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2016
Z. - Q. Du and Du, Z. - Q., Comparative transcriptome analysis reveals three potential antiviral signaling pathways in lymph organ tissue of the red swamp crayfish, Procambarus clarkii, vol. 15, no. 4, p. -, 2016.
Conflicts of interest The authors declare no conflicts of interest. ACKNOWLEDGMENTS Research supported by the National Natural Science Foundation of China (Grant #31460698). REFERENCES Agaisse H, Perrimon N, et al (2004). The roles of JAK/STAT signaling in Drosophila immune responses. Immunol. Rev. 198: 72-82. http://dx.doi.org/10.1111/j.0105-2896.2004.0133.x Ali MY, Pavasovic A, Mather PB, Prentis PJ, et al (2015). Transcriptome analysis and characterisation of gill-expressed carbonic anhydrase and other key osmoregulatory genes in freshwater crayfish Cherax quadricarinatus. Data Brief 5: 187-193. http://dx.doi.org/10.1016/j.dib.2015.08.018 Banani H, Marcet-Houben M, Ballester AR, Abbruscato P, et al (2016). Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum. BMC Genomics 17: 19. http://dx.doi.org/10.1186/s12864-015-2347-x Chen K, Li E, Li T, Xu C, et al (2015a). Transcriptome and molecular pathway analysis of the hepatopancreas in the Pacific white shrimp Litopenaeus vannamei under chronic low-salinity stress. PLoS One 10: e0131503. http://dx.doi.org/10.1371/journal.pone.0131503 Chen K, Li E, Xu Z, Li T, et al (2015b). Comparative transcriptome analysis in the hepatopancreas tissue of Pacific white shrimp Litopenaeus vannamei fed different lipid sources at low salinity. PLoS One 10: e0144889. http://dx.doi.org/10.1371/journal.pone.0144889 Christie AE, Chi M, Lameyer TJ, Pascual MG, et al (2015). Neuropeptidergic signaling in the American lobster Homarus americanus: new insights from high-throughput nucleotide sequencing. PLoS One 10: e0145964. http://dx.doi.org/10.1371/journal.pone.0145964 Dedeine F, Weinert LA, Bigot D, Josse T, et al (2015). Comparative analysis of transcriptomes from secondary reproductives of three Reticulitermes termite species. PLoS One 10: e0145596. http://dx.doi.org/10.1371/journal.pone.0145596 Di Lena P, Domeniconi G, Margara L, Moro G, et al (2015). GOTA: GO term annotation of biomedical literature. BMC Bioinformatics 16: 346. http://dx.doi.org/10.1186/s12859-015-0777-8 Du Z, Jin Y, Ren D, et al (2016). In-depth comparative transcriptome analysis of intestines of red swamp crayfish, Procambarus clarkii, infected with WSSV. Sci. Rep. 6: 26780. http://dx.doi.org/10.1038/srep26780 Du ZQ, Jin YH, et al (2015). Molecular characterization and antibacterial activity analysis of two novel penaeidin isoforms from Pacific white shrimp, Litopenaeus vannamei. Appl. Biochem. Biotechnol. 177: 1607-1620. http://dx.doi.org/10.1007/s12010-015-1840-7 Du ZQ, Li XC, Wang ZH, Zhao XF, et al (2010). A single WAP domain (SWD)-containing protein with antipathogenic relevance in red swamp crayfish, Procambarus clarkii. Fish Shellfish Immunol. 28: 134-142. http://dx.doi.org/10.1016/j.fsi.2009.10.009 Du ZQ, Lan JF, Weng YD, Zhao XF, et al (2013). BAX inhibitor-1 silencing suppresses white spot syndrome virus replication in red swamp crayfish, Procambarus clarkii. Fish Shellfish Immunol. 35: 46-53. http://dx.doi.org/10.1016/j.fsi.2013.03.376 Ermolaeva MA, Schumacher B, et al (2014). Insights from the worm: the C. elegans model for innate immunity. Semin. Immunol. 26: 303-309. http://dx.doi.org/10.1016/j.smim.2014.04.005 Feng D, Li Q, Yu H, Zhao X, et al (2015). Comparative transcriptome analysis of the Pacific oyster Crassostrea gigas characterized by shell colors: identification of genetic bases potentially involved in pigmentation. PLoS One 10: e0145257. http://dx.doi.org/10.1371/journal.pone.0145257 Gao Y, Zhang X, Wei J, Sun X, et al (2015). Whole transcriptome analysis provides insights into molecular mechanisms for molting in Litopenaeus vannamei. PLoS One 10: e0144350. http://dx.doi.org/10.1371/journal.pone.0144350 Gupta P, Goel R, Agarwal AV, Asif MH, et al (2015). Comparative transcriptome analysis of different chemotypes elucidates withanolide biosynthesis pathway from medicinal plant Withania somnifera. Sci. Rep. 5: 18611. http://dx.doi.org/10.1038/srep18611 Gurskaya OY, Dobryakova YV, Markevich VA, et al (2015). A role of the Wnt signaling in the regulation of brain function. Zh. Vyssh. Nerv. Deiat. Im. I P Pavlova 65: 387-399. Harel S, Higgins CA, Cerise JE, Dai Z, et al (2015). Pharmacologic inhibition of JAK-STAT signaling promotes hair growth. Sci. Adv. 1: e1500973. http://dx.doi.org/10.1126/sciadv.1500973 He W, Zhuang H, Fu Y, Guo L, et al (2015). De novo transcriptome assembly of a Chinese locoweed (Oxytropis ochrocephala) species provides insights into genes associated with drought, salinity, and cold tolerance. Front. Plant Sci. 6: 1086. http://dx.doi.org/10.3389/fpls.2015.01086 Jiang H, Xing Z, Lu W, Qian Z, et al (2014). Transcriptome analysis of red swamp crawfish Procambarus clarkii reveals genes involved in gonadal development. PLoS One 9: e105122. http://dx.doi.org/10.1371/journal.pone.0105122 Lai Z, Lin Y, et al (2013). Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using Illumina paired-end sequencing. BMC Genomics 14: 561. http://dx.doi.org/10.1186/1471-2164-14-561 Langmead B, Salzberg SL, et al (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9: 357-359. http://dx.doi.org/10.1038/nmeth.1923 Leng X, Jia H, Sun X, Shangguan L, et al (2015). Comparative transcriptome analysis of grapevine in response to copper stress. Sci. Rep. 5: 17749. http://dx.doi.org/10.1038/srep17749 Li D, Liang Y, Wang X, Wang L, et al (2015). Transcriptomic analysis of Musca domestica to reveal key genes of the prophenoloxidase-activating system. G3 (Bethesda) 5: 1827-1841. http://dx.doi.org/10.1534/g3.115.016899 Li S, Zhang X, Sun Z, Li F, et al (2013). Transcriptome analysis on Chinese shrimp Fenneropenaeus chinensis during WSSV acute infection. PLoS One 8: e58627. http://dx.doi.org/10.1371/journal.pone.0058627 Li ST, Zhang P, Zhang M, Fu CH, et al (2012a). Transcriptional profile of Taxus chinensis cells in response to methyl jasmonate. BMC Genomics 13: 295-305. http://dx.doi.org/10.1186/1471-2164-13-295 Li Y, Deng W, Yang K, Wang W, et al (2012b). The expression of prophenoloxidase mRNA in red swamp crayfish, Procambarus clarkii, when it was challenged. Genomics 99: 355-360. http://dx.doi.org/10.1016/j.ygeno.2012.04.001 Livak KJ, Schmittgen TD, et al (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Δ Δ C(T)) Method. Methods 25: 402-408. http://dx.doi.org/10.1006/meth.2001.1262 Manfrin C, Tom M, De Moro G, Gerdol M, et al (2015). The eyestalk transcriptome of red swamp crayfish Procambarus clarkii. Gene 557: 28-34. http://dx.doi.org/10.1016/j.gene.2014.12.001 Mao X, Cai T, Olyarchuk JG, Wei L, et al (2005). Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21: 3787-3793. http://dx.doi.org/10.1093/bioinformatics/bti430 Martin JA, Wang Z, et al (2011). Next-generation transcriptome assembly. Nat. Rev. Genet. 12: 671-682. http://dx.doi.org/10.1038/nrg3068 Mortazavi A, Williams BA, McCue K, Schaeffer L, et al (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628. http://dx.doi.org/10.1038/nmeth.1226 Mousavi S, Alisoltani A, Shiran B, Fallahi H, et al (2014). De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress. PLoS One 9: e104541. http://dx.doi.org/10.1371/journal.pone.0104541 Shen H, Hu Y, Ma Y, Zhou X, et al (2014). In-depth transcriptome analysis of the red swamp crayfish Procambarus clarkii. PLoS One 9: e110548. http://dx.doi.org/10.1371/journal.pone.0110548 Sun C, Shao HL, Zhang XW, Zhao XF, et al (2011). Molecular cloning and expression analysis of signal transducer and activator of transcription (STAT) from the Chinese white shrimp Fenneropenaeus chinensis. Mol. Biol. Rep. 38: 5313-5319. http://dx.doi.org/10.1007/s11033-011-0681-x Taffoni C, Pujol N, et al (2015). Mechanisms of innate immunity in C. elegans epidermis. Tissue Barriers 3: e1078432. http://dx.doi.org/10.1080/21688370.2015.1078432 Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, et al (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41. http://dx.doi.org/10.1186/1471-2105-4-41 Wang P, Wang J, Su YQ, Mao Y, et al (2016). Transcriptome analysis of the Larimichthys crocea liver in response to Cryptocaryon irritans. Fish Shellfish Immunol. 48: 1-11. http://dx.doi.org/10.1016/j.fsi.2015.11.011 Young MD, Wakefield MJ, Smyth GK, Oshlack A, et al (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 11: R14. http://dx.doi.org/10.1186/gb-2010-11-2-r14 Zeng DG, Chen XL, Xie DX, Zhao YZ, et al (2015). Identification of highly expressed host microRNAs that respond to white spot syndrome virus infection in the Pacific white shrimp Litopenaeus vannamei (Penaeidae). Genet. Mol. Res. 14: 4818-4828. http://dx.doi.org/10.4238/2015.May.11.14
Z. - Q. Du and Du, Z. - Q., Comparative transcriptome analysis reveals three potential antiviral signaling pathways in lymph organ tissue of the red swamp crayfish, Procambarus clarkii, vol. 15, no. 4, p. -, 2016.
Conflicts of interest The authors declare no conflicts of interest. ACKNOWLEDGMENTS Research supported by the National Natural Science Foundation of China (Grant #31460698). REFERENCES Agaisse H, Perrimon N, et al (2004). The roles of JAK/STAT signaling in Drosophila immune responses. Immunol. Rev. 198: 72-82. http://dx.doi.org/10.1111/j.0105-2896.2004.0133.x Ali MY, Pavasovic A, Mather PB, Prentis PJ, et al (2015). Transcriptome analysis and characterisation of gill-expressed carbonic anhydrase and other key osmoregulatory genes in freshwater crayfish Cherax quadricarinatus. Data Brief 5: 187-193. http://dx.doi.org/10.1016/j.dib.2015.08.018 Banani H, Marcet-Houben M, Ballester AR, Abbruscato P, et al (2016). Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum. BMC Genomics 17: 19. http://dx.doi.org/10.1186/s12864-015-2347-x Chen K, Li E, Li T, Xu C, et al (2015a). Transcriptome and molecular pathway analysis of the hepatopancreas in the Pacific white shrimp Litopenaeus vannamei under chronic low-salinity stress. PLoS One 10: e0131503. http://dx.doi.org/10.1371/journal.pone.0131503 Chen K, Li E, Xu Z, Li T, et al (2015b). Comparative transcriptome analysis in the hepatopancreas tissue of Pacific white shrimp Litopenaeus vannamei fed different lipid sources at low salinity. PLoS One 10: e0144889. http://dx.doi.org/10.1371/journal.pone.0144889 Christie AE, Chi M, Lameyer TJ, Pascual MG, et al (2015). Neuropeptidergic signaling in the American lobster Homarus americanus: new insights from high-throughput nucleotide sequencing. PLoS One 10: e0145964. http://dx.doi.org/10.1371/journal.pone.0145964 Dedeine F, Weinert LA, Bigot D, Josse T, et al (2015). Comparative analysis of transcriptomes from secondary reproductives of three Reticulitermes termite species. PLoS One 10: e0145596. http://dx.doi.org/10.1371/journal.pone.0145596 Di Lena P, Domeniconi G, Margara L, Moro G, et al (2015). GOTA: GO term annotation of biomedical literature. BMC Bioinformatics 16: 346. http://dx.doi.org/10.1186/s12859-015-0777-8 Du Z, Jin Y, Ren D, et al (2016). In-depth comparative transcriptome analysis of intestines of red swamp crayfish, Procambarus clarkii, infected with WSSV. Sci. Rep. 6: 26780. http://dx.doi.org/10.1038/srep26780 Du ZQ, Jin YH, et al (2015). Molecular characterization and antibacterial activity analysis of two novel penaeidin isoforms from Pacific white shrimp, Litopenaeus vannamei. Appl. Biochem. Biotechnol. 177: 1607-1620. http://dx.doi.org/10.1007/s12010-015-1840-7 Du ZQ, Li XC, Wang ZH, Zhao XF, et al (2010). A single WAP domain (SWD)-containing protein with antipathogenic relevance in red swamp crayfish, Procambarus clarkii. Fish Shellfish Immunol. 28: 134-142. http://dx.doi.org/10.1016/j.fsi.2009.10.009 Du ZQ, Lan JF, Weng YD, Zhao XF, et al (2013). BAX inhibitor-1 silencing suppresses white spot syndrome virus replication in red swamp crayfish, Procambarus clarkii. Fish Shellfish Immunol. 35: 46-53. http://dx.doi.org/10.1016/j.fsi.2013.03.376 Ermolaeva MA, Schumacher B, et al (2014). Insights from the worm: the C. elegans model for innate immunity. Semin. Immunol. 26: 303-309. http://dx.doi.org/10.1016/j.smim.2014.04.005 Feng D, Li Q, Yu H, Zhao X, et al (2015). Comparative transcriptome analysis of the Pacific oyster Crassostrea gigas characterized by shell colors: identification of genetic bases potentially involved in pigmentation. PLoS One 10: e0145257. http://dx.doi.org/10.1371/journal.pone.0145257 Gao Y, Zhang X, Wei J, Sun X, et al (2015). Whole transcriptome analysis provides insights into molecular mechanisms for molting in Litopenaeus vannamei. PLoS One 10: e0144350. http://dx.doi.org/10.1371/journal.pone.0144350 Gupta P, Goel R, Agarwal AV, Asif MH, et al (2015). Comparative transcriptome analysis of different chemotypes elucidates withanolide biosynthesis pathway from medicinal plant Withania somnifera. Sci. Rep. 5: 18611. http://dx.doi.org/10.1038/srep18611 Gurskaya OY, Dobryakova YV, Markevich VA, et al (2015). A role of the Wnt signaling in the regulation of brain function. Zh. Vyssh. Nerv. Deiat. Im. I P Pavlova 65: 387-399. Harel S, Higgins CA, Cerise JE, Dai Z, et al (2015). Pharmacologic inhibition of JAK-STAT signaling promotes hair growth. Sci. Adv. 1: e1500973. http://dx.doi.org/10.1126/sciadv.1500973 He W, Zhuang H, Fu Y, Guo L, et al (2015). De novo transcriptome assembly of a Chinese locoweed (Oxytropis ochrocephala) species provides insights into genes associated with drought, salinity, and cold tolerance. Front. Plant Sci. 6: 1086. http://dx.doi.org/10.3389/fpls.2015.01086 Jiang H, Xing Z, Lu W, Qian Z, et al (2014). Transcriptome analysis of red swamp crawfish Procambarus clarkii reveals genes involved in gonadal development. PLoS One 9: e105122. http://dx.doi.org/10.1371/journal.pone.0105122 Lai Z, Lin Y, et al (2013). Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using Illumina paired-end sequencing. BMC Genomics 14: 561. http://dx.doi.org/10.1186/1471-2164-14-561 Langmead B, Salzberg SL, et al (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9: 357-359. http://dx.doi.org/10.1038/nmeth.1923 Leng X, Jia H, Sun X, Shangguan L, et al (2015). Comparative transcriptome analysis of grapevine in response to copper stress. Sci. Rep. 5: 17749. http://dx.doi.org/10.1038/srep17749 Li D, Liang Y, Wang X, Wang L, et al (2015). Transcriptomic analysis of Musca domestica to reveal key genes of the prophenoloxidase-activating system. G3 (Bethesda) 5: 1827-1841. http://dx.doi.org/10.1534/g3.115.016899 Li S, Zhang X, Sun Z, Li F, et al (2013). Transcriptome analysis on Chinese shrimp Fenneropenaeus chinensis during WSSV acute infection. PLoS One 8: e58627. http://dx.doi.org/10.1371/journal.pone.0058627 Li ST, Zhang P, Zhang M, Fu CH, et al (2012a). Transcriptional profile of Taxus chinensis cells in response to methyl jasmonate. BMC Genomics 13: 295-305. http://dx.doi.org/10.1186/1471-2164-13-295 Li Y, Deng W, Yang K, Wang W, et al (2012b). The expression of prophenoloxidase mRNA in red swamp crayfish, Procambarus clarkii, when it was challenged. Genomics 99: 355-360. http://dx.doi.org/10.1016/j.ygeno.2012.04.001 Livak KJ, Schmittgen TD, et al (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Δ Δ C(T)) Method. Methods 25: 402-408. http://dx.doi.org/10.1006/meth.2001.1262 Manfrin C, Tom M, De Moro G, Gerdol M, et al (2015). The eyestalk transcriptome of red swamp crayfish Procambarus clarkii. Gene 557: 28-34. http://dx.doi.org/10.1016/j.gene.2014.12.001 Mao X, Cai T, Olyarchuk JG, Wei L, et al (2005). Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21: 3787-3793. http://dx.doi.org/10.1093/bioinformatics/bti430 Martin JA, Wang Z, et al (2011). Next-generation transcriptome assembly. Nat. Rev. Genet. 12: 671-682. http://dx.doi.org/10.1038/nrg3068 Mortazavi A, Williams BA, McCue K, Schaeffer L, et al (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628. http://dx.doi.org/10.1038/nmeth.1226 Mousavi S, Alisoltani A, Shiran B, Fallahi H, et al (2014). De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress. PLoS One 9: e104541. http://dx.doi.org/10.1371/journal.pone.0104541 Shen H, Hu Y, Ma Y, Zhou X, et al (2014). In-depth transcriptome analysis of the red swamp crayfish Procambarus clarkii. PLoS One 9: e110548. http://dx.doi.org/10.1371/journal.pone.0110548 Sun C, Shao HL, Zhang XW, Zhao XF, et al (2011). Molecular cloning and expression analysis of signal transducer and activator of transcription (STAT) from the Chinese white shrimp Fenneropenaeus chinensis. Mol. Biol. Rep. 38: 5313-5319. http://dx.doi.org/10.1007/s11033-011-0681-x Taffoni C, Pujol N, et al (2015). Mechanisms of innate immunity in C. elegans epidermis. Tissue Barriers 3: e1078432. http://dx.doi.org/10.1080/21688370.2015.1078432 Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, et al (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41. http://dx.doi.org/10.1186/1471-2105-4-41 Wang P, Wang J, Su YQ, Mao Y, et al (2016). Transcriptome analysis of the Larimichthys crocea liver in response to Cryptocaryon irritans. Fish Shellfish Immunol. 48: 1-11. http://dx.doi.org/10.1016/j.fsi.2015.11.011 Young MD, Wakefield MJ, Smyth GK, Oshlack A, et al (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 11: R14. http://dx.doi.org/10.1186/gb-2010-11-2-r14 Zeng DG, Chen XL, Xie DX, Zhao YZ, et al (2015). Identification of highly expressed host microRNAs that respond to white spot syndrome virus infection in the Pacific white shrimp Litopenaeus vannamei (Penaeidae). Genet. Mol. Res. 14: 4818-4828. http://dx.doi.org/10.4238/2015.May.11.14