Comparative transcriptome analysis reveals key genes and pathways related to gonad development in the sea cucumber Apostichopus japonicus

Ying Wei1, Dexiang Huang1, Zhiqing Ye1, Zhijing Jiang1, Lifei Ge1, Yucheng Ren1, Jixiu Wang1, Xiuwen Xu1, Jingwen Yang1, Tianming Wang1
1National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China

Tài liệu tham khảo

Anderson, 2008, Stra8 and its inducer, retinoic acid, regulate meiotic initiation in both spermatogenesis and oogenesis in mice, Proc. Natl. Acad. Sci., 105, 14976, 10.1073/pnas.0807297105 Bader, 2003, An automated method for finding molecular complexes in large protein interaction networks, BMC Bioinform., 4, 2, 10.1186/1471-2105-4-2 Bertho, 2016, Foxl2 and its relatives are evolutionary conserved players in gonadal sex differentiation, Sex. Dev., 10, 111, 10.1159/000447611 Chaiyamoon, 2019, Existence of two mature sequences of cubifrin neuropeptide and their effects on spawning in the sea cucumber, Holothuria scabra, Aquaculture, 519, 734753, 10.1016/j.aquaculture.2019.734753 Choo, 2008, Population status, fisheries and trade of sea cucumbers in Asia, 81 Clement, 2007, Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes, Reproduction, 134, 455, 10.1530/REP-06-0341 Eddy, 1998, Profile hidden Markov models, Bioinformatics, 14, 755, 10.1093/bioinformatics/14.9.755 Edelbrock, 2013, Structural, molecular and cellular functions of MSH2 and MSH6 during DNA mismatch repair, damage signaling and other noncanonical activities, Mutat. Res., 743-744, 53, 10.1016/j.mrfmmm.2012.12.008 Edmonds, 2010, Insulin/FOXO signaling regulates ovarian prostaglandins critical for reproduction, Dev. Cell, 19, 858, 10.1016/j.devcel.2010.11.005 Feng, 2023, dmrtb1 is involved in the testicular development in Larimichthys crocea, Reproduction, 165, 159, 10.1530/REP-22-0214 Fujiwara, 2010, Spawning induced by cubifrin in the Japanese common sea cucumber Apostichopus japonicus, Fish. Sci., 76, 795, 10.1007/s12562-010-0262-2 Gao, 2022, A time-course transcriptome analysis of gonads from yellow catfish (Pelteobagrus fulvidraco) reveals genes associated with gonad development, BMC Genomics, 23, 409, 10.1186/s12864-022-08651-0 Gene Ontology, 2021, The Gene Ontology resource: enriching a GOld mine, Nucleic Acids Res., 49, D325, 10.1093/nar/gkaa1113 Gridley, 2003, Notch signaling and inherited disease syndromes, Hum. Mol. Genet., 12, R9, 10.1093/hmg/ddg052 Hamada, 2018, Interaction of WDR60 intermediate chain with TCTEX1D2 light chain of the dynein-2 complex is crucial for ciliary protein trafficking, Mol. Biol. Cell, 29, 1628, 10.1091/mbc.E18-03-0173 Han, 2015, High-throughput sequencing reveals hypothalamic microRNAs as novel partners involved in timing the rapid development of chicken (Gallus gallus) gonads, PLoS One, 10, 10.1371/journal.pone.0129738 Huang, 2021, Genome-wide prediction and comparative transcriptomic analysis reveals the G protein-coupled receptors involved in gonadal development of Apostichopus japonicus, Genomics, 113, 967, 10.1016/j.ygeno.2020.10.030 Huerta-Cepas, 2019, eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses, Nucleic Acids Res., 47, D309, 10.1093/nar/gky1085 Hussain, 2016, Neuropeptides modulate female chemosensory processing upon mating in Drosophila, PLoS Biol., 14, 10.1371/journal.pbio.1002455 Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317 Lafont, 2007, Steroids in aquatic invertebrates, Ecotoxicology, 16, 109, 10.1007/s10646-006-0113-1 Lan, 2020, Rad51 facilitates filament assembly of meiosis-specific Dmc1 recombinase, Proc. Natl. Acad. Sci., 117, 11257, 10.1073/pnas.1920368117 Langfelder, 2008, WGCNA: an R package for weighted correlation network analysis, BMC Bioinform., 9, 559, 10.1186/1471-2105-9-559 Li, 2022, CDT1 is the major functional regulatory subunit of the pre-replication complex in zygotes, Cell Prolif., 56 Liu, 2023, Identification and functional analysis of Dmrt1 gene and the SoxE gene in the sexual development of sea cucumber, Apostichopus japonicus, Front. Genet., 14 Liu, X., Sun, Z., Zhang, M., Meng, X., Xia, X., Yuan, W., Xue, F., Liu, C., 2012. Antioxidant and antihyperlipidemic activities of polysaccharides from sea cucumber Apostichopus japonicus. Carbohydr. Polym. 90(4), 1664–1670. Doi:doi:https://doi.org/10.1016/j.carbpol.2012.07.047. Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method, Methods, 25, 402, 10.1006/meth.2001.1262 Machado, 2022, The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: identification of sex-related and lipid biosynthesis genes, Aquacult. Rep., 22, 100936 Mita, 2013, Relaxin-like gonad-stimulating substance in an echinoderm, the starfish: a novel relaxin system in reproduction of invertebrates, Gen. Comp. Endocrinol., 181, 241, 10.1016/j.ygcen.2012.07.015 Perez-Portela, 2016, Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq, Mol. Ecol. Resour., 16, 794, 10.1111/1755-0998.12500 Pertea, 2015, StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nat. Biotechnol., 33, 290, 10.1038/nbt.3122 Piprek, 2019, Transcriptome profiling reveals male- and female-specific gene expression pattern and novel gene candidates for the control of sex determination and gonad development in Xenopus laevis, Dev. Genes Evol., 229, 53, 10.1007/s00427-019-00630-y Planells, 2020, Gene expression profiles of bovine genital ridges during sex determination and early differentiation of the gonadsdagger, Biol. Reprod., 102, 38 Pozo, 2016, Regulation and function of Cdt1; a key factor in cell proliferation and genome stability, Genes (Basel), 8, 10.3390/genes8010002 Qin, 2000, Effects of flavonoids of semen cuscutae on reproductive function of animals, Tradit. Chin. Drug Res. Clin. Pharmacol., 11, 349 Sanderson, 2006, The steroid hormone biosynthesis pathway as a target for endocrine-disrupting chemicals, Toxicol. Sci., 94, 3, 10.1093/toxsci/kfl051 Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498, 10.1101/gr.1239303 Song, 2006, Oogenesis: single cell development and differentiation, Dev. Biol., 300, 385, 10.1016/j.ydbio.2006.07.041 Sreenivasan, 2013, Gonad differentiation in zebrafish is regulated by the canonical Wnt signaling pathway, Biol. Reprod., 90 Sun, 2022, Identification and functional analysis of foxl2 and nodal in sea cucumber, Apostichopus japonicus, Gene Expr. Patterns, 44, 119245, 10.1016/j.gep.2022.119245 Takemoto, 2020, Sycp2 is essential for synaptonemal complex assembly, early meiotic recombination and homologous pairing in zebrafish spermatocytes, PLoS Genet., 16, 10.1371/journal.pgen.1008640 Thirumal Kumar, 2019, Elucidating the role of interacting residues of the MSH2-MSH6 complex in DNA repair mechanism: a computational approach, Adv. Protein Chem. Struct. Biol., 115, 325, 10.1016/bs.apcsb.2018.11.005 Uhlenhaut, 2009, Somatic sex reprogramming of adult ovaries to testes by FOXL2 ablation, Cell, 139, 1130, 10.1016/j.cell.2009.11.021 Walker, C.W., Lesser, M.P., Unuma, T., 2013. Chapter 3 — Sea urchin gametogenesis – structural, functional and molecular/genomic biology, in: J.M. Lawrence (Ed.), Dev. Aquac. Fish. Sci. Elsevier, 25-43. Wang, 2010, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26, 136, 10.1093/bioinformatics/btp612 Wang, 2015, Reproductive biology, 87, 10.1016/B978-0-12-799953-1.00006-4 Wang, 2020, Existence and functions of a kisspeptin neuropeptide signaling system in a non-chordate deuterostome species, Elife, 9 Wang, 2022, Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study, BMC Genomics, 23, 391, 10.1186/s12864-022-08632-3 Wasson, 1998, Synthesis of testosterone and 5α-androstanediols during nutritionally stimulated gonadal growth in Lytechinus variegatus Lamarck (Echinodermata:Echinoidea), Gen. Comp. Endocrinol., 111, 197, 10.1006/gcen.1998.7105 Xie, 2011, KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases, Nucleic Acids Res., 39, W316, 10.1093/nar/gkr483 Xu, 2021, Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination, Nucleic Acids Res., 49, 13135, 10.1093/nar/gkab1141 Yan, 2013, Expression pattern of vasa in gonads of sea cucumber Apostichopus japonicus during gametogenesis and reproductive cycle, Gene Expr. Patterns, 13, 171, 10.1016/j.gep.2013.03.001 Yang, 2016, Transcriptome analysis of male and female mature gonads of Japanese scallop Patinopecten yessonsis, Genes Genom., 38, 1041, 10.1007/s13258-016-0449-8 Young, 2010, Gene ontology analysis for RNA-seq: accounting for selection bias, Genome Biol., 11, R14, 10.1186/gb-2010-11-2-r14 Yu, 2012, clusterProfiler: an R package for comparing biological themes among gene clusters, Omics, 16, 284, 10.1089/omi.2011.0118 Zhang, 2021, Transcriptome analysis of gender-biased CYP genes in gonads of the sea cucumber Apostichopus japonicus, Comp. Biochem. Physiol. Part D Genomics Proteomics, 38, 100790, 10.1016/j.cbd.2021.100790 Zhang, 2017, The sea cucumber genome provides insights into morphological evolution and visceral regeneration, PLoS Biol., 15, 10.1371/journal.pbio.2003790 Zhang, 2018, Transcriptome sequencing and molecular markers discovery in the gonads of Portunus sanguinolentus, Sci. Data, 5, 180131, 10.1038/sdata.2018.131 Zhu, 2016, Gene structure, expression, and DNA methylation characteristics of sea cucumber cyclin B gene during aestivation, Gene, 594, 82, 10.1016/j.gene.2016.09.006 Zou, 2010, Aquatic invertebrate endocrine disruption, 112