Transcriptome analysis of body wall reveals growth difference between the largest and smallest individuals in the pure and hybrid populations of Apostichopus japonicus

Allen, 1974, Effects of stocking density and water exchange rate on growth and survival of channel catfish Ictalurus punctatus in circular tanks, Aquaculture., 4, 29, 10.1016/0044-8486(74)90016-7 Ambudkar, 2003, P-glycoprotein: from genomics to mechanism, Oncogene., 22, 7468, 10.1038/sj.onc.1206948 Azaza, 2013, The effects of rearing density on growth, size heterogeneity and inter-individual variation of feed intake in monosex male Nile tilapia Oreochromis niloticus L, Animal., 7, 1865, 10.1017/S1751731113001493 Bang, 2004, Individual variation in the rate of oxygen consumption by zebrafish embryos, J. Fish Biol., 64, 1285, 10.1111/j.0022-1112.2004.00391.x Bennien, 2018, Rare genetic variants in the sodium-dependent organic anion transporter SOAT (SLC10A6): effects on transport function and membrane expression, J. Steroid Biochem. Mol. Biol., 179, 26, 10.1016/j.jsbmb.2017.09.004 Biro, 2014, Individual and sex-specific differences in intrinsic growth rate covary with consistent individual differences in behaviour, J. Anim. Ecol., 83, 1186, 10.1111/1365-2656.12210 Blobel, 2005, ADAMs: key components in EGFR signalling and development, Nat. Rev. Mol. Cell Biol., 6, 32, 10.1038/nrm1548 Bronkhorst, 2013, Risk of infection and sepsis in severely injured patients related to single nucleotide polymorphisms in the lectin pathway, Br. J. Surg., 100, 1818, 10.1002/bjs.9319 Bustin, 2009, The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments, Clin. Chem., 55, 611, 10.1373/clinchem.2008.112797 Chen, 2010, Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin, Pharmacogenet. Genomics, 20, 687, 10.1097/FPC.0b013e32833fe789 Crosby, 1998, Chimaeric analysis reveals role of Pdgf receptors in all muscle lineages, Nat. Genet., 18, 385, 10.1038/ng0498-385 Cui, 2014, Dominance hierarchy and social relationships in a group of captive black-and-white snub-nosed monkeys (Rhinopithecus bieti), Dongwuxue Yanjiu, 35, 204 Cui, 2015, Transcriptional profiling reveals differential gene expression of Amur Ide. Leuciscus waleckii during spawning migration, Int. J. Mol. Sci., 16, 13959, 10.3390/ijms160613959 Dean, 2001, The human ATP-binding cassette transporter superfamily, Genome Res., 11, 1156, 10.1101/gr.GR-1649R Dong, 2004, The essential ATP-binding cassette protein RLI1 functions in translation by promoting preinitiation complex assembly, J. Biol. Chem., 279, 42157, 10.1074/jbc.M404502200 Dong, 2010, Intra-specific effects of sea cucumber (Apostichopus japonicus) with reference to stocking density and body size, Aquac. Res., 41, 1170 Feder, 1999, Heat-shock proteins, molecular chaperones, and the stress response: evolutionary and ecological physiology, Annu. Rev. Physiol., 61, 243, 10.1146/annurev.physiol.61.1.243 Ferreira, 2015, Insect midgut carboxypeptidases with emphasis on S10 hemipteran and M14 lepidopteran carboxypeptidases, Insect Mol. Biol., 24, 222, 10.1111/imb.12151 Florea, 2013, Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues, F1000Research., 2, 188, 10.12688/f1000research.2-188.v1 Fouts, 2008, Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice, PLoS Genet., 4, 10.1371/journal.pgen.1000141 Franceschini, 2013, STRING v9. 1: protein-protein interaction networks, with increased coverage and integration, Nucleic Acids Res., 41, D808, 10.1093/nar/gks1094 Gao, 2017, Transcriptome analysis of the sea cucumber (apostichopus japonicus) with variation in individual growth, PLoS One, 12, 10.1371/journal.pone.0181471 Giebeler, 2016, A Disintegrin and Metalloprotease (ADAM): historical overview of their functions, Toxins (Basel), 23, 122, 10.3390/toxins8040122 Griffen, 2012, The role of individual behavior type in mediating indirect interactions, Ecology., 93, 1935, 10.1890/11-2153.1 Hiadlovská, 2015, Shaking the myth: body mass, aggression, steroid hormones, and social dominance in wild house mouse, Gen. Comp. Endocrinol., 1223, 16, 10.1016/j.ygcen.2015.09.033 Hruban, 1969, Microbodies and related particles. Morphology, biochemistry, and physiology, Int. Rev. Cytol., 1, 1 Itkonen, 2017, Lipid degradation promotes prostate cancer cell survival, Oncotarget, 13, 38264, 10.18632/oncotarget.16123 Iwama, 1998, Heat shock protein expression in fish, Rev. Fish Biol. Fish., 8, 35, 10.1023/A:1008812500650 Jiang, 2017, Comparative study of three phenoloxidases in the sea cucumber Apostichopus japonicus, Fish Shellfish Immunol., 67, 11, 10.1016/j.fsi.2017.05.061 Jimenez, 2015, Micro-scale environmental variation amplifies physiological variation among individual mussels, Proc. Biol. Sci., 282, 10.1098/rspb.2015.2273 Jobling, 1994, The influence of environmental manipulations on inter- and intra-individual variation in food acquisition and growth performance of Arctic charr, (Salvelinus alpinus), J. Fish Biol., 44, 1069, 10.1111/j.1095-8649.1994.tb01277.x Kamstra, 1993, The effect of size grading on individual growth in eel, Anguilla anguilla, measured by individual marking, Aquaculture., 112, 67, 10.1016/0044-8486(93)90159-V Kanehisa, 2004, The KEGG resource for deciphering the genome, Nucleic Acids Res., 32, D277, 10.1093/nar/gkh063 Khoshnevis, 2010, The iron-sulphur protein RNase L inhibitor functions in translation termination, EMBO Rep., 11, 214, 10.1038/embor.2009.272 Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36 Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25 Lee, 2010, The Hippo-Salvador pathway restrains hepatic oval cell proliferation, liver size, and liver tumorigenesis, Proc. Natl. Acad. Sci. U. S. A., 107, 8248, 10.1073/pnas.0912203107 Leng, 2013, EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments, Bioinformatics., 29, 1035, 10.1093/bioinformatics/btt087 Liberale, 2017, Treatment with proprotein convertase Subtilisin/Kexin type 9 (PCSK9) inhibitors to reduce cardiovascular inflammation and outcomes, Curr. Med. Chem., 24, 1403, 10.2174/0929867324666170303123734 Liu, 1999, beta-Trcp couples beta-catenin phosphorylation-degradation and regulates Xenopus axis formation, Proc. Natl. Acad. Sci. U. S. A., 96, 6273, 10.1073/pnas.96.11.6273 Lo, 2004, Cloning and molecular characterization of heat shock cognate 70 from tiger shrimp (Penaeus monodon), Cell Stress Chaperones, 9, 332, 10.1379/CSC-47R.1 Lu, 2010, Hippo signaling is a potent in vivo growth and tumor suppressor pathway in the mammalian liver, Proc. Natl. Acad. Sci. U. S. A., 107, 1437, 10.1073/pnas.0911427107 Mao, 2005, Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary, Bioinformatics., 21, 3787, 10.1093/bioinformatics/bti430 Marchand, 1988, Influence of fish density on the energy allocation pattern of juvenile 106 brook trout (Salvelinus fontinahs), Can. J. Fish. Aquat. Sci., 55, 796, 10.1139/f97-301 Martins, 2005, Size distribution in African catfish (Clarias gariepinus) affects feeding behaviour but not growth, Aquaculture, 250, 300, 10.1016/j.aquaculture.2005.05.034 McCarthy, 1992, The effect of feeding hierarchy on individual variability in daily feeding of rainbow trout Oncorhynchus mykiss (Walbaum), J. Fish Biol., 41, 257, 10.1111/j.1095-8649.1992.tb02655.x McDonald, 1996, Fish simulation culture model (FIS-C): a bioenergetics based model for aquaculture wasteload application, Aquac. Eng., 15, 243, 10.1016/0144-8609(96)00260-9 Michel, 2017, Protocol for assessing the relative effects of environment and genetics on antler and body growth for a long-lived cervid, J. Vis. Exp., 8, 126 Miller, 2014, Simulating the effects of fluctuating dissolved oxygen on growth, reproduction, and survival of fish and shrimp, J. Theor. Biol., 343, 54, 10.1016/j.jtbi.2013.11.004 Pei, 2014, Effects of stocking density and body physical contact on growth of sea cucumber, Apostichopus japonicus, Aquac. Res., 45, 629, 10.1111/are.12004 Percilia, 2005, Chemical cues related to conspecific size in pintado catfish, Pseudoplatystoma coruscans, Acta. Ethol., 8, 65, 10.1007/s10211-005-0001-3 Pérez-Casanova, 2008, The immune and stress responses of Atlantic cod to long-term increases in water temperature, Fish Shellfish Immunol., 24, 600, 10.1016/j.fsi.2008.01.012 Ren, 2016, Two proprotein convertase subtilisin/kexin type 9 (PCSK9) paralogs from the tropical sea cucumber (Stichopus monotuberculatus): molecular characterization and inducible expression with immune challenge, Fish Shellfish Immunol., 56, 255, 10.1016/j.fsi.2016.07.013 Robert, 2003, Evolution of heat shock protein and immunity, Dev. Comp. Immunol., 27, 449, 10.1016/S0145-305X(02)00160-X Sahu, 2018, Knockdown of chondroitin-4-sulfotransferase-1, but not of dermatan-4-sulfotransferase-1, accelerates regeneration of zebrafish after spinal cord injury, FASEB J., 19 Scheving, 1983, Primary amino acid sequence similarity between human epidermal growth factor-urogastrone, human pancreatic secretory trypsin inhibitor, and members of porcine secretin family, Arch. Biochem. Biophys., 226, 411, 10.1016/0003-9861(83)90309-0 Schneider, 2005, Organic cation transporter 3 modulates murine basophil functions by controlling intracellular histamine levels, J. Exp. Med., 202, 387, 10.1084/jem.20050195 Semlitsch, 2015, Intermediate pond sizes contain the highest density, richness, and diversity of pond-breeding amphibians, PLoS One, 10, 10.1371/journal.pone.0123055 Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498, 10.1101/gr.1239303 Sun, 2016, Effects of stocking density on the individual growth and differentiation of the oriental river prawn macrobrachium Nipponense (de haan, 1849) (caridea: palaemonidae), J. Crustac. Biol., 36, 1 Temple, 2014, Skeletal growth in early and late Neolithic foragers from the Cis-Baikal region of Eastern Siberia, Am. J. Phys. Anthropol., 153, 377, 10.1002/ajpa.22436 Tong, 2016, Subcellular localization of five singular WSC domain-containing proteins and their roles in Beauveria bassiana responses to stress cues and metal ions, Environ. Microbiol. Rep., 8, 295, 10.1111/1758-2229.12380 Walker, 2013, The ATP synthase: the understood, the uncertain and the unknown, Biochem. Soc. Trans., 1, 1, 10.1042/BST20110773 Wang, 2018, Comparative transcriptome analysis reveals growth-related genes in juvenile Chinese sea cucumber, Russian sea cucumber, and their hybrids, Mar. Biotechnol., 20, 193, 10.1007/s10126-018-9796-6 Wang, 2018, Integration of small RNAs and mRNAs by high-throughput sequencing reveals a complex regulatory network in Chinese sea cucumber, Russian sea cucumber and their hybrids, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 1, 10.1016/j.cbd.2018.10.003 Watanabe, 2004, M-phase kinases induce phospho-dependent ubiquitination of somatic Wee1 by SCFbeta-TrCP, Proc. Natl. Acad. Sci. U. S. A., 101, 4419, 10.1073/pnas.0307700101 Wu, 2009, Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis, J. Bacteriol., 191, 4492, 10.1128/JB.00315-09 Young, 2010, Gene ontology analysis for RNA-seq: accounting for selection bias, Genome Biol., 11, R14, 10.1186/gb-2010-11-2-r14 Zhai, 2014, The regulatory roles of MicroRNA-146b-5p and its target platelet-derived growth factor receptor α (PDGFRA) in erythropoiesis and megakaryocytopoiesis, J. Biol. Chem., 289, 22600, 10.1074/jbc.M114.547380 Zhang, 2004, Natural resources, culture and problems of sea cucumber worldwide, Mar. Fish Res., 25, 89 Zhang, 2013, Growth comparison of juvenile F1Hybrids between Russia population and China population of sea cucumber, Apostichopus japonicus, Fish. Sci., 32 Zhang, 2017, The sea cucumber genome provides insights into morphological evolution and visceral regeneration, PLoS Biol., 15, 10.1371/journal.pbio.2003790 Zhao, 2007, Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control, Genes Dev., 21, 2747, 10.1101/gad.1602907 Zhou, 2016, Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus, PeerJ., 4, e1779, 10.7717/peerj.1779