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Lowell N, Suhrbier A, Tarpey C, May S, Carson H, Hauser L. Population structure and adaptive differentiation in the sea cucumber Apostichopus californicus and implications for spatial resource management. PLoS One 2023; 18:e0280500. [PMID: 36928497 PMCID: PMC10019739 DOI: 10.1371/journal.pone.0280500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/03/2023] [Indexed: 03/18/2023] Open
Abstract
A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species' range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driving two patterns of differentiation: isolation-by-distance and a latitudinal gradient of differentiation. Notably, we found detectable population differences among collection sites within the Salish Sea (pairwise FST = 0.001-0.006). Using FST outlier detection and gene-environment association, we identified 10.2% of total SNPs as putatively adaptive. Environmental variables (e.g., temperature, salinity) from the sea surface were more correlated with genetic variation than those same variables measured near the benthos, suggesting that selection on pelagic larvae may drive adaptive differentiation to a greater degree than selection on adults. Our results were consistent with previous estimates of and patterns in population structure for this species in other extents of the range. Additionally, we found that patterns of neutral and adaptive differentiation co-varied, suggesting that adaptive barriers may limit dispersal. Our study provides guidance to decision-makers regarding the designation of management units for A. californicus and adds to the growing body of literature identifying genetic population differentiation in marine species despite large, nominally connected populations.
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Affiliation(s)
- Natalie Lowell
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Andy Suhrbier
- Pacific Shellfish Institute, Olympia, Washington, United States of America
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Samuel May
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Henry Carson
- Washington Department of Fish and Wildlife, Olympia, Washington, United States of America
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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Yang Z, Hu K, Hou Y, Wang Y, Yao Y, Lei X, Yan B, Jiang Q, Xiong C, Xu L, Zeng L. Transcriptome analysis of hepatopancreas of Eriocheir sinensis with hepatopancreatic necrosis disease (HPND). PLoS One 2020; 15:e0228623. [PMID: 32084152 PMCID: PMC7034867 DOI: 10.1371/journal.pone.0228623] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 01/20/2020] [Indexed: 11/19/2022] Open
Abstract
Hepatopancreatic necrosis disease (HPND) is a newly emerging disease in the Chinese mitten crab, Eriocheir sinensis, which has resulted in large economic losses. However, the underlying cause of this disease remains unclear. To better understand the pathogenesis and pathogenic mechanism of HPND, we compared the transcriptome differences of the hepatopancreas of E. sinensis with and without HPND. The analysis yielded > 30 million reads for each sample of three test (with HPND) and three control groups (without HPND). We observed 978 downregulated genes and 644 upregulated genes. Among the gene ontology categories "biological process," "cellular component," and "molecular function", the subcategories cellular process, single-organism process, biological regulation, metabolic process, cell part, organelle, organelle part, binding, and catalytic were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that "metabolism of xenobiotics by cytochrome P450," "drug metabolism-cytochrome P450," "chemical carcinogenesis," and "material metabolism" were the "five" most significantly enriched pathways in the hepatopancreas of E. sinensis with HPND. The results revealed that material metabolic abnormalities and drug effects from the external environment might be associated with HPND in the Chinese mitten crab. Considering the wide use of pyrethroids for pond cleaning in Xinghua city, we speculated that pyrethroids might cause HPND in the Chinese mitten crab. Our study provided useful information about the cause and pathogenetic mechanisms of HPND and could help to prevent this disease in production practice.
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Affiliation(s)
- Zongying Yang
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Kun Hu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Pudong, Shanghai, China
| | - Yujie Hou
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Yulan Wang
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Yi Yao
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Xiaoqing Lei
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Baohua Yan
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Qinglong Jiang
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Chunxian Xiong
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Liangqing Xu
- Nanchang Academy of Agricultural Sciences, Nanchang, China
| | - Liugen Zeng
- Nanchang Academy of Agricultural Sciences, Nanchang, China
- * E-mail:
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Gan L, Jiang T, Yi W, Lu R, Xu F, Liu C, Li Z, Han Y, Hu Y, Chen J, Tu H, Huang H, Li J. Study on potential biomarkers of energy metabolism‐related to early‐stage Yin‐deficiency‐heat syndrome based on metabolomics and transcriptomics. Anat Rec (Hoboken) 2020; 303:2109-2120. [PMID: 31909898 DOI: 10.1002/ar.24355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Lin Gan
- South China University of Technology School of Medicine Guangzhou China
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Ting‐Ting Jiang
- South China University of Technology School of Medicine Guangzhou China
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Wen‐Jing Yi
- Medical Research Center, Yuebei People's Hospital Shaoguan China
| | - Ren Lu
- Health Management Center, The People's Liberation Army No.117 Hospital Hangzhou China
| | - Fang‐Yan Xu
- Xiaoshan Hospital of Traditional Chinese Medicine Hangzhou China
| | - Chang‐Ming Liu
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Zhi‐Bin Li
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Yu‐Shuai Han
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Yu‐Ting Hu
- Medical Research Center, Yuebei People's Hospital Shaoguan China
| | - Jing Chen
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Hui‐Hui Tu
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
| | - Huai Huang
- Medical Research Center, Yuebei People's Hospital Shaoguan China
| | - Ji‐Cheng Li
- Department of Anatomy and Embryology Zhejiang University Hangzhou China
- Medical Research Center, Yuebei People's Hospital Shaoguan China
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Huang Y, Xiong JL, Gao XC, Sun XH. Transcriptome analysis of the Chinese giant salamander ( Andrias davidianus) using RNA-sequencing. GENOMICS DATA 2017; 14:126-131. [PMID: 29159068 PMCID: PMC5675895 DOI: 10.1016/j.gdata.2017.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/21/2017] [Accepted: 10/21/2017] [Indexed: 12/21/2022]
Abstract
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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Transcriptional responses in the hepatopancreas of Eriocheir sinensis exposed to deltamethrin. PLoS One 2017; 12:e0184581. [PMID: 28910412 PMCID: PMC5599000 DOI: 10.1371/journal.pone.0184581] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/26/2017] [Indexed: 11/19/2022] Open
Abstract
Deltamethrin is an important pesticide widely used against ectoparasites. Deltamethrin contamination has resulted in a threat to the healthy breeding of the Chinese mitten crab, Eriocheir sinensis. In this study, we investigated transcriptional responses in the hepatopancreas of E. sinensis exposed to deltamethrin. We obtained 99,087,448, 89,086,478, and 100,117,958 raw sequence reads from control 1, control 2, and control 3 groups, and 92,094,972, 92,883,894, and 92,500,828 raw sequence reads from test 1, test 2, and test 3 groups, respectively. After filtering and quality checking of the raw sequence reads, our analysis yielded 79,228,354, 72,336,470, 81,859,826, 77,649,400, 77,194,276, and 75,697,016 clean reads with a mean length of 150 bp from the control and test groups. After deltamethrin treatment, a total of 160 and 167 genes were significantly upregulated and downregulated, respectively. Gene ontology terms "biological process," "cellular component," and "molecular function" were enriched with respect to cell killing, cellular process, other organism part, cell part, binding, and catalytic. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes showed that the metabolic pathways were significantly enriched. We found that the CYP450 enzyme system, carboxylesterase, glutathione-S-transferase, and material (including carbohydrate, lipid, protein, and other substances) metabolism played important roles in the metabolism of deltamethrin in the hepatopancreas of E. sinensis. This study revealed differentially expressed genes related to insecticide metabolism and detoxification in E. sinensis for the first time and will help in understanding the toxicity and molecular metabolic mechanisms of deltamethrin in E. sinensis.
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Rivera-Casas C, González-Romero R, Vizoso-Vazquez Á, Cheema MS, Cerdán ME, Méndez J, Ausió J, Eirin-Lopez JM. Characterization of mussel H2A.Z.2: a new H2A.Z variant preferentially expressed in germinal tissues from Mytilus. Biochem Cell Biol 2016; 94:480-490. [DOI: 10.1139/bcb-2016-0056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Histones are the fundamental constituents of the eukaryotic chromatin, facilitating the physical organization of DNA in chromosomes and participating in the regulation of its metabolism. The H2A family displays the largest number of variants among core histones, including the renowned H2A.X, macroH2A, H2A.B (Bbd), and H2A.Z. This latter variant is especially interesting because of its regulatory role and its differentiation into 2 functionally divergent variants (H2A.Z.1 and H2A.Z.2), further specializing the structure and function of vertebrate chromatin. In the present work we describe, for the first time, the presence of a second H2A.Z variant (H2A.Z.2) in the genome of a non-vertebrate animal, the mussel Mytilus. The molecular and evolutionary characterization of mussel H2A.Z.1 and H2A.Z.2 histones is consistent with their functional specialization, supported on sequence divergence at promoter and coding regions as well as on varying gene expression patterns. More precisely, the expression of H2A.Z.2 transcripts in gonadal tissue and its potential upregulation in response to genotoxic stress might be mirroring the specialization of this variant in DNA repair. Overall, the findings presented in this work complement recent reports describing the widespread presence of other histone variants across eukaryotes, supporting an ancestral origin and conserved role for histone variants in chromatin.
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Affiliation(s)
- Ciro Rivera-Casas
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Rodrigo González-Romero
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Ángel Vizoso-Vazquez
- Exprela Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Manjinder S. Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - M. Esperanza Cerdán
- Exprela Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Josefina Méndez
- Xenomar Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Jose M. Eirin-Lopez
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
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Kanth BK, Kumari S, Choi SH, Ha HJ, Lee GJ. Generation and analysis of expressed sequence tags (ESTs) of Camelina sativa to mine drought stress-responsive genes. Biochem Biophys Res Commun 2015; 467:83-93. [PMID: 26410535 DOI: 10.1016/j.bbrc.2015.09.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/21/2015] [Indexed: 01/02/2023]
Abstract
Camelina sativa is an oil-producing crop belonging to the family of Brassicaceae. Due to exceptionally high content of omega fatty acid, it is commercially grown around the world as edible oil, biofuel, and animal feed. A commonly referred 'false flax' or gold-of-pleasure Camelina sativa has been interested as one of biofuel feedstocks. The species can grow on marginal land due to its superior drought tolerance with low requirement of agricultural inputs. This crop has been unexploited due to very limited transcriptomic and genomic data. Use of gene-specific molecular markers is an important strategy for new cultivar development in breeding program. In this study, Illumina paired-end sequencing technology and bioinformatics tools were used to obtain expression profiling of genes responding to drought stress in Camelina sativa BN14. A total of more than 60,000 loci were assembled, corresponding to approximately 275 K transcripts. When the species was exposed to 10 kPa drought stress, 100 kPa drought stress, and rehydrated conditions, a total of 107, 2,989, and 982 genes, respectively, were up-regulated, while 146, 3,659, and 1189 genes, respectively, were down-regulated compared to control condition. Some unknown genes were found to be highly expressed under drought conditions, together with some already reported gene families such as senescence-associated genes, CAP160, and LEA under 100 kPa soil water condition, cysteine protease, 2OG, Fe(II)-dependent oxygenase, and RAD-like 1 under rehydrated condition. These genes will be further validated and mapped to determine their function and loci. This EST library will be favorably applied to develop gene-specific molecular markers and discover genes responsible for drought tolerance in Camelina species.
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Affiliation(s)
| | - Shipra Kumari
- Chungnam National University, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Seo Hee Choi
- Chungnam National University, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Hye-Jeong Ha
- Chungnam National University, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Geung-Joo Lee
- Chungnam National University, Yuseong-gu, Daejeon, 305-764, Republic of Korea.
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Moreira R, Pereiro P, Canchaya C, Posada D, Figueras A, Novoa B. RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues. BMC Genomics 2015; 16:728. [PMID: 26400066 PMCID: PMC4581086 DOI: 10.1186/s12864-015-1817-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background The Mediterranean mussel (Mytilus galloprovincialis) is a cosmopolitan, cultured bivalve with worldwide commercial and ecological importance. However, there is a qualitative and quantitative lack of knowledge of the molecular mechanisms involved in the physiology and immune response of this mollusc. In order to start filling this gap, we have studied the transcriptome of mantle, muscle and gills from naïve Mediterranean mussels and hemocytes exposed to distinct stimuli. Results A total of 393,316 million raw RNA-Seq reads were obtained and assembled into 151,320 non-redundant transcripts with an average length of 570 bp. Only 55 % of the transcripts were shared across all tissues. Hemocyte and gill transcriptomes shared 60 % of the transcripts while mantle and muscle transcriptomes were most similar, with 77 % shared transcripts. Stimulated hemocytes showed abundant defense and immune-related proteins, in particular, an extremely high amount of antimicrobial peptides. Gills expressed many transcripts assigned to both structure and recognition of non-self patterns, while in mantle many transcripts were related to reproduction and shell formation. Moreover, this tissue presented additional and interesting hematopoietic, antifungal and sensorial functions. Finally, muscle expressed many myofibril and calcium-related proteins and was found to be unexpectedly associated with defense functions. In addition, many metabolic routes related to cancer were represented. Conclusions Our analyses indicate that whereas the transcriptomes of these four tissues have characteristic expression profiles in agreement with their biological structures and expected functions, tissue-specific transcriptomes reveal a complex and specialized functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1817-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebeca Moreira
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.
| | - Patricia Pereiro
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.
| | - Carlos Canchaya
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Unidad Asociada CSIC, Universidade de Vigo, 36310, Vigo, Spain.
| | - David Posada
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Unidad Asociada CSIC, Universidade de Vigo, 36310, Vigo, Spain.
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.
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RNA-Seq analysis and gene discovery of Andrias davidianus using Illumina short read sequencing. PLoS One 2015; 10:e0123730. [PMID: 25874626 PMCID: PMC4395309 DOI: 10.1371/journal.pone.0123730] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 03/05/2015] [Indexed: 11/19/2022] Open
Abstract
The Chinese giant salamander, Andrias davidianus, is an important species in the course of evolution; however, there is insufficient genomic data in public databases for understanding its immunologic mechanisms. High-throughput transcriptome sequencing is necessary to generate an enormous number of transcript sequences from A. davidianus for gene discovery. In this study, we generated more than 40 million reads from samples of spleen and skin tissue using the Illumina paired-end sequencing technology. De novo assembly yielded 87,297 transcripts with a mean length of 734 base pairs (bp). Based on the sequence similarities, searching with known proteins, 38,916 genes were identified. Gene enrichment analysis determined that 981 transcripts were assigned to the immune system. Tissue-specific expression analysis indicated that 443 of transcripts were specifically expressed in the spleen and skin. Among these transcripts, 147 transcripts were found to be involved in immune responses and inflammatory reactions, such as fucolectin, β-defensins and lymphotoxin beta. Eight tissue-specific genes were selected for validation using real time reverse transcription quantitative PCR (qRT-PCR). The results showed that these genes were significantly more expressed in spleen and skin than in other tissues, suggesting that these genes have vital roles in the immune response. This work provides a comprehensive genomic sequence resource for A. davidianus and lays the foundation for future research on the immunologic and disease resistance mechanisms of A. davidianus and other amphibians.
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Santos CA, Blanck DV, de Freitas PD. RNA-seq as a powerful tool for penaeid shrimp genetic progress. Front Genet 2014; 5:298. [PMID: 25221571 PMCID: PMC4147233 DOI: 10.3389/fgene.2014.00298] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/11/2014] [Indexed: 11/27/2022] Open
Abstract
The sequences of all different RNA transcripts present in a cell or tissue that are related to the gene expression and its functional control represent what it is called a transcriptome. The transcripts vary between cells, tissues, ontogenetic and environmental conditions, and the knowledge that can be gained through them is of a solid relevance for genetic applications in aquaculture. Some of the techniques used in transcriptome studies, such as microarrays, are being replaced for next-generation sequencing approaches. RNA-seq emerges as a new possibility for the transcriptome complexity analysis as well as for the candidate genes and polymorphisms identification of penaeid species. Thus, it may also help to understand the determination of complex traits mechanisms and genetic improvement of stocks. In this review, it is first introduced an overview of transcriptome analysis by RNA-seq, followed by a discussion of how this approach may be applied in genetic progress within penaeid stocks.
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Affiliation(s)
- Camilla A Santos
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
| | - Danielly V Blanck
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
| | - Patrícia D de Freitas
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
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Jonsson B, Jonsson N. Early environment influences later performance in fishes. JOURNAL OF FISH BIOLOGY 2014; 85:151-88. [PMID: 24961386 DOI: 10.1111/jfb.12432] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 04/28/2014] [Indexed: 05/19/2023]
Abstract
Conditions fish encounter during embryogenesis and early life history can leave lasting effects not only on morphology, but also on growth rate, life-history and behavioural traits. The ecology of offspring can be affected by conditions experienced by their parents and mother in particular. This review summarizes such early impacts and their ecological influences for a variety of teleost species, but with special reference to salmonids. Growth and adult body size, sex ratio, egg size, lifespan and tendency to migrate can all be affected by early influences. Mechanisms behind such phenotypically plastic impacts are not well known, but epigenetic change appears to be one central mechanism. The thermal regime during development and incubation is particularly important, but also early food consumption and intraspecific density can all be responsible for later life-history variation. For behavioural traits, early experiences with effects on brain, sensory development and cognition appear essential. This may also influence boldness and other social behaviours such as mate choice. At the end of the review, several issues and questions for future studies are given.
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Affiliation(s)
- B Jonsson
- Norwegian Institute for Nature Research, Gaustadalléen 21, N-0349 Oslo, Norway
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Gomez-Uchida D, Seeb LW, Warheit KI, McKinney GJ, Seeb JE. Deep sequencing of the transcriptome and mining of single nucleotide polymorphisms (SNPs) provide genomic resources for applied studies in Chinook salmon (Oncorhynchus tshawytscha). CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0235-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cui Z, Li X, Liu Y, Song C, Hui M, Shi G, Luo D, Li Y. Transcriptome profiling analysis on whole bodies of microbial challenged Eriocheir sinensis larvae for immune gene identification and SNP development. PLoS One 2013; 8:e82156. [PMID: 24324760 PMCID: PMC3852986 DOI: 10.1371/journal.pone.0082156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/21/2013] [Indexed: 01/04/2023] Open
Abstract
To study crab immunogenetics of individuals, newly hatched Eriocheir sinensis larvae were stimulated with a mixture of three pathogen strains (Gram-positive bacteria Micrococcus luteus, Gram-negative bacteria Vibrio alginolyticus and fungi Pichia pastoris; 108 cfu·mL-1). A total of 44,767,566 Illumina clean reads corresponding to 4.52 Gb nucleotides were generated and assembled into 100,252 unigenes (average length: 1,042 bp; range: 201-19,357 bp). 17,097 (26.09%) of 65,535 non-redundant unigenes were annotated in NCBI non-redundant protein (Nr) database. Moreover, 23,188 (35.38%) unigenes were assigned to three Gene Ontology (GO) categories, 15,071 (23.00%) to twenty-six Clusters of orthologous Groups (COG) and 8,574 (13.08%) to six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. Numerous genes were further identified to be associated with multiple immune pathways, including Toll, immune deficiency (IMD), janus kinase (JAK)-signal transducers and activators of transcription (STAT) and mitogen-activated protein kinase (MAPK) pathways. Some of them, such as tumor necrosis factor receptor associated factor 6 (TRAF6), fibroblast growth factor (FGF), protein-tyrosine phosphatase (PTP), JNK-interacting protein 1 (JIP1), were first identified in E. sinensis. TRAF6 was even first discovered in crabs. Additionally, 49,555 single nucleotide polymorphisms (SNPs) were developed from over 13,309 unigenes. This is the first transcriptome report of whole bodies of E. sinensis larvae after immune challenge. Data generated here not only provide detail information to identify novel genes in genome reference-free E. sinensis, but also facilitate our understanding on host immunity and defense mechanism of the crab at whole transcriptome level.
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Affiliation(s)
- Zhaoxia Cui
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- National & Local Joint Engineering Laboratory for Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
| | - Xihong Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 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
| | - Min Hui
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Guohui Shi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - 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
| | - Yingdong Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Guo H, Ye CX, Wang AL, Xian JA, Liao SA, Miao YT, Zhang SP. Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq. FISH & SHELLFISH IMMUNOLOGY 2013; 35:2008-16. [PMID: 24055647 DOI: 10.1016/j.fsi.2013.09.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 05/26/2023]
Abstract
In the present study, transcriptome of nitrite-exposed Litopenaeus vannamei was performed using a newly developed high-throughput sequencing technology (Illumina RNA-seq). As many as 42,336 unigenes were generated with 561 bp of average length and 736 bp of unigene N50 after filtering and assembly. These unigenes from the de novo assembly were further annotated using BLAST and BLAST2GO softwares. A total of 23,532 unigenes were unambiguous alignments to the reference when BLAST against non-redundant protein sequence (Nr), non-redundant nucleotide (Nt), Swiss-Prot, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases available at NCBI. Numerous candidate genes associated with immune response, detoxification, apoptosis pathway were identified. Ten candidate genes related to immune responses and apoptosis were selected for validating the results of assembly and annotation by real-time quantitative PCR. Results revealed that the expressions of all these ten genes were up-regulated after nitrite exposure. Combining to our previous study, we speculate that all these selected genes may be involved in the response to nitrite stress. The study shows a systematic overview of the transcriptome analysis in L. vannamei, and provides valuable gene information for studying molecular mechanisms under nitrite exposure.
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Affiliation(s)
- Hui Guo
- Key Laboratory of Ecology and Environmental Science of Guangdong Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou 510631, People's Republic of China
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Transcriptome analysis and discovery of genes involved in immune pathways from hepatopancreas of microbial challenged mitten crab Eriocheir sinensis. PLoS One 2013; 8:e68233. [PMID: 23874555 PMCID: PMC3714283 DOI: 10.1371/journal.pone.0068233] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 06/01/2013] [Indexed: 12/02/2022] Open
Abstract
Background The Chinese mitten crab Eriocheir sinensis is an important economic crustacean and has been seriously attacked by various diseases, which requires more and more information for immune relevant genes on genome background. Recently, high-throughput RNA sequencing (RNA-seq) technology provides a powerful and efficient method for transcript analysis and immune gene discovery. Methods/Principal Findings A cDNA library from hepatopancreas of E. sinensis challenged by a mixture of three pathogen strains (Gram-positive bacteria Micrococcus luteus, Gram-negative bacteria Vibrio alginolyticus and fungi Pichia pastoris; 108 cfu·mL−1) was constructed and randomly sequenced using Illumina technique. Totally 39.76 million clean reads were assembled to 70,300 unigenes. After ruling out short-length and low-quality sequences, 52,074 non-redundant unigenes were compared to public databases for homology searching and 17,617 of them showed high similarity to sequences in NCBI non-redundant protein (Nr) database. For function classification and pathway assignment, 18,734 (36.00%) unigenes were categorized to three Gene Ontology (GO) categories, 12,243 (23.51%) were classified to 25 Clusters of Orthologous Groups (COG), and 8,983 (17.25%) were assigned to six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Potentially, 24, 14, 47 and 132 unigenes were characterized to be involved in Toll, IMD, JAK-STAT and MAPK pathways, respectively. Conclusions/Significance This is the first systematical transcriptome analysis of components relating to innate immune pathways in E. sinensis. Functional genes and putative pathways identified here will contribute to better understand immune system and prevent various diseases in crab.
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