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Yu ST, Zhao R, Sun XQ, Hou MX, Cao YM, Zhang J, Chen YJ, Wang KK, Zhang Y, Li JT, Wang Q. DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp ( Cyprinus carpio). Int J Mol Sci 2024; 25:1635. [PMID: 38338913 PMCID: PMC10855618 DOI: 10.3390/ijms25031635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
DNA methylation and chromatin accessibility play important roles in gene expression, but their function in subgenome expression dominance remains largely unknown. We conducted comprehensive analyses of the transcriptome, DNA methylation, and chromatin accessibility in liver and muscle tissues of allotetraploid common carp, aiming to reveal the function of epigenetic modifications in subgenome expression dominance. A noteworthy overlap in differential expressed genes (DEGs) as well as their functions was observed across the two subgenomes. In the promoter and gene body, the DNA methylation level of the B subgenome was significantly different than that of the A subgenome. Nevertheless, differences in DNA methylation did not align with changes in homoeologous biased expression across liver and muscle tissues. Moreover, the B subgenome exhibited a higher prevalence of open chromatin regions and greater chromatin accessibility, in comparison to the A subgenome. The expression levels of genes located proximally to open chromatin regions were significantly higher than others. Genes with higher chromatin accessibility in the B subgenome exhibited significantly elevated expression levels compared to the A subgenome. Contrastingly, genes without accessibility exhibited similar expression levels in both subgenomes. This study contributes to understanding the regulation of subgenome expression dominance in allotetraploid common carp.
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Affiliation(s)
- Shuang-Ting Yu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
- Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Xiao-Qing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Ming-Xi Hou
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Yi-Ming Cao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Jin Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Ying-Jie Chen
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Kai-Kuo Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (S.-T.Y.); (R.Z.); (X.-Q.S.); (M.-X.H.); (Y.-M.C.); (J.Z.); (Y.-J.C.); (K.-K.W.); (Y.Z.)
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2
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Ren L, Gao X, Cui J, Zhang C, Dai H, Luo M, He S, Qin Q, Luo K, Tao M, Xiao J, Wang J, Zhang H, Zhang X, Zhou Y, Wang J, Zhao X, Liu G, Wang G, Huo L, Wang S, Hu F, Zhao R, Zhou R, Wang Y, Liu Q, Yan X, Wu C, Yang C, Tang C, Duan W, Liu S. Symmetric subgenomes and balanced homoeolog expression stabilize the establishment of allopolyploidy in cyprinid fish. BMC Biol 2022; 20:200. [PMID: 36100845 PMCID: PMC9472340 DOI: 10.1186/s12915-022-01401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
Background Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids. Results We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis. Conclusions Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01401-4.
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Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Mengxue Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shaofang He
- Wuhan Carbon Code Biotechnologies Corporation, Wuhan, 430070, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Hong Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yi Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jing Wang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xin Zhao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Linhe Huo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rong Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qinfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiaojing Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Wei Duan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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Cui J, Zhang H, Gao X, Zhang X, Luo M, Ren L, Liu S. Correlations of expression of nuclear and mitochondrial genes in triploid fish. G3 GENES|GENOMES|GENETICS 2022; 12:6655693. [PMID: 35924985 PMCID: PMC9434317 DOI: 10.1093/g3journal/jkac197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022]
Abstract
Abstract
The expression of nuclear and mitochondrial genes, as well as their coordinated control, regulates cell proliferation, individual development, and disease in animals. However, the potential coregulation between nuclear and mitochondrial genes is unclear in triploid fishes. The two triploids (R2C and RC2) with distinct mitochondrial genomes but similar nuclear genomes exhibit different embryonic development times and growth rates. They are an excellent model for studying how nuclear and mitochondrial genes coordinate. Here, we performed the mRNA-seq of four stages of embryonic development (blastula, gastrula, segmentation, and hatching periods) in the two triploids (R2C and RC2) and their diploid inbred parents (red crucian carp and common carp). After establishing the four patterns of mitochondrial and nuclear gene expression, 270 nuclear genes regulated by mitochondrial genes were predicted. The expression levels of APC16 and Trim33 were higher in RC2 than in R2C, suggesting their potential effects on regulating embryonic development time. In addition, 308 differentially expressed genes filtered from the list of nuclear-encoded mitochondrial genes described by Mercer et al. in 2011 were considered potential genes for which nuclear genes regulate mitochondrial function. The findings might aid in our understanding of the correlation between mitochondrial and nuclear genomes as well as their synergistic effects on embryonic development.
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Affiliation(s)
- Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Hong Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Mengxue Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
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4
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Ren L, Zhang H, Luo M, Gao X, Cui J, Zhang X, Liu S. Heterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish. Epigenetics Chromatin 2022; 15:19. [PMID: 35597966 PMCID: PMC9123727 DOI: 10.1186/s13072-022-00455-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022] Open
Abstract
Background Heterosis of growth traits in allotriploid fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Now, an allotriploid complex, including two triploids and their diploid inbred parents, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis. Results Here, we performed a series of analyses on DNA methylation modification and miRNA expression in combination with gene expression in the allotriploid complex. We first established a model of cis- and trans-regulation related to DNA methylation and miRNA in allotriploids. Then, comparative analyses showed that DNA methylation contributed to the emergence of a dosage compensation effect, which reduced gene expression levels in the triploid to the diploid state. We detected 31 genes regulated by DNA methylation in the subgenomes of the allotriploids. Finally, the patterns of coevolution between small RNAs and their homoeologous targets were classified and used to predict the regulation of miRNA expression in the allotriploids. Conclusions Our results uncovered the regulatory network between DNA methylation and miRNAs in allotriploids, which not only helps us understand the regulatory mechanisms of heterosis of growth traits but also benefits the study and application of epigenetics in aquaculture. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00455-6.
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Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Hong Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Mengxue Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China. .,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
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5
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The formation and biological characterization of two allotriploid fish derived from interploid crosses. REPRODUCTION AND BREEDING 2022. [DOI: 10.1016/j.repbre.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Ren L, Zhang X, Li J, Yan X, Gao X, Cui J, Tang C, Liu S. Diverse transcriptional patterns of homoeologous recombinant transcripts in triploid fish (Cyprinidae). SCIENCE CHINA. LIFE SCIENCES 2021; 64:1491-1501. [PMID: 33420922 DOI: 10.1007/s11427-020-1749-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/13/2020] [Indexed: 11/29/2022]
Abstract
Homoeologous recombination (HR), the exchange of homoeologous chromosomes, contributes to subgenome adaptation to diverse environments by producing various phenotypes. However, the potential relevance of HR and innate immunity is rarely described in triploid cyprinid fish species. In our study, two allotriploid genotypes (R2C and RC2), whose innate immunity was stronger than their inbred parents (Carassius auratus red var. and Cyprinus carpio L.), were obtained from backcrossing between male allotetraploids of C. auratus red var.×C. carpio L. and females of their two inbred parents, respectively. The work detected 140 HRs shared between the two triploids at the genomic level. Further, transcriptions of 54 homoeologous recombinant genes (HRGs) in R2C and 65 HRGs in RC2 were detected using both Illumina and PacBio data. Finally, by comparing expressed recombinant reads to total expressed reads in each of the genes, a range of 0.1%-10% was observed in most of the 99-193 HRGs, of which six recombinant genes were classified as "response to stimulus". These results not only provide a novel way to predict HRs in allopolyploids based on cross prediction at both genomic and transcriptional levels, but also insight into the potential relationship between HRs related to innate immunity and adaptation of the triploids and allotetraploids.
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Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jiaming Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiaojing Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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