Agarwal, V., Bell, G. W., Nam, J. W., & Bartel, D. P. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4:e05005. https://doi.org/10.7554/ eLife.05005.001.
Allendorf, F. W. & Thorgaard, G. H. Tetraploidy and the evolution of salmonid fishes. Plenum Press.1984;1-53. https://doi.org/10.1007/978-1-4684-4652-4_1.
Al-Tobasei R, Paneru B, Salem M. Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout. PLoS One. 2016;11(2):e0148940. https://doi.org/ 10.1371/journal.pone.0148940.
Ambady, S., Wu, Z., & Dominko, T. Identification of novel microRNAs in Xenopus laevis metaphase II arrested eggs. Genesis. 2012;50(3):286-299. https://doi.org/ 10.1002/dvg.22010.
Anjali Gupta Hinch, Philipp W. Becker, Tao Li, et al. The Configuration of RPA, RAD51, and DMC1 Binding in Meiosis Reveals the Nature of Critical Recombination Intermediates. Molecular Cell. 2020;79(4):689-701.e10. https://doi.org/10.1016/j. molcel.2020.06.015
Barak Y, Liao D, He W, et al. Effects of peroxisome proliferator-activated receptor delta on placentation, adiposity, and colorectal cancer. Proceedings of the National Academy of Sciences. 2002;99(1):303-308. https://doi.org/10.1073/pnas. 012610299.
Barker HM, Brewis ND, Street AJ, Spurr NK, Cohen PT. 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. 1994;1220(2):212. https://doi.org/10.1016/0167-4889(94)90138-4.
Benfey, T., J. The physiology and behavior of triploid fishes. Reviews in Fisheries Science. 1999;7:45–48. https://doi.org/10.1080/10641269991319162.
Berthelot C , Brunet, Frédéric, Chalopin D , et al. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun. 2014;5:3567. https://doi.org/10.1038/ncomms4657.
Betel D, Koppal A, Agius P, et al. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biology, 2010;11(8): R90. https://doi.org/10.1186/gb-2010-11-8-r90.
Bogacka I, Kurzynska A, Bogacki M, & Chojnowska K. Peroxisome proliferator-activated receptors in the regulation of female reproductive functions. Folia Histochemica Cytobiologica. 2015;53(3):189-200. https://doi.org/10.5603/fhc.a 2015.0023.
Bonache S, Algaba F, Franco E, et al. Altered gene expression signature of early stages of the germ line supports the pre-meiotic origin of human spermatogenic failure. Andrology. 2014;2(4):596-606. https://doi.org/10.1111/j.2047-2927.2014. 00217.x.
Buchfink, B., Xie, C., & Huson, H. D. Fast and sensitive protein alignment using DIAMOND. Nature Methods. 2014;12(1):59-60. https://doi.org/10.1038/nmeth.3176.
Chang J, Niu H X, Jia Y D, et al. Effects of dietary lipid levels on growth, feed utilization, digestive tract enzyme activity and lipid deposition of juvenile Manchurian trout, Brachymystax lenok (Pallas). Aquaculture Nutrition, 2017;24(2). https://10.1111/anu.12598.
Chassot, A. A., Gregoire, E. P., Lavery, R., Taketo, M. M., de Rooij, D. G., Adams, I. R., & Chaboissier, M. C. RSPO1/beta-catenin signaling pathway regulates oogonia differentiation and entry into meiosis in the mouse fetal ovary. PLoS One. 2011;6(10): e25641. https://doi.org/10.1371/journal.pone.0025641.
Chassot, A. A., Ranc, F., Gregoire, E. P., Roepers-Gajadien, H. L., Taketo, M. M., Camerino, G., de Rooij, D. G., Schedl, A. & Chaboissier, M. C. Activation of beta-catenin signaling by Rspo1 controls differentiation of the mammalian ovary. Hum Mol Genet. 2008;17(9):1264-1277. https://doi.org/10.1093/hmg/ddn016.
Chen J, Cui X, Jia S, et al. Disruption of dmc1 Produces Abnormal Sperm in Medaka (Oryzias latipes). Scientific Reports. 2016;6:30912. https://doi.org/10.1038/ srep30912.
Chen L, Zhang BY, Feng GD, Xiang W, Ma YX, Chen H, Chu MX, Wang PQ. The mechanism of miRNA-mediated PGR signaling pathway in regulating female reproduction. Hereditas. 2016;38(1):40-51. https://doi.org/10.16288/j.yczz.15-293.
Cimino MC. Meiosis in triploid all-female fish (Poeciliopsis, Poeciliidae). Science. 1972;175(4029):1484-6. https://doi.org/10.1126/science.175.4029.1484.
Comai L. The advantages and disadvantages of being polyploid. Nat Rev Genet. 2005;6(11):836-846. https://doi.org/10.1038/nrg1711.
Feist, G. & Schreck, C. B. Brain-pituitary-gonadal axis during early development and sexual differentiation in the rainbow trout, Oncorhynchus mykiss. Gen Comp Endocrinol, 1996;102(3):394-409. https://doi.org/10.1006/gcen.1996.0083.
Francesc Piferrer, Andy Beaumont, Jean-Claude Falguière, et al. Polyploid fish and shellfish: Production, biology and applications to aquaculture for performance improvement and genetic containment. Aquaculture. 2009;293(3):125-156. https://doi.org/10. 1016/j.aquaculture.2009.04.036.
Frazee, A. C., Pertea, G., Jaffe, A. E., Langmead, B., Salzberg, S. L. & Leek, J. T. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol. 2015;33(3):243-246. https://doi.org/10.1038/nbt.3172.
Glover K. A. et al. Three Decades of Farmed Escapees in the Wild: A Spatio-Temporal Analysis of Atlantic Salmon Population Genetic Structure throughout Norway. PloS one. 2018;e43129. https://doi.org/10.1371/journal.pone. 0043129.
Gregory M. Weber, Mark A. Hostuttler, Beth M. Cleveland, et al. Growth performance comparison of intercross-triploid, induced triploid, and diploid rainbow trout. Aquaculture. 2014;433:85-93. https://doi.org/10.1016/j.aquaculture.2014.06. 003.
Guo, L., Zhao, Y., Yang, S., Zhang, H., & Chen, F. An integrated analysis of miRNA, lncRNA, and mRNA expression profiles. Biomed Res Int. 2014;345605. https://doi.org/10.1155/2014/345605.
Guo, X., et al. All-triploid Pacific oysters (Crassostrea gigas Thunberg) produced by mating tetraploids and diploids. Aquaculture. 1996;142:149-161. https://doi.org/ 10.1016/0044-8486(95)01243-5.
Herrera, L., Ottolenghi, C., Garcia-Ortiz, J. E., Pellegrini, M., Manini, F., Ko, M. S., Nagaraja, R., Forabosco, A., & Schlessinger, D. Mouse ovary developmental RNA and protein markers from gene expression profiling. Dev Biol. 2005;279(2): 271-290. https://doi.org/10.1016/j.ydbio.2004.11.029.
Jaillon, O. et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004;431(7011):946-57. https://doi.org/ 10.1038/nature03025.
Jaillon, O., et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004;431:946-957. https://doi.org/ 10.1038/nature03025.
Juanchich A, Bardou P, Rué O, Gabillard JC, Gaspin C, Bobe J, Guiguen Y. Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing. BMC Genomics. 2016;17:164. https://doi.org/ 10.1186/s12864-016-2505-9.
Kang, L., Yang, C., Wu, H., Chen, Q., Huang, L., Li, X., Tang, H., & Jiang, Y. miR-26a-5p regulates TNRC6A Expression and Facilitates Theca Cell Proliferation in Chicken Ovarian Follicles. DNA Cell Biol. 2017;36(11):922-929. https://doi.org/ 10.1089/dna.2017.3863.
Kawashima, I., & Kawamura, K. Regulation of follicle growth through hormonal factors and mechanical cues mediated by Hippo signaling pathway. Syst Biol Reprod Med. 2017;64(1):3-11. https://doi.org/10.1080/19396368.2017.1411990.
Kong, L., Zhang, Y., Ye, Z. Q., Liu, X. Q., Zhao, S. Q., Wei, L., & Gao, G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;35(Web Server issue):W345-349. https://doi.org/10.1093/nar/gkm391.
Kouznetsova, A. 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. 2005;118(10):2271-8. https://doi.org/10.1242/jcs.02362.
Krisfalusi M, Cloud JG. Gonadal sex reversal in triploid rainbow trout (Oncorhynchus mykiss). J Exp Zool. 1999;284(4):466-72. https://doi.org/10.1002/(sici)1097-010x (19990901)284:4<466::aid-jez13>3.3.co;2-7.
Laetitia Martinerie, Marcia Manterola, Sanny S. W. Chung, et al. Mammalian E-type Cyclins Control Chromosome Pairing, Telomere Stability and CDK2 Localization in Male Meiosis. Plos Genetics. 2014;10(2):e1004165. https://doi.org/10.1371/journal. pgen.1004350.
Laiho, A., Kotaja, N., Gyenesei, A., & Sironen, A. Transcriptome profiling of the murine testis during the first wave of spermatogenesis. PLoS One. 2013;8(4): e61558. https://doi.org/10.1371/journal.pone.0061558.
Leitch, A.R. & Leitch, I.J. Genomic plasticity and the diversity of polyploid plants. Science. 2008;320(5875):481-483. https://doi.org/10.1126/science.1153585.
Manyes L, Holst S, Lozano M, Santos E, Fernandez-Medarde A. Spatial learning and long-term memory impairments in RasGrf1 KO, Pttg1 KO, and double KO mice. Brain Behav. 2018;8(11):e01089. https://doi.org/10.1002/brb3.1089.
Mark, M., Jacobs, H., Oulad-Abdelghani, M., Dennefeld, C., Feret, B., Vernet, N., Codreanu, C. A., Chambon, P., & Ghyselinck, N. B. STRA8-deficient spermatocytes initiate, but fail to complete, meiosis and undergo premature chromosome condensation. J Cell Sci. 2008;121(19):3233-3242. https://doi.org/10.1242/jcs.035071
Near, T. J. et al. Resolution of ray-finned fish phylogeny and timing of diversification. Proc. Natl Acad. Sci. USA. 2012;109(34):13698-13703 . https://doi.org/10.1073/pnas. 1206625109.
Nwachi O F, Esa Yuzine B. Comparative growth and survival of diploid and triploid Mozambique tilapia (Oreochromism ossambicus) reared in indoor tanks. Journal of environmental biology. 2016;37(4 Spec No):839-843.
Offenberg H H, Schalk J A, Meuwissen R L, van Aalderen M, KesterH A, Dietrich A J, Heyting C. SCP2: A major protein component of the axial elements of synaptonemal complexes of the rat. Nucleic AcidsResearch, 1998;26(11):2572-2579. https:// doi.org/10.1093/nar/26.11.2572.
Paneru B, Ali A, Al-Tobasei R, Kenney B, Salem M. Crosstalk among lncRNAs, microRNAs and mRNAs in the muscle 'degradome' of rainbow trout. Sci Rep. 2018 ;8(1):8416. https://doi.org/10.1038/s41598-018-26753-2.
Park In-Seok, Gil Hyun Woo, Lee Tae Ho, et al. Comparative Study of Growth and Gonad Maturation in Diploid and Triploid Marine Medaka, Oryzias dancena. Developmant & Reproduction. 2016;20(4):305-314. https://doi.org/10.12717/DR. 2016.20.4.305.
Pittman,D.L., Cobb,J., Schimenti,K.J., Wilson,L.A., Cooper,D.M., Brignull,E., Handel, M.A. and Schimenti,J.C. Meiotic prophase arrest with failure of chromosome synapsis in mice deficient for Dmc1, a germline-specific Rec A homolog. Molecular Cell. 1998;1(5), 697-705. https://doi.org/10.1016/S1097-2765(00)80069-6.
Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E. L., Eddy, S. R., Bateman, A., & Finn, R. D. The Pfam protein families database. Nucleic Acids Res. 2012;40(Database issue):D290-301. https://doi.org/10.1093/ nar/gkr1065.
Reza AMMT, Choi YJ, Han SG, Song H, Park C, Hong K, Kim JH. Roles of microRNAs in mammalian reproduction: from the commitment of germ cells to peri-implantation embryos. Biol Rev Camb Philos Soc. 2019;94(2):415-438. https://doi.org/10.1111/brv.12459.
Sauer K, Lehner CF. The role of cyclin E in the regulation of entry into Sphase. Progress Cell Cycle Res. 1995;1:125-39. https://doi.org/10.1007/978-1-4615-1809 -9-10.
Schalk J A, Offenberg H H, Peters E, Groot N P, Hoovers J M, Heyting C. Isolation and characterization of the human SCP2 cDNA and chromosomal localization of the gene. Mammalian Genome,1999;10(6):642-644. https://doi.org/10.1007/s003359 901062.
Shu Y, Zhang H, Cai Q, Tang D, Wang G, Liu T, Lv B, Wu H. 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. 2019;332(3-4):69-80. https://doi.org/10.1002/jez.b.22851.
Stenberg, P., & Saura, A. Meiosis and its deviations in polyploid animals. Cytogenet Genome Res. 2013;140(2-4):185-203. https://doi.org/10.1159/000351731.
Sun, L., Luo, H., Bu, D., Zhao, G., Yu, K., Zhang, C., Liu, Y., Chen, R., & Zhao, Y. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013;41(17):e166. https://doi.org/ 10.1093/nar/gkt646.
Takemoto K, Imai Y, Saito K, et al. Sycp2 is essential for synaptonemal complex assembly, early meiotic recombination and homologous pairing in zebrafish spermatocytes. PLoS Genetics. 2020;16(2):e1008640. https://doi.org/10.1371/journal. pgen.1008640.
Taranger GL, et al. Risk assessment of the environmental impact of Norwegian Atlantic salmon farming. ICES J. Marine Sci. 2015;72:997-1021. https://doi.org/ 10.1093/ icesjms/fsu132.
Taylor, D. H., Chu, E. T., Spektor, R., & Soloway, P. D. Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev. 2015;82(12):932-956. https://doi.org/10.1002/mrd.22581.
Teng Y, Wang Y, Fu J, Cheng X, Miao S, Wang L. Cyclin T2: a novel miR-15a target gene involved in early spermatogenesis. FEBS Lett. 2011;585(15):2493-500. https://doi.org/10.1016/j.febslet.2011.06.031.
Tiwary, B.K., Kirubagaran, R., Raym, A.K. The biology of triploid fish. Rev Fish Biol Fish. 2004;14:391-402. https://doi.org/10.1007/s11160-004-8361-8.
Van de Peer Y, et al. The evolutionary significance of ancient genome duplications. Nat Rev Genet. 2009;10:725-32. https://doi.org/10.1038/nrg2600.
Winkel K, Alsheimer M, Ollinger R, Benavente R. Protein SYCP2 provides a link between transverse filaments and lateral elements ofmammalian synaptonemal complexes. Chromosoma. 2009;118(2):259-267. https://doi.org/10.1007/s00412-008 -0194-0.
Xu, G., Huang, T., Jin, X., Cui, C., Li, D., Sun, C., Han, Y., & Mu, Z. Morphology, sex steroid level and gene expression analysis in gonadal sex reversal of triploid female (XXX) rainbow trout (Oncorhynchus mykiss). Fish Physiol Biochem. 2016;42(1):193-202. https://doi.org/10.1007/s10695-015-0129-7.
Yang F, Fuente R D L, Leu N A, et al. Mouse SYCP2 Is Required for Synaptonemal Complex Assembly and Chromosomal Synapsis during Male Meiosis. Journal of Cell Biology. 2006;173(4):497-507. https://doi.org/10.1083/jcb.200603063.
Yang, F., Guan, J., Li, R., Li, X., Niu, J., Shang, R., Qi, J., & Wang, X. miR-1388 regulates the expression of nectin2l in Paralichthys olivaceus. Comp Biochem Physiol Part D Genomics Proteomics. 2018;28:9-16. https://doi.org/10.1016/j.cbd. 2018.05.003.
Ye, W., Lv, Q., Wong, C. K., Hu, S., Fu, C., Hua, Z., Cai, G., Li, G., Yang, B. B., & Zhang, Y. The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. PLoS One. 2008;3(3):e1719. https://doi.org/ 10.1371/journal.pone.0001719.
Yin, C., Zhang, J., Shi, Z., Sun, W., Zhang, H., & Fu, Y. Identification and expression of the target gene emx2 of miR-26a and miR-26b in Paralichthys olivaceus. Gene. 2015;570(2): 205-212. https://doi.org/10.1016/j.gene.2015.06.030.
Yuan L, Liu JG, Zhao J, et al. The murine SCP3 gene is required for synaptonemal complex assembly, chromosome synapsis, and male fertility. Mol Cell. 2000;5:73-83.https://doi.org/10.1016/S1097-2765(00)80404-9.
Zhang, Y. C., Liao, J. Y., Li, Z. Y., Yu, Y., Zhang, J. P., Li, Q. F., Qu, L. H., Shu, W. S. & Chen, Y. Q. Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol. 2014;15(12):512. https://doi.org/10.1186/s13059-014-0512-1.