Genome guided, organ-specific transcriptome assembly of the European flounder (P. flesus) from the Baltic Sea

Nissling, A. & Larsson, R. Population specific sperm production in European flounder Platichthys flesus: Adaptation to salinity at spawning. J. Fish Biol. 93, 47–52, https://doi.org/10.1111/jfb.13667 (2018).Article 
PubMed 

Google Scholar 
Martinho, F., van der Veer, H. W., Cabral, H. N. & Pardal, M. A. Juvenile nursery colonization patterns for the European flounder (Platichthys flesus): A latitudinal approach. J. Sea Res. 84, 61–69, https://doi.org/10.1016/j.seares.2013.07.014 (2013).Article 
ADS 

Google Scholar 
Williams, T. D. et al. Molecular responses of European flounder (Platichthys flesus) chronically exposed to contaminated estuarine sediments. Chemosphere 108, 152–158, https://doi.org/10.1016/j.chemosphere.2014.01.028 (2014).Article 
ADS 
CAS 
PubMed 

Google Scholar 
NCBI GenBank https://identifiers.org/ncbi/insdc:HBYV00000000.1 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:ERS12067672 (2023).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRX893920 (2015).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP356374 (2022).Fletcher, C., Alexander, D. & Reed, B. The genome sequence of the European flounder, Platichthys flesus (Linnaeus, 1758). Wellcome Open Res. 8, 381, https://doi.org/10.12688/wellcomeopenres.19909.1 (2023).Article 
CAS 

Google Scholar 
Draganik, B., Ivanow, S., Tomczak, M., Maksimov, B. Y. & Psuty-Lipska, I. Status of exploited Baltic flounder stocks in the southern Baltic area (ICES SD 26). Oceanol. Hydrobiol. Stud. 36, 47–64, https://doi.org/10.2478/v10009-007-0029-y (2007).Article 

Google Scholar 
Dias, E., Daverat, F. & Morais, P. European flounder. In: Wilson, K. & Veneranta, L. (Eds). Data-limited diadromous species – review of European status. Report No. 348 https://doi.org/10.17895/ices.pub.5253 (ICES Cooperative Research, 2019).Skerritt, D. J. A review of the European flounder Platichthys flesus – biology, life history and trends in population. Eastern Sea Fisheries Joint Committee Report. Newcastle University, 13 pp (2010).McCrohan, C. R., Lu, W., Brierley, M. J., Dow, L. & Balment, R. J. Fish caudal neurosecretory system: a model for the study of neuroendocrine secretion. Gen. Comp. Endocrinol. 153, 243–250, https://doi.org/10.1016/j.ygcen.2006.12.027 (2007).Article 
CAS 
PubMed 

Google Scholar 
Hubbard, P. C., Balment, R. J. & McCrohan, C. R. Adrenergic Receptor Activation Hyperpolarizes the Caudal Neurosecretory Cells of the Flounder, Platichthys flesus. J. Neuroendocrinol. 8, 153–9, https://doi.org/10.1111/j.1365-2826.1996.tb00836.x (1996).Article 
CAS 
PubMed 

Google Scholar 
Laroche, J. et al. Variation patterns in individual fish responses to chemical stress among estuaries, seasons and genders: the case of the European flounder (Platichthys flesus) in the Bay of Biscay. Environ. Sci. Pollut. Res. Int. 20, 738–748, https://doi.org/10.1007/s11356-012-1276-3 (2013).Article 
CAS 
PubMed 

Google Scholar 
Napierska, D. & Podolska, M. Biomarkers of contaminant exposure: Results of a field study with flounder (Platichthys flesus) from the southern Baltic Sea. Mar. Pollut. Bull. 50, 758–67, https://doi.org/10.1016/j.marpolbul.2005.02.007 (2005).Article 
CAS 
PubMed 

Google Scholar 
Sheader, D. L., Williams, T. D., Lyons, B. P. & Chipman, J. K. Oxidative stress response of European flounder (Platichthys flesus) to cadmium determined by a custom cDNA microarray. Mar. Environ. Res. 62, 33–44, https://doi.org/10.1016/j.marenvres.2006.03.001 (2006).Article 
CAS 
PubMed 

Google Scholar 
Ojaveer, E. & Margers, K. The impact of climate change on the adaptation of marine fish in the Baltic Sea. ICES J. Mar. Sci. 62, 1492–1500, https://doi.org/10.1016/j.icesjms.2005.08.002 (2005).Article 

Google Scholar 
Jokinen, H. et al. Decline of flounder (Platichthys flesus (L.)) at the margin of the species’ distribution range. J. Sea Res. 105, 1–9, https://doi.org/10.1016/j.seares.2015.08.001 (2015).Article 
ADS 

Google Scholar 
Bond, H., Winter, M. J., Warne, J. M., McCrohan, C. R. & Balment, R. J. Plasma concentrations of arginine vasotocin and urotensin II are reduced following transfer of the euryhaline flounder (Platichthys flesus) from seawater to fresh water. Gen. Comp. Endocrinol. 125, 113–120, https://doi.org/10.1006/gcen.2001.7736 (2002).Article 
CAS 
PubMed 

Google Scholar 
Warne, J. M. & Balment, R. J. Effect of acute manipulation of blood volume and osmolality on plasma [AVT] in seawater flounder. Am. J. Physiol. 269, 1107–1112, https://doi.org/10.1152/ajpregu.1995.269.5.R1107 (1995).Article 

Google Scholar 
Florin, A.-B. & Höglund, J. Population structure of flounder (Platichthys flesus) in the Baltic Sea: Differences among demersal and pelagic spawners. Heredity 101, 27–38, https://doi.org/10.1038/hdy.2008.22 (2008).Article 
CAS 
PubMed 

Google Scholar 
Pomianowski, K., Burzyński, A., Kulczykowska, E. A de novo transcriptome assembly of the European Flounder (Platichthys flesus): The preselection of transcripts encoding active forms of enzymes. Front. Mar. Sci. 8. https://doi.org/10.3389/fmars.2021.618779 (2021).Pomianowski, K., Gozdowska, M., Sokołowska, E. & Kulczykowska, E. The cutaneous stress response system in three-spined stickleback and European flounder exposed to oxidative stress: Different mode of action. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 285, 111493, https://doi.org/10.1016/j.cbpa.2023.111493 (2023).Article 
CAS 
PubMed 

Google Scholar 
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652, https://doi.org/10.1038/nbt.1883 (2011).Article 
CAS 
PubMed 

Google Scholar 
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21, https://doi.org/10.1093/bioinformatics/bts635 (2013).Article 
CAS 
PubMed 

Google Scholar 
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659, (version 4.8.1) https://doi.org/10.1093/bioinformatics/btl158 (2006).Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212, https://doi.org/10.1093/bioinformatics/btv351 (2015).Article 
CAS 
PubMed 

Google Scholar 
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B. & Wu, C. H. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31, 926–932, https://doi.org/10.1093/bioinformatics/btu739 (2015).Article 
CAS 
PubMed 

Google Scholar 
Finn, R. D. et al. The Pfam protein families database. Nucleic Acids Res. 38, 11–22 (version 32.0) https://doi.org/10.1093/nar/gkp985 (2010).Thomas, P. D. et al. PANTHER: A Library of Protein Families and Subfamilies Indexed by Function. Genome Res. 13, 2129–2141, (version 15.0) https://doi.org/10.1101/gr.772403 (2003).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Mirdita, M., Steinegger, M. & Söding, J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics 35, 2856–2858, https://doi.org/10.1093/bioinformatics/bty1057 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29, https://doi.org/10.1038/75556 (2000).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Mitchell, A. L. et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47, 351–360, https://doi.org/10.1093/nar/gky1100 (2019).Article 
CAS 

Google Scholar 
Leinonen, R., Sugawara, H. & Shumway, M. The Sequence Read Archive. Nucleic Acids Res. 39, D19–D21, https://doi.org/10.1093/nar/gkq1019 (2011).Article 
CAS 
PubMed 

Google Scholar 
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP266160 (2024).NCBI GenBank https://identifiers.org/ncbi/insdc:GKXD01000000 (2024).