Comparative de novo assembly and annotation of mantle tissue transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus)

Andrews Bierne, 2003, Introgression patterns in a mosaic hybrid zone between Mytilus edulis and Mytilus galloprovoincialis, Mol. Ecol., 12, 447, 10.1046/j.1365-294X.2003.01730.x Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinfiormatics., 30, 2114, 10.1093/bioinformatics/btu170 Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics., 21, 3674, 10.1093/bioinformatics/bti610 Freer, 2013, Biomineral proteins from Mytilus edulis mantle tissue transcriptome, Mar. Biotechnol., 16, 34, 10.1007/s10126-013-9516-1 Grabherr, 2011, Full-length transcriptome assembly from RNA-seq data without a reference genome, Nat. Biotechnol., 29, 644, 10.1038/nbt.1883 Kijewsk, 2006, Introgression and mitochondrial heteroplasmy in the Baltic populations of mussels Mytilus trossulus and M. edulis, Marine Biology, 149, 1371, 10.1007/s00227-006-0316-2 Koehn, 1991, The genetics and taxonomy of species in the genus Mytilus, Aquaculture, 94, 125, 10.1016/0044-8486(91)90114-M Langmead, 2012, Fast gapped-read alignment with Bowtie2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Larsson, 2016, Regional genetic differentiation in the blue mussel from the Baltic Sea area, Estuar. Coast. Shelf Sci. Lesser, 2016, Transcriptomic resources for the rocky intertidal blue mussel Mytilus edulis from the Gulf of Maine, J. Shellfish Res., 35, 435, 10.2983/035.035.0218 Li, 2006, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics., 22, 1658, 10.1093/bioinformatics/btl158 Moreira, 2015, RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues, BMC Genomics, 16, 728, 10.1186/s12864-015-1817-5 Murgarella, 2016, A first insight into the genome of the filter-feeder mussel Mytilus galloprovincialis, PLoS One, 11, 10.1371/journal.pone.0151561 Philipp, 2012, Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis, PLoS One, 7, 10.1371/journal.pone.0033091 Riginos, 2005, Local adaptation and species 1segregation in two mussel (Mytilus edulis x Mytilus trossulus) hybrid zones, Mol. Ecol., 14, 381, 10.1111/j.1365-294X.2004.02379.x Riginos, 2002, Evidence for selection at multiple allozyme loci across a mussel hybrid zone, Molecular Biolology and Evolution, 19, 347, 10.1093/oxfordjournals.molbev.a004088 Riisgård, 2014, Dwarfism of blue mussels in the low saline Baltic Sea—growth to the lower salinity limit, Mar Ecol-Prog Ser, 517, 181, 10.3354/meps11011 Simão, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics., 31, 3210, 10.1093/bioinformatics/btv351 Stuckas, 2009, Evolutionary implications of discordant clines across the Baltic Mytilus hybrid zone (Mytilus edulis, Mytilus trossulus), Heredity., 103, 146, 10.1038/hdy.2009.37 Stuckas, 2017, Combining hydrodynamic modelling with genetics: can passive larval drift shape the genetic structure of Baltic Mytilus populations?, Mol. Ecol., 26, 2765, 10.1111/mec.14075 Thomsen, 2015, Impact of seawater arbonate chemistry on the calcification of marine bivalves, Biogeosciences., 12, 4209, 10.5194/bg-12-4209-2015 Utermann, 2018, Combined genotyping, microbial diversity and metabolite profiling studies on farmed Mytilus spp. from Kiel Fjord, Sci. Rep., 8, 7983, 10.1038/s41598-018-26177-y Waterhouse, 2018, BUSCO applications from quality assessments to gene prediction and phylogenomics, Mol. Biol. Evol., 35, 543, 10.1093/molbev/msx319 Yilmaz, 2011, Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications, Nat. Biotechnol., 29, 415, 10.1038/nbt.1823 Zbawicka, 2014, New SNP markers reveal lergely concordant clinal variation across the hybrid zone between Mytilus spp. in the Baltic Sea, Aquat. Biol., 21, 25, 10.3354/ab00566