Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)

Genomics - Tập 113 - Trang 3533-3543 - 2021
Tianqing Huang1, Wei Gu1, Enhui Liu1, Xiulan Shi1, Bingqian Wang1, Wenhua Wu1, Fulin Dong1, Gefeng Xu1
1Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China

Tài liệu tham khảo

Comai, 2005, The advantages and disadvantages of being polyploid, Nat. Rev. Genet., 6, 836, 10.1038/nrg1711 Leitch, 2008, Genomic plasticity and the diversity of polyploid plants, Science., 320, 481, 10.1126/science.1153585 Allendorf, 1984, 1 Near, 2012, Resolution of ray-finned fish phylogeny and timing of diversification, Proc. Natl. Acad. Sci. U. S. A., 109, 13698, 10.1073/pnas.1206625109 Jaillon, 2004, Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, Nature., 431, 946, 10.1038/nature03025 Piferrer, 2009, Polyploid fish and shellfish: production, biology and applications to aquaculture for performance improvement and genetic containment, Aquaculture., 293, 125, 10.1016/j.aquaculture.2009.04.036 Stenberg, 2013, Meiosis and its deviations in polyploid animals, Cytogenet Genome Res., 140, 185, 10.1159/000351731 Benfey, 1999, J. the physiology and behavior of triploid fishes, Rev. Fish. Sci., 7, 45, 10.1080/10641269991319162 Tiwary, 2004, The biology of triploid fish, Rev. Fish Biol. Fish., 14, 391, 10.1007/s11160-004-8361-8 Taranger, 2015, Risk assessment of the environmental impact of Norwegian Atlantic salmon farming, ICES J. Marine Sci., 72, 997, 10.1093/icesjms/fsu132 Glover, 2012, Three decades of farmed escapees in the wild: a spatio-temporal analysis of atlantic salmon population genetic structure throughout Norway, PLoS One, 7, e43129, 10.1371/journal.pone.0043129 Krisfalusi, 1999, Gonadal sex reversal in triploid rainbow trout (Oncorhynchus mykiss), J. Exp. Zool., 284, 466, 10.1002/(SICI)1097-010X(19990901)284:4<466::AID-JEZ13>3.0.CO;2-G Zhang, 2014, Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice, Genome Biol., 15, 512, 10.1186/s13059-014-0512-1 Taylor, 2015, Long non-coding RNA regulation of reproduction and development, Mol. Reprod. Dev., 82, 932, 10.1002/mrd.22581 Herrera, 2005, Mouse ovary developmental RNA and protein markers from gene expression profiling, Dev. Biol., 279, 271, 10.1016/j.ydbio.2004.11.029 Laiho, 2013, Transcriptome profiling of the murine testis during the first wave of spermatogenesis, PLoS One, 8, 10.1371/journal.pone.0061558 Chen, 2016, Disruption of dmc1 produces abnormal sperm in Medaka (Oryzias latipes), Sci. Rep., 6, 30912, 10.1038/srep30912 Reza, 2019, Roles of microRNAs in mammalian reproduction: from the commitment of germ cells to peri-implantation embryos, Biol. Rev. Camb. Philos. Soc., 94, 415, 10.1111/brv.12459 Shu, 2019, Integrated mRNA and miRNA expression profile analyses reveal the potential roles of sex-biased miRNA-mRNA pairs in gonad tissues of the Chinese concave-eared torrent frog (Odorrana tormota), J. Exp. Zool. B Mol. Dev. Evol., 332, 69, 10.1002/jez.b.22851 Ng, 2012, Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility, Curr. Opin. Plant Biol., 15, 154, 10.1016/j.pbi.2012.01.007 Liu, 2019, Transcriptome and miRNAs analyses enhance our understanding of the evolutionary advantages of polyploidy, Crit. Rev. Biotechnol., 39, 173, 10.1080/07388551.2018.1524824 Ha, 2008, Interspecies regulation of microRNAs and their targets, Biochim. Biophys. Acta, 1779, 735, 10.1016/j.bbagrm.2008.03.004 Tao, 2018, MicroRNA alternations in the testes related to the sterility of triploid fish, Mar. Biotechnol. (NY)., 20, 739, 10.1007/s10126-018-9845-1 Sessegolo, 2016, Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies, Biol. Lett., 12, 2016407, 10.1098/rsbl.2016.0407 Grover, 2010, Recent insights into mechanisms of genome size change in plants, Aust. J. Bot., 382732 Wendel, 2018, The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation, Curr. Opin. Genet. Dev., 49, 1, 10.1016/j.gde.2018.01.004 Covelo-Soto, 2015, Genome-wide methylation study of diploid and triploid brown trout (Salmo trutta L.), Anim. Genet., 46, 280, 10.1111/age.12287 Thorgaard, 1977, Heteromorphic sex chromosomes in male rainbow trout, Science., 196, 900, 10.1126/science.860122 Alfaqih, 2009, Mapping of five candidate sex-determining loci in rainbow trout (Oncorhynchus mykiss), BMC Genet., 10, 2, 10.1186/1471-2156-10-2 Bertho, 2018, The unusual rainbow trout sex determination gene hijacked the canonical vertebrate gonadal differentiation pathway, Proc. Natl. Acad. Sci. U. S. A., 115, 12781, 10.1073/pnas.1803826115 Rud, 2015, Sex identification of the rainbow trout Oncorhynchus mykiss by polymerase chain reaction, Ontogenez., 46, 87 Pérez, 2018, Sex hormone-binding globulin b expression in the rainbow trout ovary prior to sex differentiation, Gen. Comp. Endocrinol., 259, 165, 10.1016/j.ygcen.2017.11.021 Al-Tobasei, 2016, Genome-wide discovery of long non-coding RNAs in rainbow trout, PLoS One, 11, 10.1371/journal.pone.0148940 Juanchich, 2016, Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing, BMC Genomics, 17, 164, 10.1186/s12864-016-2505-9 Salmena, 2011, A ceRNA hypothesis: the Rosetta stone of a hidden RNA language?, Cell., 146, 353, 10.1016/j.cell.2011.07.014 Berthelot, 2014, The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates, Nat. Commun., 5, 3567, 10.1038/ncomms4657 Paneru, 2018, Crosstalk among lncRNAs, microRNAs and mRNAs in the muscle ‘degradome’ of rainbow trout, Sci. Rep., 8, 8416, 10.1038/s41598-018-26753-2 Feist, 1996, Brain-pituitary-gonadal axis during early development and sexual differentiation in the rainbow trout, Oncorhynchus mykiss, Gen. Comp. Endocrinol., 102, 394, 10.1006/gcen.1996.0083 Xu, 2016, Morphology, sex steroid level and gene expression analysis in gonadal sex reversal of triploid female (XXX) rainbow trout (Oncorhynchus mykiss), Fish Physiol. Biochem., 42, 193, 10.1007/s10695-015-0129-7 Chang, 2017, Effects of dietary lipid levels on growth, feed utilization, digestive tract enzyme activity and lipid deposition of juvenile Manchurian trout, Brachymystax lenok (Pallas), Aquac. Nutr., 24, 10.1111/anu.12598 Martin, 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. J., 17, 10, 10.14806/ej.17.1.200 Langmead, 2012, Fast gapped-read alignment with bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, 1, 10.1186/gb-2013-14-4-r36 Frazee, 2015, Ballgown bridges the gap between transcriptome assembly and expression analysis, Nat. Biotechnol., 33, 243, 10.1038/nbt.3172 Agarwal, 2015, Predicting effective microRNA target sites in mammalian mRNAs, Elife., 4, 10.7554/eLife.05005 Kong, 2007, CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine, Nucleic Acids Res., 35, W345, 10.1093/nar/gkm391 Sun, 2013, Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts, Nucleic Acids Res., 41, e166, 10.1093/nar/gkt646 Punta, 2012, The Pfam protein families database, Nucleic Acids Res., 40, D290, 10.1093/nar/gkr1065 Ambady, 2012, Identification of novel microRNAs in Xenopus laevis metaphase II arrested eggs, Genesis., 50, 286, 10.1002/dvg.22010 Buchfink, 2014, Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59, 10.1038/nmeth.3176 Betel, 2010, Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites, Genome Biol., 11, R90, 10.1186/gb-2010-11-8-r90 Olsen, 1997, A vasa-like gene in Zebrafish identifies putative primordial germ cells, Mech. Dev., 66, 95, 10.1016/S0925-4773(97)00099-3 Blázquez, 2011, Cloning and sequence analysis of a vasa homolog in the European Sea bass (Dicentrarchus labrax): tissue distribution and mRNA expression levels during early development and sex differentiation, Gen. Comp. Endocrinol., 170, 322, 10.1016/j.ygcen.2010.10.007 Kang, 2017, miR-26a-5p regulates TNRC6A expression and facilitates Theca cell proliferation in chicken ovarian follicles, DNA Cell Biol., 36, 922, 10.1089/dna.2017.3863 Yang, 2018, miR-1388 regulates the expression of nectin2l in Paralichthys olivaceus, Comp. Biochem. Physiol. Part D Genomics Proteomics., 28, 9, 10.1016/j.cbd.2018.05.003 Kouznetsova, 2005, SYCP2 and SYCP3 are required for cohesin core integrity at diplotene but not for centromere cohesion at the first meiotic division, J. Cell ence., 118, 2271 Hinch, 2020, The configuration of RPA, RAD51, and DMC1 binding in meiosis reveals the nature of critical recombination intermediates, Mol. Cell, 79, 10.1016/j.molcel.2020.06.015 Chen, 2016, The mechanism of miRNA-mediated PGR signaling pathway in regulating female reproduction, Hereditas., 38, 40 Sauer, 1995, The role of cyclin E in the regulation of entry into Sphase, Prog. Cell Cycle Res., 1, 125, 10.1007/978-1-4615-1809-9_10 Barker, 1994, Three genes for protein phosphatase 1 map to different human chromosomes: sequence, expression and gene localisation of protein serine/threonine phosphatase 1 beta (PPP1CB), Biochim. Biophys. Acta, 1220, 212, 10.1016/0167-4889(94)90138-4 Manyes, 2018, Spatial learning and long-term memory impairments in RasGrf1 KO, Pttg1 KO, and double KO mice, Brain Behav., 8, 10.1002/brb3.1089 Cimino, 1972, Meiosis in triploid all-female fish (Poeciliopsis, Poeciliidae), Science., 175, 1484, 10.1126/science.175.4029.1484 Offenberg, 1998, SCP2: a major protein component of the axial elements of synaptonemal complexes of the rat, Nucleic Acids Res., 26, 2572, 10.1093/nar/26.11.2572 Schalk, 1999, Isolation and characterization of the human SCP2 cDNA and chromosomal localization of the gene, Mamm. Genome, 10, 642, 10.1007/s003359901062 Winkel, 2009, Protein SYCP2 provides a link between transverse filaments and lateral elements ofmammalian synaptonemal complexes, Chromosoma., 118, 259, 10.1007/s00412-008-0194-0 Kouznetsova, 2005, SYCP2 and SYCP3 are required for cohesin core integrity at diplotene but not for centromere cohesion at the first meiotic division, Journal of Cell ence., 118, 2271 Yang, 2006, Mouse SYCP2 is required for Synaptonemal complex assembly and chromosomal synapsis during male meiosis, J. Cell Biol., 173, 497, 10.1083/jcb.200603063 Yuan, 2000, The murine SCP3 gene is required for synaptonemal complex assembly, chromosome synapsis, and male fertility, Mol. Cell, 5, 73, 10.1016/S1097-2765(00)80404-9 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 Pittman, 1998, Meiotic prophase arrest with failure of chromosome synapsis in mice deficient for Dmc1, a germline-specific rec a homolog, Mol. Cell, 1, 697, 10.1016/S1097-2765(00)80069-6 Bonache, 2014, Altered gene expression signature of early stages of the germ line supports the pre-meiotic origin of human spermatogenic failure, Andrology., 2, 596, 10.1111/j.2047-2927.2014.00217.x Martinerie, 2014, Mammalian E-type cyclins control chromosome pairing, telomere stability and CDK2 localization in male meiosis, PLoS Genet., 10, 10.1371/journal.pgen.1004165 Teng, 2011, Cyclin T2: a novel miR-15a target gene involved in early spermatogenesis, FEBS Lett., 585, 2493, 10.1016/j.febslet.2011.06.031 Kawashima, 2017, Regulation of follicle growth through hormonal factors and mechanical cues mediated by hippo signaling pathway, Syst Biol Reprod Med, 64, 3, 10.1080/19396368.2017.1411990 Bogacka, 2015, Peroxisome proliferator-activated receptors in the regulation of female reproductive functions, Folia Histochem. Cytobiol., 53, 189, 10.5603/fhc.a2015.0023 Barker, 1994, Three genes for protein phosphatase 1 map to different human chromosomes: sequence, expression and gene localisation of protein serine/threonine phosphatase 1 beta (PPP1CB), Biochim. Biophys. Acta, 1220, 212, 10.1016/0167-4889(94)90138-4 Chassot, 2008, Activation of beta-catenin signaling by Rspo1 controls differentiation of the mammalian ovary, Hum. Mol. Genet., 17, 1264, 10.1093/hmg/ddn016 Mark, 2008, STRA8-deficient spermatocytes initiate, but fail to complete, meiosis and undergo premature chromosome condensation, J. Cell Sci., 121, 3233, 10.1242/jcs.035071 Ye, 2008, The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation, PLoS One, 3, 10.1371/journal.pone.0001719 Guo, 2014, An integrated analysis of miRNA, lncRNA, and mRNA expression profiles, Biomed. Res. Int., 345605 Yin, 2015, Identification and expression of the target gene emx2 of miR-26a and miR-26b in Paralichthys olivaceus, Gene., 570, 205, 10.1016/j.gene.2015.06.030 Kang, 2017, miR-26a-5p regulates TNRC6A expression and facilitates Theca cell proliferation in chicken ovarian follicles, DNA Cell Biol., 36, 922, 10.1089/dna.2017.3863