Iso-seq analysis and functional annotation of the Santa Fe cave crayfish (Procambarus erythrops) transcriptome
Tài liệu tham khảo
American Veterinary Medical Association (AVMA)
Al Kaddissi, 2012, Are antioxidant and transcriptional responses useful for discriminating between chemo- and radiotoxicity of uranium in the crayfish Procambarus clarkii?, Ecotoxicol. Environ. Saf., 80, 266, 10.1016/j.ecoenv.2012.03.010
Breinholt, 2012
Cho, 2014, High-resolution transcriptome analysis with long-read RNA sequencing, PLoS One, 9, 10.1371/journal.pone.0108095
Chow, 2019, Utility of PacBio Iso-Seq for transcript and gene discovery in Hevea latex, J. Rubber Res., 22, 169, 10.1007/s42464-019-00026-7
Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610
Du, 2016, In-depth comparative transcriptome analysis of intestines of red swamp crayfish, Procambarus clarkii, infected with WSSV, Sci. Report., 6, 26780, 10.1038/srep26780
El-Din, 2013, Antiviral immunity in the red swamp crayfish, Procambarus clarkii: hemocyte production, proliferation and apoptosis, J. Egypt. Soc. Parasitol., 43, 71
Franz, 1994, Review of biologically significant caves and their faunas in Florida and South Georgia, Brimleyana, 20, 1
Huntley, 2015, The GOA database: gene ontology annotation updates for 2015, Nucleic Acids Res., 43, D1057, 10.1093/nar/gku1113
Kubec, 2019, Communication, behavior, and decision making in crayfish: a review, Zool. Anz., 278, 28, 10.1016/j.jcz.2018.10.009
Pootakham, 2020, A novel full-length transcriptome resource for black tiger shrimp (Penaeus monodon) developed using isoform sequencing (Iso-Seq), Front. Mar. Sci., 7, 172, 10.3389/fmars.2020.00172
Rhoads, 2015, PacBio sequencing and its applications, Genomics Proteomics Bioinforma., 13, 278, 10.1016/j.gpb.2015.08.002
Richman, 2015, Multiple drivers of decline in theglobal status of freshwater crayfish (Decapoda: Astacidea), Phil. Trans Roy. Soc. B, 370, 20140060, 10.1098/rstb.2014.0060
Sambrook, 2012
Shen, 2014, In-depth transcriptome analysis of the red swamp crayfish Procambarus clarkii, PLoS One, 9, 10.1371/journal.pone.0110548
Simão, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351
Speiser, 2014, Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms, BMC Bioinforma., 15, 350, 10.1186/s12859-014-0350-x
Stern, 2018, The evolution of gene expression underlying vision loss in cave animals, Mol. Biol. Evol., 35, 2005, 10.1093/molbev/msy106
Tardaguila, 2018, SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification, Genome Res., 28, 396, 10.1101/gr.222976.117
Theissinger, 2016, De Novo assembly and annotation of the freshwater crayfish Astacus astacus transcriptome, Mar. Genomics, 28, 7, 10.1016/j.margen.2016.02.006
Van Nguyen, 2009, PLAST: parallel local alignment search tool for database comparison, BMC Bioinforma., 10, 329, 10.1186/1471-2105-10-329
Vogt, 2018, Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: a review and perspectives, J. Biosci., 43, 189, 10.1007/s12038-018-9741-x
Walsh, 2001, Freshwater macrofauna in Florida karst habitats, 78
Wu, 2005, GMAP: a genomic mapping and alignment program for mRNA and EST sequences, Bioinformatics, 21, 1859, 10.1093/bioinformatics/bti310
