Transcriptome Profile Analysis on Ovarian Tissues of Autotetraploid Fish and Diploid Red Crucian Carp

Overview

Journal Front Genet

Date 2019 Apr 4

PMID 30941161

Citations 2

Authors

Yude Wang

Minghe Zhang

Qinbo Qin

Yajun Peng

Xu Huang

Chongqing Wang

Liu Cao

Wuhui Li

Min Tao

Chun Zhang

Shaojun Liu

Affiliations

Soon will be listed here.

Abstract

Polyploidization can significantly alter the size of animal gametes. Autotetraploid fish (RRRR, 4nRR = 200) (4nRR) possessing four sets of chromosomes were derived from whole-genome duplication in red crucian carp (RR, 2 = 100) (RCC). The diploid eggs of the 4nRR fish were significantly larger than the eggs of RCC. To explore the differences between the ovaries of these two ploidies of fishes at the molecular level, we compared the ovary transcriptome profiles of 4nRR fish and RCC and identified differentially expressed genes (DEGs). A total of 19,015 unigenes were differentially expressed between 4nRR fish and RCC, including 12,591 upregulated and 6,424 downregulated unigenes in 4nRR fish. Functional analyses revealed that eight genes (, , , , , , , and ) were involved in the regulation of cell proliferation, cell division, gene transcription, ovary development and energy metabolism, suggesting that these eight genes were related to egg size in 4nRR fish and RCC. We validated the expression levels of these eight DEGs in 4nRR fish and RCC using quantitative PCR. The study results provided insights into the regulatory mechanisms underlying the differences in crucian carp egg sizes.

Citing Articles

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Xu X, Zhou Y, Wang C, Huang X, Zhang K, Xu X Zool Res. 2024; 45(2):381-397.

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Whole-Genome Re-sequencing and Transcriptome Reveal Oogenesis-Related Genes in Autotetraploid Carassius auratus.

Wang C, Qin H, Zhao C, Yang L, Yu T, Zhang Y Mar Biotechnol (NY). 2021; 23(2):233-241.

PMID: 33675430 DOI: 10.1007/s10126-021-10018-7.

References

Pfaffl M . A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001; 29(9):e45. PMC: 55695. DOI: 10.1093/nar/29.9.e45. View

Storey J, Tibshirani R . Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003; 100(16):9440-5. PMC: 170937. DOI: 10.1073/pnas.1530509100. View

de Hoon M, Imoto S, Nolan J, Miyano S . Open source clustering software. Bioinformatics. 2004; 20(9):1453-4. DOI: 10.1093/bioinformatics/bth078. View

Dubrac S, Lear S, Ananthanarayanan M, Balasubramaniyan N, Bollineni J, Shefer S . Role of CYP27A in cholesterol and bile acid metabolism. J Lipid Res. 2004; 46(1):76-85. DOI: 10.1194/jlr.M400219-JLR200. View

Menges M, de Jager S, Gruissem W, Murray J . Global analysis of the core cell cycle regulators of Arabidopsis identifies novel genes, reveals multiple and highly specific profiles of expression and provides a coherent model for plant cell cycle control. Plant J. 2005; 41(4):546-66. DOI: 10.1111/j.1365-313X.2004.02319.x. View

Comai L . The advantages and disadvantages of being polyploid. Nat Rev Genet. 2005; 6(11):836-46. DOI: 10.1038/nrg1711. View

Knoll-Gellida A, Andre M, Gattegno T, Forgue J, Admon A, Babin P . Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals. BMC Genomics. 2006; 7:46. PMC: 1488847. DOI: 10.1186/1471-2164-7-46. View

Finn R, Kristoffersen B . Vertebrate vitellogenin gene duplication in relation to the "3R hypothesis": correlation to the pelagic egg and the oceanic radiation of teleosts. PLoS One. 2007; 2(1):e169. PMC: 1770952. DOI: 10.1371/journal.pone.0000169. View

Chen Z . Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol. 2007; 58:377-406. PMC: 1949485. DOI: 10.1146/annurev.arplant.58.032806.103835. View

10.

Santos E, Workman V, Paull G, Filby A, Van Look K, Kille P . Molecular basis of sex and reproductive status in breeding zebrafish. Physiol Genomics. 2007; 30(2):111-22. DOI: 10.1152/physiolgenomics.00284.2006. View

11.

Liu S, Duan W, Tao M, Zhang C, Sun Y, Shen J . Establishment of the diploid gynogenetic hybrid clonal line of red crucian carp x common carp. Sci China C Life Sci. 2007; 50(2):186-93. DOI: 10.1007/s11427-007-0032-2. View

12.

Stupar R, Bhaskar P, Yandell B, Rensink W, Hart A, Ouyang S . Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics. 2007; 176(4):2055-67. PMC: 1950613. DOI: 10.1534/genetics.107.074286. View

13.

Masterson J . Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science. 1994; 264(5157):421-4. DOI: 10.1126/science.264.5157.421. View

14.

Gaeta R, Pires J, Iniguez-Luy F, Leon E, Osborn T . Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell. 2007; 19(11):3403-17. PMC: 2174891. DOI: 10.1105/tpc.107.054346. View

15.

Leitch I, Hanson L, Lim K, Kovarik A, Chase M, Clarkson J . The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Ann Bot. 2008; 101(6):805-14. PMC: 2710205. DOI: 10.1093/aob/mcm326. View

16.

Knight C, Beaulieu J . Genome size scaling through phenotype space. Ann Bot. 2008; 101(6):759-66. PMC: 2710210. DOI: 10.1093/aob/mcm321. View

17.

Mullin B, Prince R, Dick I, Hart D, Spector T, Dudbridge F . Identification of a role for the ARHGEF3 gene in postmenopausal osteoporosis. Am J Hum Genet. 2008; 82(6):1262-9. PMC: 2427258. DOI: 10.1016/j.ajhg.2008.04.016. View

18.

Doyle J, Flagel L, Paterson A, Rapp R, Soltis D, Soltis P . Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet. 2008; 42:443-61. DOI: 10.1146/annurev.genet.42.110807.091524. View

19.

McCarthy D, Smyth G . Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics. 2009; 25(6):765-71. PMC: 2654802. DOI: 10.1093/bioinformatics/btp053. View

20.

Cao X, Wang W . Histology and mucin histochemistry of the digestive tract of yellow catfish, Pelteobagrus fulvidraco. Anat Histol Embryol. 2009; 38(4):254-61. DOI: 10.1111/j.1439-0264.2009.00932.x. View