Volume 46 Issue 8
Aug.  2022
Turn off MathJax
Article Contents
Abstract
References
Related Articles
CHEN Jie, DONG Meng, CUI Yue, FANG Cui-Lian, CHEN Xu-Tang, LIU Zi-Ming. TRANSCRIPTOME ANALYSIS OF TWO DIFFERENT MORPHOLOGICAL POPULATIONS OF SCYLLA PARAMAMOSAIN UNDER COLD STRESS[J]. ACTA HYDROBIOLOGICA SINICA, 2022, 46(8): 1256-1264. DOI: 10.7541/2022.2021.129
Citation: CHEN Jie, DONG Meng, CUI Yue, FANG Cui-Lian, CHEN Xu-Tang, LIU Zi-Ming. TRANSCRIPTOME ANALYSIS OF TWO DIFFERENT MORPHOLOGICAL POPULATIONS OF SCYLLA PARAMAMOSAIN UNDER COLD STRESS[J]. ACTA HYDROBIOLOGICA SINICA, 2022, 46(8): 1256-1264. DOI: 10.7541/2022.2021.129
shu

TRANSCRIPTOME ANALYSIS OF TWO DIFFERENT MORPHOLOGICAL POPULATIONS OF SCYLLA PARAMAMOSAIN UNDER COLD STRESS

  • 1.

    College of Ecology, Lishui University, Lishui 323000, China

  • 2.

    Lishui Institute for Ecological Economy Research, Lishui 323000, China

Funds: Supported by the National Natural Science Foundation of China (32002407)
  • Received Date: July 05, 2021
  • Rev Recd Date: January 25, 2022
  • Available Online: May 06, 2022
  • Published Date: August 14, 2022
    Graphical Abstract
    • Abstract
  • Scylla paramamosain is an economically important crab species mainly distribute in the southern reaches of the Yangtze River. Based on many years of breeding experience, it is speculated that different morphological populations of Scylla paramamosain have acquired different adaptations to temperature changes. In this study, Sp1 populations, with “one spine on the outer margin of the carpus of cheliped ” and Sp2 populations, with “two spines” were designated research objects, and 8℃ low temperature stress and 20℃ control groups were established. The hepatopancreas was used as a transcriptome source, and an Illumina Hiseq4000 platform was used for sequencing. A total of 81853 Unigenes were obtained by sequencing, with an average length of 420 bp, and an N50 of 1460 bp. Among these, 22.33% were known genes. Screening for differentially expressed genes identified 15773 Unigenes displaying significant differential expression in the Sp1 population under low temperature stress. Of these, 15628 Unigenes were down-regulated, and 145 Unigenes were up-regulated. Functional enrichment analysis revealed that the differentially expressed genes encode abundant cytosolic, RNA binding, and ribosome structural constituent proteins, and were further enriched in signal pathway components including ribosome, spliceosome, and protein processing components in the endoplasmic reticulum. 323 Unigenes were significantly differentially expressed in the Sp2 population under low temperature stress, of which, 209 Unigenes were down-regulated, and 114 Unigenes were up-regulated. Functional enrichment analysis revealed that the differentially expressed genes include abundant contributors to steroid hydroxylase activity, DNA integration, and bicarbonate transmembrane transporter activity, and were also enriched in signal pathways including lysine degradation, glycine, serine, and threonine metabolism, and arginine and proline metabolism. The above results indicated that as water temperature droped from 20℃ to 8℃, expression of a large number of genes was down-regulated in the Sp1 population, and physiological activities were drastically reduced. This may correspond to winter behaviors of Scylla paramamosain, including fasting and dwelling in burrows. By contrast, the Sp2 population mainly adjusted its material metabolism, indicating that the Sp2 population was relatively slow to respond to sudden temperature drops. Transcriptome data has been verified by RT-qPCR, supporting the feasibility of comparing responses of two morphological populations to low temperature stress based on transcriptome analysis. This study will inform selection of cold-tolerant and high-quality varieties for breeding of Scylla paramamosain.
    • FullText(HTML)
    • References (30)
  • [1]
    马凌波, 张凤英, 乔振国, 等. 中国东南沿海青蟹线粒体COI基因部分序列分析 [J]. 水产学报, 2006, 30(4): 463-468.

    Ma L B, Zhang F Y, Qiao Z G, et al. Sequence analysis of mitochondrial COI gene of Scylla spp. along coast of southeastern China [J]. Journal of Fisheries of China, 2006, 30(4): 463-468.
    [2]
    高天翔, 王玉江, 刘进贤, 等. 基于线粒体12S rRNA序列探讨4种青蟹系统发育关系及中国沿海青蟹的分类地位 [J]. 中国海洋大学学报(自然科学版), 2007, 37(1): 57-60.

    Gao T X, Wang Y J, Liu J X, et al. Study on phylogenetic relationships of four Scylla species and taxonomic status of mud crab in China based on mitochondrial 12S rRNA sequences [J]. Periodical of Ocean University of China, 2007, 37(1): 57-60.
    [3]
    林琪, 李少菁, 黎中宝, 等. 中国东南沿海青蟹属不同种类的mtDNA COI基因序列分析及其系统发育 [J]. 厦门大学学报(自然科学版), 2008, 47(2): 268-273.

    Lin Q, Li S J, Li Z B, et al. Sequence analysis of mtDNA COI gene and molecular phylogeny of four spcies in Scylla from the coast of southeast China [J]. Journal of Xiamen University (Natural Science), 2008, 47(2): 268-273.
    [4]
    Liu Z M, Zhu X L, Lu J, et al. Effect of high temperature stress on heat shock protein expression and antioxidant enzyme activity of two morphs of the mud crab Scylla paramamosain [J]. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 2018(223): 10-17.
    [5]
    Liu Z M, Wang G Z, Wu L S, et al. Seasonal change in mitochondrial function and metabolic enzyme activity of different populations of the mud crab, Scylla paramamosain, from China [J]. Aquaculture, 2013(376-379): 68-75. doi: 10.1016/j.aquaculture.2012.11.007
    [6]
    Kong X, Wang G, Li S. Seasonal variations of ATPase activity and antioxidant defenses in gills of the mud crab Scylla serrata (Crustacea, Decapoda) [J]. Marine Biology, 2008, 154(2): 269-276. doi: 10.1007/s00227-008-0920-4
    [7]
    Kong X, Wang G, Li S. Effects of low temperature acclimation on antioxidant defenses and ATPase activities in the muscle of mud crab (Scylla paramamosain) [J]. Aquaculture, 2012(370-371): 144-149. doi: 10.1016/j.aquaculture.2012.10.012
    [8]
    Saranyan P V, Ross N W, Benfey T J. Erythrocyte heat shock protein responses to chronic (in vivo) and acute (in vitro) temperature challenge in diploid and triploid salmonids [J]. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 2017(206): 95-104.
    [9]
    Zheng J, Li L, Dong H, et al. Molecular cloning of heat shock protein 60 from Marsupenaeus japonicus and its expression profiles at early developmental stages and response to heat stress [J]. Aquaculture Research, 2018, 49(1): 301-312. doi: 10.1111/are.13461
    [10]
    Houde A L S, Akbarzadeh A, Günther O P, et al. Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity and temperature, but not dissolved oxygen [J]. The Journal of Experimental Biology, 2019, 222(Pt 13): jeb198036.
    [11]
    Huang A M, Geng Y, Wang K Y, et al. Molecular cloning and expression analysis of heat shock protein 90 (Hsp90) of the mud crab, Scylla paramamosain [J]. Journal of Agricultural Science, 2013, 5(7): 1-11.
    [12]
    Yang Y N, Ye H, Huang H, et al. Expression of Hsp70 in the mud crab, Scylla paramamosain in response to bacterial, osmotic, and thermal stress [J]. Cell Stress & Chaperones, 2013, 18(4): 475-482.
    [13]
    Yang Y N, Ye H, Huang H, et al. Characterization and expression of SpHsp60 in hemocytes after challenge to bacterial, osmotic and thermal stress from the mud crab Scylla paramamosain [J]. Fish & Shellfish Immunology, 2013, 35(4): 1185-1191.
    [14]
    Ding J, Chen F Y, Ren S Y, et al. Molecular characterization and promoter analysis of crustacean heat shock protein 10 in Scylla paramemosain [J]. Genome, 2013, 56(5): 273-281. doi: 10.1139/gen-2013-0002
    [15]
    Grabherr M G, Haas B J, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome [J]. Nature Biotechnology, 2011, 29(7): 644-652. doi: 10.1038/nbt.1883
    [16]
    Mortazavi A, Williams B A, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-seq [J]. Nature Methods, 2008, 5(7): 621-628. doi: 10.1038/nmeth.1226
    [17]
    Robinson M D, McCarthy D J, Smyth G K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data [J]. Bioinformatics (Oxford, England) , 2010, 26(1): 139-140. doi: 10.1093/bioinformatics/btp616
    [18]
    Young M D, Wakefield M J, Smyth G K, et al. Gene ontology analysis for RNA-seq: accounting for selection bias [J]. Genome Biology, 2010, 11(2): R14. doi: 10.1186/gb-2010-11-2-r14
    [19]
    Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and the environment [J]. Nucleic Acids Research, 2008(36): D480-D484.
    [20]
    Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔ CT method [J]. Methods, 2001, 25(4): 402-408. doi: 10.1006/meth.2001.1262
    [21]
    Hsieh S L, Chiu Y C, Kuo C M. Molecular cloning and tissue distribution of ferritin in Pacific white shrimp (Litopenaeus vannamei) [J]. Fish & Shellfish Immunology, 2006, 21(3): 279-283.
    [22]
    Xu Z, Liu A, Li S, et al. Hepatopancreas immune response during molt cycle in the mud crab, Scylla paramamosain [J]. Scientific Reports, 2020(10): 13102. doi: 10.1038/s41598-020-70139-2
    [23]
    孔祥会, 王桂忠, 王克坚, 等. 低温驯化下锯缘青蟹肝胰腺蛋白质表达及脂肪酸组成的变化 [J]. 水生生物学报, 2005, 29(5): 524-532. doi: 10.3321/j.issn:1000-3207.2005.05.009

    Kong X H, Wang G Z, Wang K J, et al. Changes of protein expression and fatty acid composition in hepatopancreas of Scylla serrata under low temperature acclimation [J]. Acta Hydrobiologica Sinica, 2005, 29(5): 524-532. doi: 10.3321/j.issn:1000-3207.2005.05.009
    [24]
    刘子明, 王桂忠, 李少菁, 等. 低温季节不同种群拟穴青蟹线粒体呼吸速率和酶活性的差异 [J]. 厦门大学学报(自然科学版), 2018, 57(3): 354-362.

    Liu Z M, Wang G Z, Li S J, et al. Mitochondrial respiration rate and enzyme activity of two populations of Scylla paramamosain during low temperature seasons [J]. Journal of Xiamen University (Natural Science), 2018, 57(3): 354-362.
    [25]
    Guderley H, St-Pierre J. Going with the flow or life in the fast lane: contrasting mitochondrial responses to thermal change [J]. The Journal of Experimental Biology, 2002, 205(Pt 15): 2237-2249.
    [26]
    Yan Y, Xie X. Liver mitochondrial and whole-animal level metabolic compensation in a catfish during seasonal acclimatization [J]. Current Zoology, 2011, 57(1): 109-115. doi: 10.1093/czoolo/57.1.109
    [27]
    Berner N J, Bessay E P. Correlation of seasonal acclimatization in metabolic enzyme activity with preferred body temperature in the Eastern red spotted newt (Notophthalmus viridescens viridescens) [J]. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 2006, 144(4): 429-436.
    [28]
    董丽君, 孟宪红, 孔杰, 等. 基于转录组分析筛选凡纳滨对虾低温胁迫下的差异表达基因 [J]. 中国水产科学, 2019, 26(1): 161-171. doi: 10.3724/SP.J.1118.2019.18061

    Dong L J, Meng X H, Kong J, et al. Screening of differentially expressed genes related to the cold tolerance in Litopenaeus vannamei based on high-throughput transcriptome sequencing [J]. Journal of Fishery Sciences of China, 2019, 26(1): 161-171. doi: 10.3724/SP.J.1118.2019.18061
    [29]
    Shi M, Zhang Q, Li Y, et al. Global gene expression profile under low-temperature conditions in the brain of the grass carp (Ctenopharyngodon idellus) [J]. PLoS One, 2020, 15(9): e0239730. doi: 10.1371/journal.pone.0239730
    [30]
    Liu L, Zhang R, Wang X, et al. Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona) [J]. BMC Genomics, 2020, 21(1): 737. doi: 10.1186/s12864-020-07139-z
    • Related Articles

  • Related Articles

    [1]ZHANG Si-Yuan, ZHAO Yan, GAO Jian. TRANSCRIPTOME ANALYSIS REVEALES THE ROLE OF ELOV4B IN LC-PUFAS BIOSYNTHESIS IN ZEBRAFISH[J]. ACTA HYDROBIOLOGICA SINICA, 2024, 48(11): 1915-1925. DOI: 10.7541/2024.2024.0182
    [2]BIAN Guang-Ming, WANG Na-Ling, HU Ze-Hui, WANG Yue-Bin, HU Cheng-Shuo, CHAI Xue-Jun. A COMPARATIVE ANALYSIS ON THE GENETIC DIVERSITY OF TRICHIURUS LEPTURUS[J]. ACTA HYDROBIOLOGICA SINICA, 2019, 43(2): 282-290. DOI: 10.7541/2019.035
    [3]LIAO De-Jie, CAO Shan-Mao, TONG Jin-Gou, ZHOU Ying, YU Xiao-Mu, LIU Yang, WANG Xiao. GENETIC VARIATION AND RELATIONSHIP ANALYSIS OF SCALLOPS BASED ON THE SEQUENCES OF ITS1 AND 5S rDNA[J]. ACTA HYDROBIOLOGICA SINICA, 2018, 42(3): 494-502. DOI: 10.7541/2018.062
    [4]WANG Shen-Tong, ZHANG Meng, DANG Yun-Fei, LI Li-Sen, HUANG Wen-Ji, FANG Yuan, WANG Feng, SHEN Yu-Bang, LI Jia-Le. GENETIC VARIATION OF MITOCHONDRIAL DNA D-LOOP REGION IN WILD AND BREEDING POPULATIONS OF GRASS CARP[J]. ACTA HYDROBIOLOGICA SINICA, 2017, 41(5): 947-955. DOI: 10.7541/2017.118
    [5]MA Jin-Wu, LÜ Jian-Jian, LIU Ping, GAO Bao-Quan, LI Jian. NA+/H+-EXCHANGER IN SWIMMING CRAB (PORTUNUS TRITUBERCULATUS): CLONING, CHARACTERIZATION AND MRNA EXPRESSION UNDER SALINITY STRESS[J]. ACTA HYDROBIOLOGICA SINICA, 2016, 40(5): 902-907. DOI: 10.7541/2016.116
    [6]DUAN Li-Peng, HUANG Bei, ZHOU Li-Hong, LIANG Ying, NIE Pin, HUANG Wen-Shu. MOLECULAR CLONING, CHARACTERIZATION AND EXPRESSION OF TWO NOVEL LECTINS IN MUD CRAB, SCYLLA PARAMAMOSAIN[J]. ACTA HYDROBIOLOGICA SINICA, 2015, 39(2): 321-330. DOI: 10.7541/2015.43
    [7]LI Zhong, LIANG Hong-Wei, ZOU Gui-Wei. A RAPID PCR-QUALITY DNA EXTRACTION METHOD IN FISH[J]. ACTA HYDROBIOLOGICA SINICA, 2012, 36(2): 365-367. DOI: 10.3724/SP.J.1035.2012.00365
    [8]Shahid Mahboob, Bilal Hussain, Zahid Iqbal, Abdul Shakoor Chaudhry. ESTIMATION OF VOLATILE CONSTITUENTS IN THE FISH FLESH FROM WILD AND FARMED CIRRHINA MRIGALA AND CYPRINUS CARPIO[J]. ACTA HYDROBIOLOGICA SINICA, 2009, 33(3): 484-491.
    [9]Chen Yueqin, He Jiawan, Zhuang Li, Zeng Longmei, Qu Lianghu. SEQUENCE ANALYSIS OF rDNA 16S-23S INTERGENIC SPACER FROM MICROCYSTIS AERUGINOSA AND MICROCYSTIS WESENBERGII IN DONGHU LAKE, CHINA[J]. ACTA HYDROBIOLOGICA SINICA, 1999, 23(1): 41-46.
    [10]Wu Jihua, Liang Yanling, Sun Xida. NEWLY RECORDED SPECIES OF FREE-LIVING NEMATODES FROM CHINA (CHROMADORIDA,ENOPLIDA ARAEOLAIMIDA)[J]. ACTA HYDROBIOLOGICA SINICA, 1997, 21(4): 320-321.

  • Cited by

    Periodical cited type(3)

    1. 罗丽霞，刘莹莹，曾晓辉，吴熙文，汪波. 低温胁迫下小兰屿蝴蝶兰叶片转录组分析. 现代农业科技. 2024(06): 162-165 .
    2. 甄梦婷，胡韵月，高丽娟，申情雨，吴露晨，刘子明. 拟穴青蟹四种形态群体的形态比较和聚类分析. 丽水学院学报. 2023(05): 45-52 .
    3. 刘勤，刘堃，王茜，沈映君，余丽萍，高凌，陆亚男. 基于文献计量的青蟹研究态势分析. 渔业信息与战略. 2022(04): 267-276 .

    Other cited types(1)

Catalog

    Get Citation
    PDF
    XML
    Article views (1546) PDF downloads (61) Cited by(4)
    Related

    Editorial Office of Acta Hydrobiologica Sinica

    Address：No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, China

    Tel：027-68780701；027-68780800 E-mail：acta@ihb.ac.cn  

    Supported byBeijing Renhe Information Technology Co. Ltd  Technical support：info@rhhz.net

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return