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Identification of Genes Involved in Digestion from Transcriptome of Parasesarma pictum and Parasesarma affine Hepatopancreas

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Abstract

Although the representative species of Sesarmidaes, mudflat crab Parasesarma pictum and P. affine, are primarily herbivorous crabs, very little information is available about these transcriptomes. To identify the key genes those are responsible for the digestion systems in these crabs, we investigated transcriptomic profiles of the hepatopancreas in P. pictum and P. affine. Hundreds of unigenes in P. pictum and P. affine were classified related to food digestion and absorption by blast annotation, and many of them were annotated as digestive enzymes that played key roles during food digestion process. Remarkably, we presented the first report that these two Parasesarma genus species had four types of alpha amylase genes and two types of EGs. This transcriptomic information about P. pictum and P. affine will be helpful in further study of crustacean biology and the molecular basis of the herbivorous diet in crabs.

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References

  • Allardyce BJ, Linton SM (2008) Purification and characterisation of endo-beta-1,4-glucanase and laminarinase enzymes from the gecarcinid land crab Gecarcoidea natalis and the aquatic crayfish Cherax destructor. J Exp Biol 211(14):2275–2287

    Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402

    Google Scholar 

  • Azam M, Lifat RM, Tuan NV, Mather PB, Hurwood DA (2016) A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense). Peerj 4(10):e2520

    Google Scholar 

  • Bain PA, Gregg AL, Kumar A (2016) De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water. BMC Genomics 17(1):890

    Google Scholar 

  • Bom RA, Gils JAV, Molenaar K, Kwarteng AY, Folmer EO (2020) The intertidal mudflats of Barr Al Hikman, Sultanate of Oman, as feeding, reproduction and nursery grounds for brachyuran crabs. Hydrobiologia 847(20):1–15

    Google Scholar 

  • Bui TH, Lee SY (2015) Endogenous cellulase production in the leaf litter foraging mangrove crab Parasesarma erythodactyla. Comp Biochem Physiol B 179:27

    Google Scholar 

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinf 10(1):421

    Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676

    Google Scholar 

  • Dammannagoda LK, Pavasovic A, Prentis PJ, Hurwood DA, Mather PB (2015) Expression and characterization of digestive enzyme genes from hepatopancreatic transcripts from redclaw crayfish (Cherax quadricarinatus). Aquac Nutr 21(6):868–880

    Google Scholar 

  • Davison A, Blaxter M (2005) Ancient origin of glycosyl hydrolase family 9 cellulase genes. Mol Biol Evol 22(5):1273–1284

    Google Scholar 

  • Fernández I, Oliva M, Carrillo O, Wormhoudt AV (1997) Digestive enzyme activities of Penaeus notialis during reproduction and moulting cycle. Comp Biochem Physiol A 118(4):1267–1271

    Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652

    Article  Google Scholar 

  • Hammer HS, Bishop CD, Watts SA (2000) Activities of three digestive enzymes during development in the crayfish Procambarus clarkii (Decapoda). J Crustacean Biol 20(4):614–620

    Google Scholar 

  • Huang S, Wang J, Yue W, Chen J, Gaughan S, Lu W, Lu G, Wang C (2015) Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis. Sci Rep-Uk 5:14015

    Google Scholar 

  • Hui BM, Song C, Liu Y, Li C (2017) Exploring the molecular basis of adaptive evolution in hydrothermal vent crab Austinograea alayseaeby transcriptome analysis. PLoS One 12(5):e0178417

  • Ji PF, Yao CL, Wang ZY (2009) Immune response and gene expression in shrimp (Litopenaeus vannamei) hemocytes and hepatopancreas against some pathogen-associated molecular patterns. Fish Shellfish Immun 27(4):563

    Google Scholar 

  • Jin W, Riley RM, Wolfinger RD, White KP, Passadorgurgel G, Gibson G (2001) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 29(4):389–395

    Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T (2007) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36(suppl_1):D480–D484

    Google Scholar 

  • Kathiresan K, Bingham BL (2001) Biology of mangroves and mangrove Ecosystems. Advmarbiol 40(01):81–251

    Google Scholar 

  • Khademi S, Guarino LA, Watanabe H, Tokuda G, Meyer EF (2002) Structure of an endoglucanase from termite, Nasutitermes takasagoensis. Acta Crystallogr A 58(4):653–659

    Google Scholar 

  • Kumagai Y, Satoh T, Inoue A, Ojima T (2013) Enzymatic properties and primary structures of two α-amylase isozymes from the Pacific abalone Haliotis discus hannai. Comp Biochem Physiol Biochem Mol Biol 164(2):80–88

    Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549

    Google Scholar 

  • Levy JN, Gemmill RM, Doane WW (1985) Molecular cloning of alpha-amylase genes from Drosophila melanogaster. II. Clone organization and verification. Genetics 110(2):313–324

    Google Scholar 

  • Linton SM (2021) Presence and activity of endo-β-1,4-mannase, an important digestive carbohydrase within the digestive fluid of terrestrial crustaceans. J Comp Physiol B 191(2):1–11

    Google Scholar 

  • Lou F, Gao T, Cai S, Han Z (2017) De novo assembly and annotation of the whole transcriptome of Oratosquilla oratoria. Mar Genomics 38:17–20

    Google Scholar 

  • Miyake K, Ura K, Chida S, Ueda Y, Baba Y, Kusube T, Yanai S (2019) Guaiacol oxidation activity of herbivorous land crabs, Chiromantes haematocheir and Chiromantes dehaani. J Biosci Bioeng 128(3):316–322

    Google Scholar 

  • Moshtaghi A, Rahi ML, Nguyen VT, Mather PB, Hurwood DA (2016) A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense). Peerj 4(10):e2520

    Google Scholar 

  • Peixoto S, Silva E, Costa CB, Nery RC, Rodrigues F, Silva JF, Bezerra R, Soares R (2017) Effect of feeding frequency on growth and enzymatic activity of Litopenaeus vannamei during nursery phase in biofloc system. Aquac Nutr 24(1):579–585

    Google Scholar 

  • Ravichandran S, Kannupandi T, Kathiresan K (2006) Mangrove leaf litter processing by Sesarmid crabs. Cey. J Sci (Bio Sci) 35(2):107–114

    Google Scholar 

  • Ravichandran S, Soundarapandian P, Kannupandi T (2011) Zonation and distribution of crabs in Pichavaram mangrove swamp, southeat scoast of India. Clin Oral Invest 4(1):42–49

    Google Scholar 

  • Scrivener AM, Slaytor M (1994) Properties of the endogenous cellulase from Panesthia cribrata saussure and purification of major endo-β-1,4-glucanase components. Insect Biochem Mol Biol 24(3):223–231

    Google Scholar 

  • Sellos D, Moal J, Degremont L, Huvet A, Daniel JY, Nicoulaud S, Boudry P, Samain JF, Van WA (2003) Structure of amylase genes in populations of Pacific Cupped oyster (Crassostrea gigas): tissue expression and allelic polymorphism. Mar Biotechnol 5(4):360

    Google Scholar 

  • Štefan J, Gabriško M (2016) Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family. Cell Mol Life Sci 73(14):1–19

    Google Scholar 

  • Strauss M (2003) The transformation of wine yeasts with glucanase, xylanase and pectinase genes for improved clarification and filterability of wine. Adv Space Res 50(5):560–575

    Google Scholar 

  • Sun M, Ting YL, Liu Y, Chin SL, Wang L (2016) Transcriptome assembly and expression profiling of molecular responses to cadmium toxicity in hepatopancreas of the freshwater crab Sinopotamon henanense. Sci Rep-Uk 6:19405

    Google Scholar 

  • Tanimura A, Liu W, Yamada K, Kishida T, Toyohara H (2013) Animal cellulases with a focus on aquatic invertebrates. Fish Sci 79(1):1–13

    Google Scholar 

  • Van WA, Sellos D (1996) Cloning and sequencing analysis of three amylase cDNAs in the shrimp Penaeus vannamei (Crustacea decapoda): evolutionary aspects. J Mol Evol 42(5):543–551

    Google Scholar 

  • Van WA, Sellos D (2003) Highly variable polymorphism of the alpha-amylase gene family in Litopenaeus vannamei (Crustacea Decapoda). J Mol Evol 57(6):659–671

    Google Scholar 

  • Wang Z, Shi X, Tao Y, Wu Q, Bai Y, Guo H, Tang D (2018a) The complete mitochondrial genome of Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) and comparison with other Brachyuran crabs. Genomics 111(4):799–807

    Google Scholar 

  • Wang Z, Sun L, Guan W, Zhou C, Tang B, Cheng Y, Huang J, Xuan F (2018b) De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II). BMC Genet 19(1):3

    Google Scholar 

  • Wang Z, Wang Z, Shi X, Wu Q, Tao Y, Guo H, Ji C, Bai Y (2018c) Complete mitochondrial genome of Parasesarma affine (Brachyura: Sesarmidae): Gene rearrangements in Sesarmidae and phylogenetic analysis of the Brachyura. Int J Biol Macromol 118:31–40

    Google Scholar 

  • Wang Z, Tang D, Guo H, Shen C, Wu L, Luo Y (2020) Evolution of digestive enzyme genes associated with dietary diversity of crabs. Genetica 148(8):87–99

    Google Scholar 

  • Wei J, Zhang X, Yu Y, Li F, Xiang J (2014) RNA-Seq reveals the dynamic and diverse features of digestive enzymes during early development of Pacific white shrimp Litopenaeus vannamei. Comp Biochem Physiol Part D Genomics Proteomics 11(5):37–44

    Google Scholar 

  • Werry J, Lee S (2005) Grapsid crabs mediate link between mangrove litter production and estuarine planktonic food chains. Mar Ecol Prog 293(1):165–176

    Google Scholar 

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(Web Server issue):W293

  • Zhu B, Tang L, Yu Y, Yu H, Wang L, Qian C, Wei G, Liu C (2017) Identification of ecdysteroid receptor-mediated signaling pathways in the hepatopancreas of the red swamp crayfish, Procambarus clarkii. Gen Comp Endocrinol 246:372–381

    Google Scholar 

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Funding

This study was funded by the National Natural Science Foundation of China (grant number 31702014), and Doctoral Scientific Research Foundation of Yancheng Teachers University to ZFW, and Open Foundation of Jiangsu Key Laboratory for Bioresources of Saline Soils (grant number JKLBS2019006).

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CCS, LW and ZFW designed and conceived the experiment. ZFW, LW, DT and CCS performed the data analysis and draft the manuscript. All authors read and approved the final manuscript.

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Correspondence to Zhengfei Wang.

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Zhengfei Wang declares that he has no conflict of interest. Dan Tang declares that she has no conflict of interest. Chenchen Shen declares that she has no conflict of interest. Lv Wu declares that she has no conflict of interest.

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The sampling location was not privately-owned or protected, and field sampling did not involve protected species.

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Wang, Z., Tang, D., Shen, C. et al. Identification of Genes Involved in Digestion from Transcriptome of Parasesarma pictum and Parasesarma affine Hepatopancreas. Thalassas 38, 93–101 (2022). https://doi.org/10.1007/s41208-021-00296-2

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  • DOI: https://doi.org/10.1007/s41208-021-00296-2

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