both up- and down-regulated genes (including fasn, accα, SCD, CPT-I, igf1, ST, AST, trdmt1, hsp70, cyp450, MHC-II, C4, tgfβ, ube4b, apoE and abcb7). Thus, our results provide the baseline information for the feed formulation and nutritional research for A. nigrocauda.
Collapse
Affiliation(s)
- Xing Lu
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China
| | - Hua Wen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China
| | - Qing Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China.
| | - Guiying Wang
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China
| | - Pei Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China
| | - Jian Chen
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China
| | - Yanhong Sun
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China
| | - Changgeng Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China
| | - Fan Wu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China
| |
Collapse
|
5
|
Liu X, Xia J, Pang H, Yue G. Who eats whom, when and why? Juvenile cannibalism in fish Asian seabass. AQUACULTURE AND FISHERIES 2017. [DOI: 10.1016/j.aaf.2016.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
6
|
Wang L, Wan ZY, Bai B, Huang SQ, Chua E, Lee M, Pang HY, Wen YF, Liu P, Liu F, Sun F, Lin G, Ye BQ, Yue GH. Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass. Sci Rep 2015; 5:16358. [PMID: 26553309 PMCID: PMC4639833 DOI: 10.1038/srep16358] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/01/2015] [Indexed: 01/06/2023] Open
Abstract
A high-density genetic map is essential for comparative genomic studies and fine mapping of QTL, and can also facilitate genome sequence assembly. Here, a high density genetic map of Asian seabass was constructed with 3321 SNPs generated by sequencing 144 individuals in a F2 family. The length of the map was 1577.67 cM with an average marker interval of 0.52 cM. A high level of genomic synteny among Asian seabass, European seabass, Nile tilapia and stickleback was detected. Using this map, one genome-wide significant and five suggestive QTL for growth traits were detected in six linkage groups (i.e. LG4, LG5, LG11, LG13, LG14 and LG15). These QTL explained 10.5–16.0% of phenotypic variance. A candidate gene, ACOX1 within the significant QTL on LG5 was identified. The gene was differentially expressed between fast- and slow-growing Asian seabass. The high-density SNP-based map provides an important tool for fine mapping QTL in molecular breeding and comparative genome analysis.
Collapse
Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Zi Yi Wan
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Bin Bai
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Shu Qing Huang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Elaine Chua
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - May Lee
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Hong Yan Pang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Yan Fei Wen
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Peng Liu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Feng Liu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Fei Sun
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Grace Lin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Bao Qing Ye
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore 117543.,School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore 637551
| |
Collapse
|
7
|
Hu YC, Kang CK, Tang CH, Lee TH. Transcriptomic Analysis of Metabolic Pathways in Milkfish That Respond to Salinity and Temperature Changes. PLoS One 2015; 10:e0134959. [PMID: 26263550 PMCID: PMC4532362 DOI: 10.1371/journal.pone.0134959] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/16/2015] [Indexed: 12/20/2022] Open
Abstract
Milkfish (Chanos chanos), an important marine aquaculture species in southern Taiwan, show considerable euryhalinity but have low tolerance to sudden drops in water temperatures in winter. Here, we used high throughput next-generation sequencing (NGS) to identify molecular and biological processes involved in the responses to environmental changes. Preliminary tests revealed that seawater (SW)-acclimated milkfish tolerated lower temperatures than the fresh water (FW)-acclimated group. Although FW- and SW-acclimated milkfish have different levels of tolerance for hypothermal stress, to date, the molecular physiological basis of this difference has not been elucidated. Here, we performed a next-generation sequence analysis of mRNAs from four groups of milkfish. We obtained 29669 unigenes with an average length of approximately 1936 base pairs. Gene ontology (GO) analysis was performed after gene annotation. A large number of genes for molecular regulation were identified through a transcriptomic comparison in a KEGG analysis. Basal metabolic pathways involved in hypothermal tolerance, such as glycolysis, fatty acid metabolism, amino acid catabolism and oxidative phosphorylation, were analyzed using PathVisio and Cytoscape software. Our results indicate that in response to hypothermal stress, genes for oxidative phosphorylation, e.g., succinate dehydrogenase, were more highly up-regulated in SW than FW fish. Moreover, SW and FW milkfish used different strategies when exposed to hypothermal stress: SW milkfish up-regulated oxidative phosphorylation and catabolism genes to produce more energy budget, whereas FW milkfish down-regulated genes related to basal metabolism to reduce energy loss.
Collapse
Affiliation(s)
- Yau-Chung Hu
- Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung, and Academia Sinica, Taipei, Taiwan
| | - Chao-Kai Kang
- Tainan Hydraulics Laboratory, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Hao Tang
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- * E-mail: (C-HT); (T-HL)
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
- * E-mail: (C-HT); (T-HL)
| |
Collapse
|
8
|
|
9
|
Fu GH, Wan ZY, Xia JH, Liu F, Liu XJ, Yue GH. The MCP-8 gene and its possible association with resistance to Streptococcus agalactiae in tilapia. FISH & SHELLFISH IMMUNOLOGY 2014; 40:331-336. [PMID: 25042289 DOI: 10.1016/j.fsi.2014.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 06/03/2023]
Abstract
Mast cell proteases play an important role in the regulation of the immune response. We identified the cDNA of the mast cell protease 8 (MCP-8) gene and analyzed its genomic structure in tilapia. The ORF of the MCP-8 was 768 bp, encoding 255 amino acids. Quantitative real-time PCR revealed that the MCP-8 gene was expressed predominantly in spleen, moderately in liver, blood, brain, gill, intestine, skin, and weakly expressed in kidney, muscle and eye. After a challenge with Streptococcus agalactiae, the gene was induced significantly (p < 0.05) in intestine, kidney, spleen and liver. Furthermore, we identified five single nucleotide polymorphisms (SNPs) in the MCP-8 gene and found that three SNPs were significantly associated (p < 0.05) with resistance against S. agalactiae. However, we found no association between four SNPs and growth traits (p > 0.05). These results suggest that the MCP-8 gene play an important role in the resistance to S. agalactiae in tilapia. The SNP markers in the MCP-8 gene associated with the resistance to the bacterial pathogen may facilitate selection of tilapia resistant to the bacterial disease.
Collapse
Affiliation(s)
- Gui Hong Fu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Xiao Jun Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
| |
Collapse
|
10
|
Das S, Chhottaray C, Das Mahapatra K, Saha JN, Baranski M, Robinson N, Sahoo PK. Analysis of immune-related ESTs and differential expression analysis of few important genes in lines of rohu (Labeo rohita) selected for resistance and susceptibility to Aeromonas hydrophila infection. Mol Biol Rep 2014; 41:7361-71. [PMID: 25081649 DOI: 10.1007/s11033-014-3625-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 07/19/2014] [Indexed: 10/25/2022]
Abstract
A total of 137,629 contigs generated via de novo transcriptome assembly from resistant and susceptible lines of rohu (first generation) raised against aeromoniasis were further analyzed in terms of defence-related genes. Out of 1,939 contigs showing homology to genes involved in immune processes, 1,866 were further categorised into different functional subgroups. Comparative analysis revealed five genes for the first time in any carp species out of which apolipoprotein h, septin 4 isoform 3 and septin isoform cra_c were identified for the first time in fish. Differential expression analysis of ten genes viz., heat shock proteins (Hsps) (Hsp30, Hsp70 and Hsp90), serum lectin isoform 1 (SLI1), linker histone H1M (LHH1M), NAD(P)H quinone 1 (NQO1), zona pellucida 2 (ZP2) and three unknown genes that were highly up-expressed in first generation resistant line fish from mRNA-seq coverage data, was carried out using susceptible and resistant individuals of the second generation selected populations in eight different tissues viz. liver, kidney, intestine, gill, brain, spleen, skin and muscle using qPCR. Significant up-regulation in Hsp90, NQO1, C_116914 and C_22454 in specific tissues of resistant line and variable expression in Hsp30 and LHH1M genes in different tissues of both lines were noticed. The expression of Hsp70 was lower in many tissues of the resistant line than in susceptible line rohu. The expression of ZP2, SLI1 and C_94589 genes was not significantly different in terms of fold difference between the two lines. Differentially expressed genes need further characterisation to explore their role in resistance to Aeromonas hydrophila infection in rohu.
Collapse
Affiliation(s)
- Sweta Das
- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India
| | | | | | | | | | | | | |
Collapse
|
11
|
Gene discovery through transcriptome sequencing for the invasive mussel Limnoperna fortunei. PLoS One 2014; 9:e102973. [PMID: 25047650 PMCID: PMC4105566 DOI: 10.1371/journal.pone.0102973] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/24/2014] [Indexed: 11/22/2022] Open
Abstract
The success of the Asian bivalve Limnoperna fortunei as an invader in South America is related to its high acclimation capability. It can inhabit waters with a wide range of temperatures and salinity and handle long-term periods of air exposure. We describe the transcriptome of L. fortunei aiming to give a first insight into the phenotypic plasticity that allows non-native taxa to become established and widespread. We sequenced 95,219 reads from five main tissues of the mussel L. fortunei using Roche’s 454 and assembled them to form a set of 84,063 unigenes (contigs and singletons) representing partial or complete gene sequences. We annotated 24,816 unigenes using a BLAST sequence similarity search against a NCBI nr database. Unigenes were divided into 20 eggNOG functional categories and 292 KEGG metabolic pathways. From the total unigenes, 1,351 represented putative full-length genes of which 73.2% were functionally annotated. We described the first partial and complete gene sequences in order to start understanding bivalve invasiveness. An expansion of the hsp70 gene family, seen also in other bivalves, is present in L. fortunei and could be involved in its adaptation to extreme environments, e.g. during intertidal periods. The presence of toll-like receptors gives a first insight into an immune system that could be more complex than previously assumed and may be involved in the prevention of disease and extinction when population densities are high. Finally, the apparent lack of special adaptations to extremely low O2 levels is a target worth pursuing for the development of a molecular control approach.
Collapse
|
12
|
Generation and characterization of the sea bass Dicentrarchus labrax brain and liver transcriptomes. Gene 2014; 544:56-66. [PMID: 24768179 DOI: 10.1016/j.gene.2014.04.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/02/2014] [Accepted: 04/17/2014] [Indexed: 12/14/2022]
Abstract
The sea bass Dicentrarchus labrax is the center of interest of an increasing number of basic or applied research investigations, even though few genomic or transcriptomic data is available. Current public data only represent a very partial view of its transcriptome. To fill this need, we characterized brain and liver transcriptomes in a generalist manner that would benefit the entire scientific community. We also tackled some bioinformatics questions, related to the effect of RNA fragment size on the assembly quality. Using Illumina RNA-seq, we sequenced organ pools from both wild and farmed Atlantic and Mediterranean fishes. We built two distinct cDNA libraries per organ that only differed by the length of the selected mRNA fragments. Efficiency of assemblies performed on either or both fragments size differed depending on the organ, but remained very close reflecting the quality of the technical replication. We generated more than 19,538Mbp of data. Over 193million reads were assembled into 35,073 contigs (average length=2374bp; N50=3257). 59% contigs were annotated with SwissProt, which corresponded to 12,517 unique genes. We compared the Gene Ontology (GO) contig distribution between the sea bass and the tilapia. We also looked for brain and liver GO specific signatures as well as KEGG pathway coverage. 23,050 putative micro-satellites and 134,890 putative SNPs were identified. Our sampling strategy and assembly pipeline provided a reliable and broad reference transcriptome for the sea bass. It constitutes an indisputable quantitative and qualitative improvement of the public data, as it provides 5 times more base pairs with fewer and longer contigs. Both organs present unique signatures consistent with their specific physiological functions. The discrepancy in fragment size effect on assembly quality between organs lies in their difference in complexity and thus does not allow prescribing any general strategy. This information on two key organs will facilitate further functional approaches.
Collapse
|
13
|
Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L, Liu XJ, Yue GH. The intestinal microbiome of fish under starvation. BMC Genomics 2014; 15:266. [PMID: 24708260 PMCID: PMC4234480 DOI: 10.1186/1471-2164-15-266] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 03/31/2014] [Indexed: 02/08/2023] Open
Abstract
Background Starvation not only affects the nutritional and health status of the animals, but also the microbial composition in the host’s intestine. Next-generation sequencing provides a unique opportunity to explore gut microbial communities and their interactions with hosts. However, studies on gut microbiomes have been conducted predominantly in humans and land animals. Not much is known on gut microbiomes of aquatic animals and their changes under changing environmental conditions. To address this shortcoming, we determined the microbial gene catalogue, and investigated changes in the microbial composition and host-microbe interactions in the intestine of Asian seabass in response to starvation. Results We found 33 phyla, 66 classes, 130 orders and 278 families in the intestinal microbiome. Proteobacteria (48.8%), Firmicutes (15.3%) and Bacteroidetes (8.2%) were the three most abundant bacteria taxa. Comparative analyses of the microbiome revealed shifts in bacteria communities, with dramatic enrichment of Bacteroidetes, but significant depletion of Betaproteobacteria in starved intestines. In addition, significant differences in clusters of orthologous groups (COG) functional categories and orthologous groups were observed. Genes related to antibiotic activity in the microbiome were significantly enriched in response to starvation, and host genes related to the immune response were generally up-regulated. Conclusions This study provides the first insights into the fish intestinal microbiome and its changes under starvation. Further detailed study on interactions between intestinal microbiomes and hosts under dynamic conditions will shed new light on how the hosts and microbes respond to the changing environment.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore.
| |
Collapse
|
14
|
Fu GH, Bai ZY, Xia JH, Liu XJ, Liu F, Wan ZY, Yue GH. Characterization of the LECT2 gene and its associations with resistance to the big belly disease in Asian seabass. FISH & SHELLFISH IMMUNOLOGY 2014; 37:131-138. [PMID: 24486631 DOI: 10.1016/j.fsi.2014.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/15/2014] [Accepted: 01/21/2014] [Indexed: 06/03/2023]
Abstract
Leukocyte cell-derived chemotaxin-2 (LECT2) is an important protein of the innate immune system for the defense against bacterial infection. We cloned and characterized the LECT2 gene from Asian seabass (Lates calcarifer). Its complete cDNA consisted of an open reading frame of 459 bp encoding a protein of 152 amino acids. The genomic DNA sequence of this gene consists of four exons and three introns. Quantitative real-time PCR revealed that the LECT2 gene was expressed predominantly in liver while its expression was moderate in spleen and heart, and weak in other tissues. The LECT2 transcript was up-regulated in the kidney, spleen and liver in response to a challenge with a pathogenic bacterium Vibrio harveyi. In addition, we identified three single nucleotide polymorphisms (SNPs) in the LECT2 gene, and found significant associations between these polymorphisms and resistance to the big belly disease. These results suggest that the LECT2 gene play an important role in resistance to bacterial pathogens in fish. The SNP markers in the gene associated with the resistance to bacterial pathogens may facilitate selecting Asian seabass resistant to bacterial diseases.
Collapse
Affiliation(s)
- Gui Hong Fu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Zhi Yi Bai
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore; Key laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai, China
| | - Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Xiao Jun Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
| |
Collapse
|
15
|
Xia JH, Lin G, He X, Yunping B, Liu P, Liu F, Sun F, Tu R, Yue GH. Mapping quantitative trait loci for omega-3 fatty acids in Asian seabass. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:1-9. [PMID: 23887675 DOI: 10.1007/s10126-013-9524-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 06/04/2013] [Indexed: 06/02/2023]
Abstract
Omega-3 fatty acids are essential fatty acids for human health. Therefore, increasing both percentage of omega-3 and a better fatty acid profile in fish fillets is one of the breeding goals in aquaculture. However, it is difficult to increase the omega-3 content in fish fillets, as the phenotypic selection of these traits is not easily feasible. To facilitate the genetic improvement of the Asian seabass for optimal fatty acid profiles, a genome-wide scan for quantitative trait loci (QTL) affecting fatty acid level in the flesh of the Asian seabass was performed on an F2 family containing 314 offspring. All family members were genotyped using 123 informative microsatellites and 22 SNPs. High percentages of n-3 polyunsaturated fatty acids (PUFA), especially C22:6 (DHA 16.48 ± 3.09 %) and C20:5 (EPA 7.19 ± 0.86 %) were detected in the flesh. One significant and 54 suggestive QTL for different fatty acids and a water content trait were detected on the whole genome. QTL for C18:0b was located on linkage groups (LG) 5. QTL for total n-3 PUFA content in flesh were mapped onto LG6 and LG23 with the phenotypic variance explained ranging from 3.8 to 6.3 %. Four QTL for C22:6 were detected on LG6, LG23, and LG24, explaining 3.9 to 4.9 % of the phenotypic variance, respectively. Mapping of QTL for contents of different fatty acids is the first step towards improving the omega-3 content in the fillets of fish by using marker-assisted selection and is important for understanding the biology of fatty acid deposition.
Collapse
Affiliation(s)
- Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Fu GH, Bai ZY, Xia JH, Liu F, Liu P, Yue GH. Analysis of two lysozyme genes and antimicrobial functions of their recombinant proteins in Asian seabass. PLoS One 2013; 8:e79743. [PMID: 24244553 PMCID: PMC3820614 DOI: 10.1371/journal.pone.0079743] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/25/2013] [Indexed: 12/03/2022] Open
Abstract
Lysozymes are important proteins of the innate immune system for the defense against bacterial infection. We cloned and analyzed chicken-type (c-type) and goose-type (g-type) lysozymes from Asian seabass (Lates calcarifer). The deduced amino acid sequence of the c-type lysozyme contained 144 residues and possessed typical structure residues, conserved catalytic residues (Glu50 and Asp67) and a “GSTDYGIFQINS” motif. The deduced g-type lysozyme contained 187 residues and possessed a goose egg white lysozyme (GEWL) domain containing three conserved catalytic residues (Glu71, Asp84, Asp95) essential for catalytic activity. Real time quantitative PCR (qRT-PCR) revealed that the two lysozyme genes were constitutively expressed in all the examined tissues. The c-type lysozyme was most abundant in liver, while the g-type lysozyme was predominantly expressed in intestine and weakly expressed in muscle. The c-type and g-type transcripts were up-regulated in the kidney, spleen and liver in response to a challenge with Vibrio harveyi. The up-regulation of the c-type lysozyme was much stronger than that of the g-type lysozyme in kidney and spleen. The recombinant proteins of the c-type and g-type lysozymes showed lytic activities against the bacterial pathogens Vibrio harveyi and Photobacterium damselae in a dosage-dependent manner. We identified single nucleotide polymorphisms (SNPs) in the two lysozyme genes. There were significant associations of these polymorphisms with resistance to the big belly disease. These results suggest that the c- and g-type genes play an important role in resistance to bacterial pathogens in fish. The SNP markers in the two genes associated with the resistance to bacterial pathogens may facilitate the selection of Asian seabass resistant to bacterial diseases.
Collapse
Affiliation(s)
- Gui Hong Fu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Zhi Yi Bai
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai, China
| | - Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Peng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
| |
Collapse
|
17
|
Liu H, Wang T, Wang J, Quan F, Zhang Y. Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis. PLoS One 2013; 8:e77062. [PMID: 24130835 PMCID: PMC3793953 DOI: 10.1371/journal.pone.0077062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 08/30/2013] [Indexed: 12/03/2022] Open
Abstract
Background Liaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed denovo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology. Results Transcriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51%) unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17%) unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes. Conclusion The transcriptome of Liaoning cashmere goat was deep sequenced, denovo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.
Collapse
Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi, China
| | - Tingting Wang
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Jinke Wang
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Fusheng Quan
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi, China
- * E-mail: (FQ); (YZ)
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi, China
- * E-mail: (FQ); (YZ)
| |
Collapse
|
18
|
Xia JH, Liu P, Liu F, Lin G, Sun F, Tu R, Yue GH. Analysis of stress-responsive transcriptome in the intestine of Asian seabass (Lates calcarifer) using RNA-seq. DNA Res 2013; 20:449-60. [PMID: 23761194 PMCID: PMC3789556 DOI: 10.1093/dnares/dst022] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 05/08/2013] [Indexed: 12/20/2022] Open
Abstract
Identification of differentially expressed genes (DEGs) and regulated pathways in response to stressors using a whole-genome approach is critical to understanding the mechanisms underlying stress responses. We challenged Asian seabass with lipopolysaccharide (LPS), Vibrio harveyi, high salinity and fasting, and sequenced six cDNA libraries of intestine samples using Roche 454 RNA-seq. Over 1 million reads (average size: 516 bp) were obtained. The de novo assembly obtained 83 911 unisequences with an average length of 747 bp. In total, 62.3% of the unisequences were annotated. We observed overall similar expression profiles among different challenges, while a number of DEGs and regulated pathways were identified under specific challenges. More than 1000 DEGs and over 200 regulated pathways for each stressor were identified. Thirty-seven genes were differentially expressed in response to all challenges. Our data suggest that there is a global coordination and fine-tuning of gene regulation during different challenges. In addition, we detected dramatic immune responses in intestines under different stressors. This study is the first step towards the comprehensive understanding of the mechanisms underlying stress responses and supplies significant transcriptome resources for studying biological questions in non-model fish species.
Collapse
Affiliation(s)
- Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore117604, Singapore
| | - Peng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore117604, Singapore
| | - Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore117604, Singapore
| | - Grace Lin
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore117604, Singapore
| | - Fei Sun
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore117604, Singapore
| | - Rongjian Tu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore117604, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| |
Collapse
|
19
|
Xia JH, Lin G, He X, Liu P, Liu F, Sun F, Tu R, Yue GH. Whole genome scanning and association mapping identified a significant association between growth and a SNP in the IFABP-a gene of the Asian seabass. BMC Genomics 2013; 14:295. [PMID: 23634810 PMCID: PMC3653795 DOI: 10.1186/1471-2164-14-295] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 04/25/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Aquaculture is the quickest growing sector in agriculture. However, QTL for important traits have been only identified in a few aquaculture species. We conducted QTL mapping for growth traits in an Asian seabass F(2) family with 359 individuals using 123 microsatellites and 22 SNPs, and performed association mapping in four populations with 881 individuals. RESULTS Twelve and nine significant QTL, as well as 14 and 10 suggestive QTL were detected for growth traits at six and nine months post hatch, respectively. These QTL explained 0.9-12.0% of the phenotypic variance. For body weight, two QTL intervals at two stages were overlapped while the others were mapped onto different positions. The IFABP-a gene located in a significant QTL interval for growth on LG5 was cloned and characterized. A SNP in exon 3 of the gene was significantly associated with growth traits in different populations. CONCLUSIONS The results of QTL mapping for growth traits suggest that growth at different stages was controlled by some common QTL and some different QTL. Positional candidate genes and association mapping suggest that the IFABP-a is a strong candidate gene for growth. Our data supply a basis for fine mapping QTL, marker-assisted selection and further detailed analysis of the functions of the IFABP-a gene in fish growth.
Collapse
Affiliation(s)
- Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Grace Lin
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Xiaoping He
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Peng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Fei Sun
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Rongjian Tu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| |
Collapse
|
20
|
Long Y, Li Q, Zhou B, Song G, Li T, Cui Z. De novo assembly of mud loach (Misgurnus anguillicaudatus) skin transcriptome to identify putative genes involved in immunity and epidermal mucus secretion. PLoS One 2013; 8:e56998. [PMID: 23437293 PMCID: PMC3577766 DOI: 10.1371/journal.pone.0056998] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/16/2013] [Indexed: 12/17/2022] Open
Abstract
Fish skin serves as the first line of defense against a wide variety of chemical, physical and biological stressors. Secretion of mucus is among the most prominent characteristics of fish skin and numerous innate immune factors have been identified in the epidermal mucus. However, molecular mechanisms underlying the mucus secretion and immune activities of fish skin remain largely unclear due to the lack of genomic and transcriptomic data for most economically important fish species. In this study, we characterized the skin transcriptome of mud loach using Illumia paired-end sequencing. A total of 40364 unigenes were assembled from 86.6 million (3.07 gigabases) filtered reads. The mean length, N50 size and maximum length of assembled transcripts were 387, 611 and 8670 bp, respectively. A total of 17336 (43.76%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. Gene ontology mapping assigned a total of 108513 GO terms to 15369 (38.08%) unigenes. KEGG orthology mapping annotated 9337 (23.23%) unigenes. Among the identified KO categories, immune system is the largest category that contains various components of multiple immune pathways such as chemokine signaling, leukocyte transendothelial migration and T cell receptor signaling, suggesting the complexity of immune mechanisms in fish skin. As for mucin biosynthesis, 37 unigenes were mapped to 7 enzymes of the mucin type O-glycan biosynthesis pathway and 8 members of the polypeptide N-acetylgalactosaminyltransferase family were identified. Additionally, 38 unigenes were mapped to 23 factors of the SNARE interactions in vesicular transport pathway, indicating that the activity of this pathway is required for the processes of epidermal mucus storage and release. Moreover, 1754 simple sequence repeats (SSRs) were detected in 1564 unigenes and dinucleotide repeats represented the most abundant type. These findings have laid the foundation for further understanding the secretary processes and immune functions of loach skin mucus.
Collapse
Affiliation(s)
- Yong Long
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P. R. China
| | - Qing Li
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P. R. China
| | - Bolan Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P. R. China
- University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Guili Song
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P. R. China
| | - Tao Li
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P. R. China
| | - Zongbin Cui
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P. R. China
- * E-mail:
| |
Collapse
|
21
|
Liu P, Xia JH, Lin G, Sun F, Liu F, Lim HS, Pang HY, Yue GH. Molecular parentage analysis is essential in breeding Asian seabass. PLoS One 2012; 7:e51142. [PMID: 23227245 PMCID: PMC3515488 DOI: 10.1371/journal.pone.0051142] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/29/2012] [Indexed: 11/18/2022] Open
Abstract
In aquaculture species, maintaining pedigree information and genetic variation in each generation is essential, but very difficult. In this study, we used nine microsatellites to genotype 2,520 offspring from four independent full-factorial crosses (10 males ×10 females) of Asian seabass to reconstruct pedigree and monitor the change of genetic variations. In all four crosses, over 96.8% of the offspring could be assigned to their parents, indicating the high power of the nine microsatellites for parentage assignment. This study revealed several interesting results: (1). In all four crosses, the contribution of parents to offspring was significantly uneven, and some dominant breeding fishes (i.e. brooders) were found; (2). In two mass crosses where the brooders were carefully checked for reproductive status, a majority (≥90%) of brooders contributed to offspring, whereas in another two crosses, where the brooders were randomly picked without checking reproductive status, only a few brooders (40.0–45.0%) produced offspring; (3). Females had more problems in successful spawning compared to males; and (4). In the two crosses where a few brooders produced offspring, there was a substantial loss in allelic (24.1–34.3%) and gene (20.5–25.7%) diversities in offspring, while in the other two crosses, the majority of allelic (96.8–97.0%) and gene diversities (94.8–97.1%) were maintained. These observations suggest that a routine molecular parentage analysis is required to maintain both allelic and gene diversity in breeding Asian seabass.
Collapse
Affiliation(s)
- Peng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Grace Lin
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Fei Sun
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Huan Sein Lim
- Marine Aquaculture Center, Agri-Food & Veterinary Authority of Singapore, Singapore
| | - Hong Yan Pang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
- * E-mail:
| |
Collapse
|
22
|
Nagpure NS, Rashid I, Pathak AK, Singh M, Singh SP, Sarkar UK. Computational analysis of transcriptome of Indian major carp, Labeo rohita (Hamilton-Buchanan, 1822) for functional annotation. Bioinformation 2012; 8:1005-11. [PMID: 23275698 PMCID: PMC3524890 DOI: 10.6026/97320630081005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 10/01/2012] [Indexed: 01/10/2023] Open
Abstract
A total of 1671 ESTs of Labeo rohita were retrieved from dbEST database and analysed for functional annotation using various computational approaches. The result indicated 1387 non-redundant (184 contigs and 1203 singletons) putative transcripts with an average length of 542 bp. These 1387 transcript sequences were matched with Refseq_RNA, UniGene and Swiss-Prot on high threshold cut-off for functional annotation along with help of gene ontology and SSRs markers. We developed extensive Perl programming based modules for processing all alignment files, comparing and extracting common hits from all files on a threshold, evaluating statistics for alignment results and assigning gene ontology terms. In this study, 92 putative transcripts predicted as orthologous genes and among those, 44 putative transcripts were annotated with gene ontology terms. The annotated orthologous gene of our result associated with some very important proteins of L. rohita involved in biotic and abiotic stresses and glucose metabolism of spermatogenic cells etc. The unidentified transcripts, if found important in expression profiling can be vital resource after re-sequencing. The predicted genes can further be used for enhancing productivity and controlling disease of L. rohita.
Collapse
Affiliation(s)
- Naresh Sahebrao Nagpure
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow-226002, India
| | - Iliyas Rashid
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow-226002, India
| | - Ajey Kumar Pathak
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow-226002, India
| | - Mahender Singh
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow-226002, India
| | - Shri Prakash Singh
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow-226002, India
| | - Uttam Kumar Sarkar
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow-226002, India
| |
Collapse
|
23
|
Khoo CK, Abdul-Murad AM, Kua BC, Mohd-Adnan A. Cryptocaryon irritans infection induces the acute phase response in Lates calcarifer: a transcriptomic perspective. FISH & SHELLFISH IMMUNOLOGY 2012; 33:788-794. [PMID: 22842150 DOI: 10.1016/j.fsi.2012.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 07/09/2012] [Accepted: 07/17/2012] [Indexed: 06/01/2023]
Abstract
Cryptocaryoniasis (also known as marine white spot disease) is mediated by Cryptocaryon irritans. This obligate ectoparasitic protozoan infects virtually all marine teleosts, which includes Lates calcarifer, a highly valuable aquaculture species. Little is known about L. calcarifer-C. irritans interactions. This study was undertaken to gain an informative snapshot of the L. calcarifer transcriptomic response over the course of C. irritans infection. An in-house fabricated cDNA microarray slides containing 3872 probes from L. calcarifer liver and spleen cDNA libraries were used as a tool to investigate the response of L. calcarifer to C. irritans infection. Juvenile fish were infected with parasites for four days, and total RNA was extracted from liver tissue, which was harvested daily. We compared the transcriptomes of C. irritans-infected liver to uninfected liver over an infection period of four days; the comparison was used to identify the genes with altered expression levels in response to C. irritans infection. The greatest number of infection-modulated genes was recorded at 2 and 3 days post-infection. These genes were mainly associated with the immune response and were associated in particular with the acute phase response. Acute phase proteins such as hepcidin, C-type lectin and serum amyloid A are among the highly modulated genes. Our results indicate that an induced acute phase response in L. calcarifer toward C. irritans infection is similar to the responses observed in bacterial infections of teleosts. This response demonstrates the importance of first line defenses in teleost innate immune responses against ectoparasite infection.
Collapse
Affiliation(s)
- Choon-Kiat Khoo
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
| | | | | | | |
Collapse
|
24
|
Ma K, Qiu G, Feng J, Li J. Transcriptome analysis of the oriental river prawn, Macrobrachium nipponense using 454 pyrosequencing for discovery of genes and markers. PLoS One 2012; 7:e39727. [PMID: 22745820 PMCID: PMC3380025 DOI: 10.1371/journal.pone.0039727] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/25/2012] [Indexed: 12/02/2022] Open
Abstract
Background The oriental river prawn, Macrobrachium nipponense, is an economically and nutritionally important species of the Palaemonidae family of decapod crustaceans. To date, the sequencing of its whole genome is unavailable as a non-model organism. Transcriptomic information is also scarce for this species. In this study, we performed de novo transcriptome sequencing to produce the first comprehensive expressed sequence tag (EST) dataset for M. nipponense using high-throughput sequencing technologies. Methodology and Principal Findings Total RNA was isolated from eyestalk, gill, heart, ovary, testis, hepatopancreas, muscle, and embryos at the cleavage, gastrula, nauplius and zoea stages. Equal quantities of RNA from each tissue and stage were pooled to construct a cDNA library. Using 454 pyrosequencing technology, we generated a total of 984,204 high quality reads (338.59Mb) with an average length of 344 bp. Clustering and assembly of these reads produced a non-redundant set of 81,411 unique sequences, comprising 42,551 contigs and 38,860 singletons. All of the unique sequences were involved in the molecular function (30,425), cellular component (44,112) and biological process (67,679) categories by GO analysis. Potential genes and their functions were predicted by KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes involved in sex determination, including DMRT1, FTZ-F1, FOXL2, FEM1 and other potentially important candidate genes, were identified for the first time in this prawn. Furthermore, 6,689 SSRs and 18,107 high-confidence SNPs were identified in this EST dataset. Conclusions The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in M. nipponense. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will be essential for accelerating aquaculture breeding programs with this species.
Collapse
Affiliation(s)
- Keyi Ma
- Key laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
| | - Gaofeng Qiu
- Key laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
- E-Institute of Shanghai Universities, Shanghai Ocean University, Shanghai, P. R. China
- * E-mail: (GQ); (JL)
| | - Jianbin Feng
- Key laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
| | - Jiale Li
- Key laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
- E-Institute of Shanghai Universities, Shanghai Ocean University, Shanghai, P. R. China
- * E-mail: (GQ); (JL)
| |
Collapse
|