RNA sequence analysis of growth-related genes in Penaeus monodon

Nifareesa CHEALOH, Sataporn DIREKBUSARAKOM, Piyapong CHOTIPUNTU, Pitchanee JARIYAPONG, Hidehiro KONDO, Ikuo HIRONO, Suwit WUTHISUTHIMETHAVEE

Abstract


Penaeus monodon is one of the most economically important shrimp species in Thailand. However, little information is available about the functional genomics related to its growth performance. In this study, Illumina paired-end sequencing was used to analyze transcriptomes related to growth performance in P. monodon muscle. A total 38.4 million reads were generated. The pooled reads from 10 libraries were de novo assembled into 117,265 transcripts. For cluster analysis, 113,991 genes were obtained with an average length of 337 bp. Gene expression was analyzed with the edgeR program, which revealed 705 differentially expressed contigs (p<0.05) in fast-growth shrimp compared to slow-growth shrimp. The InterPro scan results were merged with BLAST-derived GO annotations and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and then analyzed. The results show the 234 up-regulated contigs in fast-growth shrimp are mostly underlined genes involving the metabolism pathway. Quantitative real-time polymerase chain reaction (RT-PCR) revealed seven genes involved in the cell cycle that were expressed more in fast-growth shrimp (p<0.05) than in slow-growth shrimp and moderately to strongly correlated with shrimp body weight. These genes may be good candidates for growth performance improvement in P. monodon.

Keywords


Penaeus monodon, RNA sequencing, qRT-PCR, growth-related genes, growth improvement

References


M Saroglia and Z Liu. Functional Genomics in Aquaculture, Wiley, 2012, p. 403.

FAO. The State of World Fisheries and Aquaculture 2016, 2016.

AW Fast and LJ Lester. Marine Shrimp Culture: Principles and Practices, Elsevier, 1992, p. 879.

H Jung, RE Lyons, DA Hurwood and PB Mather. Genes and growth performance in crustacean species : a review of relevant genomic studies in crustaceans and other taxa. Reviews in Aquaculture 2013; 5, 77-110.

C De-Santis and DR Jerry. Candidate growth genes in finfish — Where should we be looking? Aquaculture 2007; 272, 22-38.

H Jung, RE Lyons, Y Li, NM Thanh, H Dinh, DA Hurwood, KR Salin and PB Mather. A Candidate Gene Association Study for Growth Performance in an Improved Giant Freshwater Prawn (Macrobrachium rosenbergii) Culture Line. Mar. Biotechnol. 2014; 16, 161-80.

A Tangprasittipap, M Tiensuwan and B Withyachumnarnkul. Characterization of candidate genes involved in growth of black tiger shrimp Penaeus monodon. Aquaculture 2010; 307, 150-6.

C Nguyen, TG Nguyen, LV Nguyen, HQ Pham, TH Nguyen, HT Pham, HT Nguyen, TT Ha, TH Dau, HT Vu, DD Nguyen, NTT Nguyen, NH Nguyen, D Van Quyen, HH Chu and KD Dinh. De novo assembly and transcriptome characterization of major growth-related genes in various tissues of Penaeus monodon. Aquaculture 2016; 464, 545-53.

CA Santos, DV Blanck and PD de Freitas. RNA-seq as a powerful tool for penaeid shrimp genetic progress. Front. Genet. 2014; 5, 1-6.

AM Bolger, M Lohse and B Usadel. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30, 2114-20.

MG Grabherr, BJ Haas, M Yassour, JZ Levin, Da Thompson, I Amit, X Adiconis, L Fan, R Raychowdhury, Q Zeng, Z Chen, E Mauceli, N Hacohen, A Gnirke, N Rhind, F di Palma, BW Birren, C Nusbaum, K Lindblad-Toh, N Friedman and A Regev. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011; 29, 1-11.

J Feng, W Li and T Jiang. Inference of isoforms from short sequence reads. J. Comput. Biol. 2011; 18, 1-21.

B Li and CN Dewey. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011; 12, 1-16.

M-A Dillies, A Rau, J Aubert, C Hennequet-Antier, M Jeanmougin, N Servant, C Keime, G Marot, D Castel, J Estelle, G Guernec, B Jagla, L Jouneau, D Laloë, C Le Gall, B Schaëffer, S Le Crom, M Guedj and F Jaffrézic. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings in Bioinformatics 2013; 14, 671-83.

S Li, X Zhang, Z Sun, F Li and J Xiang. Transcriptome Analysis on Chinese Shrimp Fenneropenaeus chinensis during WSSV Acute Infection. PLoS ONE 2013; 8, 1-15.

C Trapnell, BA Williams, G Pertea, A Mortazavi, G Kwan, MJ van Baren, SL Salzberg, BJ Wold and L Pachter. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010; 28, 511-18.

BJ Haas, A Papanicolaou, M Yassour, M Grabherr, PD Blood, J Bowden, MB Couger, D Eccles, B Li, M Lieber, MD MacManes, M Ott, J Orvis, N Pochet, F Strozzi, N Weeks, R Westerman, T William, CN Dewey, R Henschel, RD LeDuc, N Friedman and A Regev. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nat. Protocol. 2013; 8, 1-43.

MD Robinson, DJ McCarthy and GK Smyth. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26, 1-2.

S Sookruksawong, F Sun, Z Liu and A Tassanakajon. RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei. Dev. Comp. Immunol. 2013; 41, 523-33.

J Gao, X Wang, Z Zou, X Jia, Y Wang and Z Zhang. Transcriptome analysis of the differences in gene expression between testis and ovary in green mud crab (Scylla paramamosain). BMC Genomics 2014; 15, 1-15.

H Jung, RE Lyons, H Dinh, DA Hurwood, S McWilliam and PB Mather. Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery. PLoS ONE 2011; 6, 1-14.

A Conesa, S Gotz, JM Garcia-Gomez, J Terol, M Talon and M Robles. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005; 21, 3674-76.

S Götz, JM García-Gómez, J Terol, TD Williams, SH Nagaraj, MJ Nueda, M Robles, M Talón, J Dopazo and A Conesa. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic. Acids. Res. 2008; 36, 3420-35.

H Guo, C-X Ye, A-L Wang, J-A Xian, S-A Liao, Y-T Miao and S-P Zhang. Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq. Fish & Shellfish Immunology 2013; 35, 2008-16.

MW Pfaffl. A new mathematical model for relative quantification in real-time RT–PCR. Nucleic. Acids. Res. 2001; 29, 1-6.

MW Pfaffl, GW Horgan and L Dempfle. Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic. Acids. Res. 2002; 30, 1-10.

JP Baren, GD Stewart, A Stokes, K Gray, CJ Pennington, R O'Neill, DAC Deans, S Paterson-Brown, ACP Riddick, DR Edwards, KCH Fearon, JA Ross and RJE Skipworth. mRNA profiling of the cancer degradome in oesophago–gastric adenocarcinoma. Br. J. Canc. Manag. 2012; 107, 143-49.

J De Neve, O Thas, J-P Ottoy and L Clement. An extension of the Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data. Stat. Appl. Genet. Mol. Biol. 12, 333-46.

A Oshlack, MD Robinson and MD Young. From RNA-seq reads to differential expression results. Genome. Biol. 2010; 11, 1-10.

Z Wang, M Gerstein and M Snyder. RNA-Seq: a revolutionary tool for transcriptome. Nat. Rev. Genet. 2009; 10, 1-7.

JR de Oliveira Cesar, B Zhao, S Malecha, H Ako and J Yang. Morphological and biochemical changes in the muscle of the marine shrimp Litopenaeus vannamei during the molt cycle. Aquaculture 2006; 261, 688-94.

X Fu, N Fu, S Guo, Z Yan, Y Xu, H Hu, C Menzel, W Chen, Y Li, R Zeng and P Khaitovich. Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 2009; 10, 1-12.

S Xue, Y Liu, Y Zhang, Y Sun, X Geng and J Sun. Sequencing and De Novo Analysis of the Hemocytes Transcriptome in Litopenaeus vannamei Response to White Spot Syndrome Virus Infection. PLoS ONE 2013; 8, 1-12.

Q-Y Zhao, Y Wang, Y-M Kong, D Luo, X Li and P Hao. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 2011; 12, 1-12.

D Zeng, X Chen, D Xie, Y Zhao, C Yang, Y Li, N Ma, M Peng, Q Yang, Z Liao, H Wang and X Chen. Transcriptome Analysis of Pacific White Shrimp (Litopenaeus vannamei) Hepatopancreas in Response to Taura Syndrome Virus (TSV) Experimental Infection. PLoS ONE 2013; 8, 1-8.

C Li, S Weng, Y Chen, X Yu, L Lü, H Zhang, J He and X Xu. Analysis of Litopenaeus vannamei Transcriptome Using the Next-Generation DNA Sequencing Technique. PLoS ONE 2012; 7, 1-12.

J Pines and T Hunter. Cyclins A and B1 in the human cell cycle. Ciba. Found. Symp. 1992; 170, 187-96.

CF Lehner and PH O’Farrell. The Roles of Drosophila Cyclins A and B in Mitotic Control. Cell 1990; 61, 535-47.

V Visudtiphole, S Klinbunga and K Kirtikara. Molecular characterization and expression profiles of cyclin A and cyclin B during ovarian development of the giant tiger shrimp Penaeus monodon. Comp. Biochem. Physiol. A. Mol. Integr. Physiol. 2009; 152, 535-43.

L Qiu, S Jiang, F Zhou, J Huang and Y Guo. Molecular cloning and characterization of a cyclin B gene on the ovarian maturation stage of black tiger shrimp (Penaeus monodon). Mol. Biol. Rep. 2007; 24, 24.

N Perrimon, L Engstrom and AP Mahowald. A pupal lethal mutation with a paternally influenced maternal effect on embryonic development in Drosophila melanogaster. Dev. Biol. 1985; 110, 480-91.

M Furriols and J Casanova. In and out of Torso RTK signalling. EMBO J 2003; 22, 1947-52.

G Jiménez, A Guichet, A Ephrussi and J Casanova. Relief of gene repression by torso RTK signaling: role of capicua in Drosophila terminal and dorsoventral patterning. Gene. Dev. 2000; 14, 224-31.

P Li, K Wood, H Mamon, W Haser and T Roberts. Raf-1: a kinase currently without a cause but not lacking in effects. Cell 1991; 64, 479-82.

ZB Yu, CK Mu, WW Song, RH Li, YE Chen and CL Wang. Screening of genes related to ovarian development in the swimming crab, Portunus trituberculatus, by suppression subtractive hybridization. Genet. Mol. Res. 2015, 14, 18675-86.

X-J Du, J-X Wang, N Liu, X-F Zhao, F-H Li and J-H Xiang. Identification and molecular characterization of a peritrophin-like protein from fleshy prawn (Fenneropenaeus chinensis). Mol. Immunol. 2006; 43, 1633-44.

L Wang, F Li, B Wang and J Xiang. A new shrimp peritrophin-like gene from Exopalaemon carinicauda involved in white spot syndrome virus (WSSV) infection. Fish & Shellfish Immunology 2013; 35, 840-46.

M Khayat, PJ Babin, B Funkenstein, M Sammar, H Nagasawa, A Tietz and E Lubzens. Molecular Characterization and High Expression During Oocyte Development of a Shrimp Ovarian Cortical Rod Protein Homologous to Insect Intestinal Peritrophins1. Biol. Reprod. 2001; 64, 1090-99.

Y Chen, T Souaiaia and T Chen. PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 2009; 25, 2514-21.

YK Kim, N Tsutsui, I Kawazoe, T Okumura, T Kaneko and K Aida. Localization and developmental expression of mRNA for cortical rod protein in kuruma prawn Marsupenaeus japonicus. Zoolog. Sci. 2005; 22, 675-80.

W Loongyai, J-C Avarre, M Cerutti, E Lubzens and W Chotigeat. Isolation and Functional Characterization of a New Shrimp Ovarian Peritrophin with Antimicrobial Activity from Fenneropenaeus merguiensis. Mar. Biotechnol. 2007; 9, 624-37.


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