Sequencing, de novo assembly and characterization of the spotted scat <italic style="font-style: italic">Scatophagus argus</italic>(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs

杨尉; 陈华谱; 崔雪凡; 张克伟; 江东能; 邓思平; 朱春华; 李广丽

doi:10.1007/s00343-018-7090-0

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Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs

Biology | Updated：2023-05-19

- Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs
- Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs
- 海洋湖沼学报（英文） 2018年36卷第4期页码：1329-1341
- Affiliations：
  
  1.Zhanjiang City Key Laboratory of Marine Ecology and Environment, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
  2.Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
  3.Food and Environmental Engineering Department, Yangjiang Vocational and Technical College, Yangjiang 529566, China
- Author bio：
  
  LI Guangli, guangligdou@163.com
- Funds：
  
  the National Science Foundation for Young Scientists of China(41706174);the National Science Foundation for Young Scientists of China(31702326);the Marine Fishery Science and Technology Promotion Projects of Guandong Province(A201408A06);the Marine Fishery Science and Technology Promotion Projects of Guandong Province(A201608B01);the 2017 Special Fund for the Development of Marine and Fisheries(2017A0012);the Natural Science Foundation of Guangdong Province(2016A030313743);the Project of Provincial Key Platform and Major Scientific Research of Colleges and Universities in Guangdong(2015KTSCX058);Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology(2016LMFS-B12)
- DOI：10.1007/s00343-018-7090-0
  中图分类号：
- 收稿：2017-03-24，
  
  录用：2017-5-3，
  
  网络首发：2017-06-19，
  
  纸质出版：2018-07
- Accepted：
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杨尉, 陈华谱, 崔雪凡, 等. Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs[J]. 海洋湖沼学报（英文）, 2018,36(4):1329-1341.

Wei YANG, Huapu CHEN, Xuefan CUI, et al. Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs[J]. Chinese Journal of Oceanology and Limnology, 2018, 36(4): 1329-1341.
杨尉, 陈华谱, 崔雪凡, 等. Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs[J]. 海洋湖沼学报（英文）, 2018,36(4):1329-1341. DOI： 10.1007/s00343-018-7090-0.

Wei YANG, Huapu CHEN, Xuefan CUI, et al. Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs[J]. Chinese Journal of Oceanology and Limnology, 2018, 36(4): 1329-1341. DOI： 10.1007/s00343-018-7090-0.

摘要

Abstract

Spotted scat (

Scatophagus argus

) is an economically important farmed fish

particularly in East and Southeast Asia. Because there has been little research on reproductive development and regulation in this species

the lack of a mature artificial reproduction technology remains a barrier for the sustainable development of the aquaculture industry. More genetic and genomic background knowledge is urgently needed for an in-depth understanding of the molecular mechanism of reproductive process and identification of functional genes related to sexual differentiation

gonad maturation and gametogenesis. For these reasons

we performed transcriptomic analysis on spotted scat using a multiple tissue sample mixing strategy. The Illumina RNA sequencing generated 118 510 486 raw reads. After trimming

de novo assembly was performed and yielded 99 888 unigenes with an average length of 905.75 bp. A total of 45 015 unigenes were successfully annotated to the Nr

Swiss-Prot

KOG and KEGG databases. Additionally

23 783 and 27 183 annotated unigenes were assigned to 56 Gene Ontology (GO) functional groups and 228 KEGG pathways

respectively. Subsequently

2 474 transcripts associated with reproduction were selected using GO term and KEGG pathway assignments

and a number of reproduction-related genes involved in sex differentiation

gonad development and gametogenesis were identified. Furthermore

22 279 simple sequence repeat (SSR) loci were discovered and characterized. The comprehensive transcript dataset described here greatly increases the genetic information available for spotted scat and contributes valuable sequence resources for functional gene mining and analysis. Candidate transcripts involved in reproduction would make good starting points for future studies on reproductive mechanisms

and the putative sex differentiation-related genes will be helpful for sex-determining gene identification and sex-specific marker isolation. Lastly

the SSRs can serve as marker resources for future research into genetics

marker-assisted selection (MAS) and conservation biology.

关键词

Keywords

references

Barry T P, Castanos M T, Fast A W. 1991. Induced spermiation in the male spotted scat ( Scatophagus argus ) by long-term administration of 17α-methyltestosterone followed by LHRHa. Asian Fish. Sci., 4(2):137-145.

Barry T P, Castanos M T, Macahilig M P S C, Fast A W. 1993.Gonadal maturation and spawning induction in female spotted scat ( Scatophagus argus ). J. Aqua. Trop., 8:121-130.

Barry T P, Fast A W. 1992. Biology of the spotted scat( Scatophagus argus ) in the Philippines. Asian Fish. Sci., 5(3):163-179.

Cai Z P, Wang Y, Hu J W, Zhang J B, Lin Y G. 2010.Reproductive biology of Scatophagus argus and artificial induction of spawning. J. Trop. Oceanogr., 29(5):180-185. (in Chinese with English abstract)

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos P, Bealer K, Madden T L. 2009. BLAST+:architecture and applications. BMC Bioinformatics, 10:421.

Chen H P, Deng S P, Dai M L, Zhu C H, Li G L. 2016. Molecular cloning, characterization, and expression profiles of androgen receptors in spotted scat ( Scatophagus argus ). Genet. Mol. Res., 15 (2): 1-14, https://doi.org/10.4238/gmr.15027838.

Chen J H, He M X, Mu X J, Yan B L, Zhang J B, Jin S C.2015b. cDNA cloning and mRNA expression analysis of Sox9 in Scatophagus argus . Chin. J. Zool., 50(1):93-102.(in Chinese with English abstract)

Chen J H, He M X, Yan B L, Zhang J B, Jin S C, Liu L. 2015a.Molecular characterization of dax1 and SF-1 and their expression analysis during sex reversal in spotted scat, Scatophagus argus . J. World Aquac. Soc., 46(1):1-19.

Conesa A, Götz S, García-Gómez J M, Terol J, Talón M, Robles M. 2005. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18):3 674-3 676.

Deng S P, Wu B, Zhu C H, Li G L. 2014. Molecular cloning and dimorphic expression of growth hormone ( gh ) in female and male spotted scat Scatophagus argus .Fisheries Sci., 80(4):715-723.

Finseth F R, Harrison R G. 2014. A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird.PLoS One, 9(10):e108550.

Fraser B A, Weadick C J, Janowitz I, Rodd F H, Hughes K A. 2011. Sequencing and characterization of the guppy( Poecilia reticulata ) transcriptome. BMC Genomics, 12:202.

Gandhi V, Venkatesan V, Ramamoorthy N. 2014. Reproductive biology of the spotted scat Scatophagus argus (Linnaeus, 1766) from Mandapam waters, South-east coast of India.Indian J. Fish., 61(4):55-59.

Garber M, Grabherr M G, Guttman M, Trapnell C. 2011.Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods, 8(6):469-477.

Grabherr M G, Haas B J, Yassour M, Levin J Z, Thompson D A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q D, Chen Z H, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren B W, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29(7):644-652.

Gupta S. 2016. An overview on morphology, biology, and culture of spotted scat Scatophagus argus (Linnaeus 1766). Rev. Fish. Sci. Aquac., 24(2):203-212.

Herpin A, Schartl M. 2011. Dmrt1 genes at the crossroads:a widespread and central class of sexual development factors in fish. FEBS J., 278(7):1 010-1 019.

Jung H, Lyons R E, Dinh H, Hurwood D A, McWilliam S, Mather P B. 2011. Transcriptomics of a giant freshwater prawn ( Macrobrachium rosenbergii ):de novo assembly, annotation and marker discovery. PLoS One, 6(12):e27938.

Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. 2004. The KEGG resource for deciphering the genome.Nucleic Acids Res., 32(Suppl 1):D277-D280.

Lalitha S. 2000. Primer premier 5. Biotech Softw . Internet Rep., 1(6):270-272.

Levavi-Sivan B, Bogerd J, Mañanós E L, Gómez A, Lareyre J J. 2010. Perspectives on fish gonadotropins and their receptors. Gen. Comp. Endocrinol., 165(3):412-437.

Levavi-Sivan B, Safarian H, Rosenfeld H, Elizur A, Avitan A. 2012. Regulation of gonadotropin-releasing hormone(GnRH)-receptor gene expression in tilapia:effect of GnRH and dopamine. Biol. Reprod., 70(6):1 545-1 551.

Li C Z, Weng S P, Chen Y G, Yu X Q, Lü L, Zhang H Q, He J G, Xu X P. 2012. Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique. PLoS One, 7(10):e47442.

Li G L, Zhang M Z, Deng S P, Chen H P, Zhu C H. 2015.Effects of temperature and fish oil supplementation on ovarian development and foxl2 mRNA expression in spotted scat Scatophagus argus . J. Fish Biol., 86(1):248-260.

Li S H, Zhang X J, Sun Z, Li F H, Xiang J H. 2013.Transcriptome analysis on Chinese shrimp Fenneropenaeus chinensis during WSSV acute infection.PLoS One, 8(3):e58627.

Li S Q, Liu Z H, Hu P, Liang X M, Liu H F, Su M L, Zhang J B. 2014. SNP discovery using high-throughput 454 pyrosequencing and validation in the spotted scat, Scatophagus argus . Conserv. Genet. Resour., 6(4):817-820.

Liu H F, Li S Q, Hu P, Zhang Y Y, Zhang J B. 2013. Isolation and characterization of EST-based microsatellite markers for Scatophagus argus based on transcriptome analysis.Conserv. Genet. Resour., 5(2):483-485.

Liu H F, Mu X J, Gui L, Su M L, Li H, Zhang G, Liu Z H, Zhang J B. 2015. Characterization and gonadal expression of foxl2 relative to cyp19a genes in spotted scat Scatophagus argus . Gene, 561(1):6-14.

Liu H F, Zhang J B, Cai Z P, Song Y. 2010. Novel polymorphic microsatellite loci for the spotted scat Scatophagus argus .Conserv. Genet. Resour., 2(2):149-151.

Lu J G, Luan P X, Zhang X F, Xue S Q, Peng L N, Mahbooband S, Sun X W. 2014. Gonadal transcriptomic analysis of yellow catfish ( Pelteobagrus fulvidraco ):identification of sex-related genes and genetic markers. Physiol. Genomics, 46(21):798-807.

Lv J J, Liu P, Gao B Q, Wang Y, Wang Z, Chen P, Li J. 2014.Transcriptome analysis of the Portunus trituberculatus :de novo assembly, growth-related gene identification and marker discovery. PLoS One, 9(4):e94055.

Ma D Y, Ma A J, Huang Z H, Wang G N, Wang T, Xia D D, Ma B H. 2016. Transcriptome analysis for identification of genes related to gonad differentiation, growth, immune response and marker discovery in the turbot ( Scophthalmus maximus ). PLoS One, 11(2):e0149414.

Ma K Y, Qiu G F, Feng J B, Li J L. 2012. Transcriptome analysis of the oriental river prawn, Macrobrachium nipponense using 454 pyrosequencing for discovery of genes and markers. PLoS One, 7(6):e39727.

Malachowicz M, Wenne R, Burzynski A. 2017. De novo assembly of the sea trout ( Salmo trutta m. trutta ) skin transcriptome to identify putative genes involved in the immune response and epidermal mucus secretion. PLoS One, 12(2):e0172282.

Morrish B C, Sinclair A H. 2002. Vertebrate sex determination:many means to an end. Reproduction, 124(4):447-457.

Patnaik B B, Wang T H, Kang S W, Hwang H J, Park S Y, Park E B, Chung J M, Song D K, Kim C, Kim S, Lee J S, Han Y S, Park H S, Lee Y S. 2016. Sequencing, de novo assembly, and annotation of the transcriptome of the endangered freshwater pearl bivalve, Cristaria plicata , provides novel insights into functional genes and marker discovery. PLoS One, 11(2):e0148622.

Pereiro P, Balseiro P, Romero A, Dios S, Forn-Cuni G, Fuste B, Planas J V, Beltran S, Novoa B, Figueras A. 2012. Highthroughput sequence analysis of turbot ( Scophthalmus maximus ) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes. PLoS One, 7(5):e35369.

Prasad P, Ogawa S, Parhar I S. 2015. Serotonin reuptake inhibitor citalopram inhibits GnRH synthesis and spermatogenesis in the male zebrafish. Biol. Reprod., 93(4):102.

Robledo D, Ronza P, Harrison P W, Losada A P, Bermúdez R, Pardo B G, Redondo M J, Sitjà-Bobadilla A, Quiroga M I, Martínez P. 2014. RNA-seq analysis reveals significant transcriptome changes in turbot ( Scophthalmus maximus )suffering severe enteromyxosis. BMC Genomics, 15:1149.

Salem M, Rexroad C E, Wang J N, Thorgaard G H, Yao J B. 2010. Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics, 11:564.

Thiel T, Michalek W, Varshney R, Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley ( Hordeum vulgare L.). Theor. Appl. Genet., 106(3):411-422.

Tong Y, Zhang Y, Huang J M, Xiao S, Zhang Y H, Li J, Chen J H, Yu Z N. 2015. Transcriptomics analysis of Crassostrea hongkongensis for the discovery of reproduction-related genes. PLoS One, 10(8):e0134280.

Xiao S J, Li J T, Ma F S, Fang L J, Xu S B, Chen W, Wang Z Y. 2015. Rapid construction of genome map for large yellow croaker ( Larimichthys crocea ) by the wholegenome mapping in BioNano Genomics Irys system.BMC Genomics, 16:670.

Xie C, Mao X Z, Huang J J, Ding Y, Wu J M, Dong S, Kong L, Gao G, Li C Y, Wei L P. 2011. KOBAS 2.0:a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res., 39(Suppl 2):W316-W322.

Xie Z Z, Xiao L, Wang D D, Fang C, Liu Q Y, Li Z H, Liu X C, Zhang Y, Li S S, Lin H R. 2014. Transcriptome analysis of the Trachinotus ovatus :identification of reproduction, growth and immune-related genes and microsatellite markers. PLoS One, 9(10):e109419.

Ye J, Fang L, Zheng H K, Zhang Y, Chen J, Zhang Z J, Wang J, Li S T, Li R Q, Bolund L, Wang J. 2006. WEGO:a web tool for plotting GO annotations. Nucleic Acids Res., 34(Suppl 2):W293-W297.

Zhang M Z, Li G L, Zhu C H, Deng S P. 2013. Effects of fish oil on ovarian development in spotted scat ( Scatophagus argus ). Anim. Reprod. Sci., 141(1-2):90-97.

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Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs

Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs

DOI：10.1007/s00343-018-7090-0

摘要

Abstract

关键词

Keywords

references