Adamson KJ, Wang T, Zhao M, Bell F, Kuballa AV, Storey KB, Cummins SF (2015) Molecular insights into land snail neuropeptides through transcriptome and comparative gene analysis. BMC Genom 16:308. https://doi.org/10.1186/s12864-015-1510-8

Article  CAS  Google Scholar 

Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P et al (2017) Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Nat Comm 8:15451. https://doi.org/10.1038/ncomms15451

Article  CAS  Google Scholar 

Amin S, Prentis PJ, Gilding EK, Pavasovic A (2014) Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers. BMC Res Not 7:488. https://doi.org/10.1186/1756-0500-7-488

Article  PubMed Central  Google Scholar 

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25:25–29. https://doi.org/10.1038/75556

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bertucci A, Pierron F, Thebault J, Klopp C, Bellec J, Gonzalez P, Baudrimont M (2017) Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France. Environ Sci Poll Res 24:27145–27159. https://doi.org/10.1007/s11356-017-0294-6

Article  CAS  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brandies P, Peel E, Hogg CJ, Belov K (2019) The value of reference genomes in the conservation of threatened species. Genes (basel) 10:846. https://doi.org/10.3390/10110846

Article  CAS  PubMed  Google Scholar 

Cai H, Li Q, Fang X, Li J, Curtis NE, Altenburger A, Shibata T, Feng M, Maeda T, Schwartz JA, Shigenobu S, Lundholm N, Nishiyama T, Yang H, Hasebe M, Li S, Pierce SK, Wang J (2019) A draft genome assembly of the solar-powered sea slug Elysia chlorotica. Sci Data 6:190022. https://doi.org/10.1038/sdata.2019.22

Article  PubMed  PubMed Central  Google Scholar 

Campbell EM, Ball A, Hoppler S, Bowman AS (2008) Invertebrate aquaporins: a review. J Comp Physiol B 178:935–955. https://doi.org/10.1007/s00360-008-0288-2

Article  CAS  PubMed  Google Scholar 

Caurcel C, Laetsch DR, Challis R, Kumar S, Gharbi K, Blaxter M 2021. MolluscDB: a genome and transcriptome database for molluscs. Phil Trans R Soc B 376. https://doi.org/10.1098/rstb.2020.0157

Challis RJ, Kumar S, Stevens L, Blaxter M (2017). GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species. Database bax039. https://doi.org/10.1093/database/bax039

Che R, Sun Y, Wang R, Xu T (2014) Transcriptomic analysis of endangered Chinese Salamander: Identification of immune, sex and reproduction-related genes and genetic markers. PLoS ONE 9:e87940. https://doi.org/10.1371/journal.pone.0087940

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cho A, Seok SH (2013) Ethical guidelines for use of experimental animals in biomedical research. J Bacteriol Virol 43:18–26. https://doi.org/10.4167/jbv.2013.43.1.18

Article  Google Scholar 

Czypionka T, Krugman T, Altmuller J, Blaustein L, Steinfartz S, Templeton AR, Nolte AW (2015) Ecological transcriptomics- a non-lethal sampling approach for endangered fire salamanders. Methods Ecol Evol 6:1417–1425. https://doi.org/10.1111/2041-210X.12431

Article  Google Scholar 

Dhanasekaran DN, Reddy EP (2008) JNK signaling in apoptosis. Oncogene 27:6245–6251. https://doi.org/10.1038/onc.2008.301

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF (2013) KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase- an open access and searchable database of a coral genome. BMC Genom 14:509. https://doi.org/10.1186/1471-2164-14-509

Article  CAS  Google Scholar 

Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132. https://doi.org/10.1038/sj.hdy.6801001

Article  CAS  PubMed  Google Scholar 

Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II Error Probabilities Genome Res 8:186–194

Article  CAS  PubMed  Google Scholar 

Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I Accuracy Assessment Genome Res 8:175–185. https://doi.org/10.1101/gr.8.3.175

Article  CAS  PubMed  Google Scholar 

Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103–107. https://doi.org/10.1016/0168-9525(89)90039-5

Article  CAS  PubMed  Google Scholar 

Gaitanaki C, Kefaloyianni E, Marmari A, Beis I (2004) Various stressors rapidly activate the p38-MAPK signaling pathway in Mytilus galloprovincialis (Lam.). Mol Cell Biochem 260:119–127. https://doi.org/10.1023/b.mcbi.0000026064.73671.91

Article  CAS  PubMed  Google Scholar 

Gomes-dos-Santos A, Machado AM, Castro LFC, Prie V, Teixeira A, Lopes-Lima M, Froufe E (2022) The gill transcriptome of threatened European freshwater mussels. Sci Data 9:494. https://doi.org/10.1038/s41597-022-01613-x

Article  PubMed  PubMed Central  Google Scholar 

Gorbushin AM, Borisova EA (2015) Lectin-like molecules in transcriptome of Littorina littorea hemocytes. Dev Comp Immunol 48:210–220. https://doi.org/10.1016/j.dci.2014.10.007

Article  CAS  PubMed  Google Scholar 

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29:644–652. https://doi.org/10.1038/nbt.1883

Article  CAS  Google Scholar 

Guerin MN, Weinstein DJ, Bracht JR (2019) Stress adapted Mollusca and Nematoda exhibit convergently expanded Hsp70 and AIG1 gene families. J Mol Evol 87:289–297. https://doi.org/10.1007/s00239-019-09900-9

Article  CAS  PubMed  Google Scholar 

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protocols 8:1494–1512. https://doi.org/10.1038/nprot.2013.084

Article  CAS  PubMed  Google Scholar 

Hill DP, Smith B, McAndrews-Hill MS, Blake JA (2008) Gene Ontology annotations: what they mean and where they come from. BMC Bioinform 9:S2. https://doi.org/10.1186/1471-2105-9-S5-S2

Article  CAS  Google Scholar 

Hogg CJ, Ottewell K, Latch P, Rossetto M, Biggs J, Gilbert A, Richmond S, Belov K (2022) Threatened species initiative: Empowering conservation action using genomic resources. Proc Natl Acad Sci 19:e2115643118. https://doi.org/10.1073/pnas.2115643118

Article  Google Scholar 

Holzer M, Marz M (2019) De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers. Gigascience 8:giz039. https://doi.org/10.1093/gigascience/giz039

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hsiao C, Lin HH, Kang SR, Hung CY, Sun PY, Yu CC, Toh KL, Yu PJ, Ju YT et al (2022) Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer. PLoS ONE 17:e0265311. https://doi.org/10.1371/journal.pone.0265311

Article  CAS  PubMed