scholarly journals The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus

2019 ◽  
Vol 29 (11) ◽  
pp. 1805-1815 ◽  
Author(s):  
Li Ren ◽  
Wuhui Li ◽  
Qinbo Qin ◽  
He Dai ◽  
Fengming Han ◽  
...  
Keyword(s):  
Megalobrama Amblycephala ◽  
Culter Alburnus ◽  
Asymmetric Expression

scholarly journals Asymmetric expression of homoeologous genes contributes to dietary adaption of an allodiploid hybrid fish derived from Megalobrama amblycephala (♀) × Culter alburnus (♂)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wuhui Li ◽  
Shi Wang ◽  
Jie Hu ◽  
Chenchen Tang ◽  
Chang Wu ◽  
...  
Keyword(s):  
Differential Expression ◽  
Megalobrama Amblycephala ◽  
Genetic Breeding ◽  
Dietary Adaptation ◽  
Homoeologous Genes ◽  
Hybrid Fish ◽  
Culter Alburnus ◽  
Mechanistic Basis ◽  
Fish Genetic Breeding ◽  
Asymmetric Expression

Abstract Background Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with one another in a single nucleus, which may cause subgenome interaction and dominance at the gene expression level and has been observed in some allopolyploid plants. In our previous studies, newly formed allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) had herbivorous characteristic. It is thus interesting to further characterize whether the subgenome interaction and dominance derive dietary adaptation of this hybrid fish. Results Differential expression, homoeolog expression silencing and bias were investigated in the hybrid fish after 70 days of adaptation to carnivorous and herbivorous diets. A total of 2.65 × 108 clean reads (74.06 Gb) from the liver and intestinal transcriptomes were mapped to the two parent genomes based on specific SNPs. A total of 2538 and 4385 differentially expressed homoeologous genes (DEHs) were identified in the liver and intestinal tissues between the two groups of fish, respectively, and these DEHs were highly enriched in fat digestion and carbon metabolism, amino acid metabolism and steroid biosynthesis. Furthermore, subgenome dominance were observed in tissues, with paternal subgenome was more dominant than maternal subgenome. Moreover, subgenome expression dominance controlled functional pathways in metabolism, disease, cellular processes, environment and genetic information processing during the two dietary adaptation processes. In addition, few but sturdy villi in the intestine, significant fat accumulation and a higher concentration of malondialdehyde in the liver were observed in fish fed carnivorous diet compared with fish fed herbivorous diet. Conclusions Our results indicated that diet drives phenotypic and genetic variation, and the asymmetric expression of homoeologous genes (including differential expression, expression silencing and bias) may play key roles in dietary adaptation of hybrid fish. Subgenome expression dominance may contribute to uncovering the mechanistic basis of heterosis and also provide perspectives for fish genetic breeding and application.

The formation of a new type of hybrid culter derived from a hybrid lineage of Megalobrama amblycephala (♀) × Culter alburnus (♂)

Aquaculture ◽  
2020 ◽  
Vol 525 ◽  
pp. 735328 ◽  
Author(s):  
Chang Wu ◽  
Xu Huang ◽  
Qian Chen ◽  
Fangzhou Hu ◽  
Luojing Zhou ◽  
...  
Keyword(s):  
Megalobrama Amblycephala ◽  
New Type ◽  
Culter Alburnus

scholarly journals Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala ´ Culter alburnus

2020 ◽  
Author(s):  
Li Ren ◽  
Xiaojing Yan ◽  
Xin Gao ◽  
Jialin Cui ◽  
Pengcheng Yan ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Mrna Expression ◽  
Maternal Effects ◽  
Reciprocal Cross ◽  
Differentially Expressed ◽  
Megalobrama Amblycephala ◽  
Homoeologous Genes ◽  
Morphogenetic Protein ◽  
Illumina Data ◽  
Culter Alburnus

Abstract Background : Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animals. Results: Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. In a comparison of BSB- and TC- homoeolog expression from the two reciprocal cross hybrids, we identified 49–348 differentially expressed BSB-homoeologous genes and 54–354 differentially expressed TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonads, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TBF3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BTF3. These results further improve AS prediction at the homoeolog level. The various AS patterns in bmpr2a belonged to the bone morphogenetic protein family were selected as an AS model to investigate expression diversity and their potential effects to body shape traits.Conclusions: The distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects were the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.

scholarly journals Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala x Culter alburnus

2019 ◽  
Author(s):  
Li Ren ◽  
Xiaojing Yan ◽  
Xin Gao ◽  
Jialin Cui ◽  
Pengcheng Yan ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Mrna Expression ◽  
Maternal Effects ◽  
Reciprocal Cross ◽  
Differentially Expressed ◽  
Megalobrama Amblycephala ◽  
Homoeologous Gene ◽  
Gene Pairs ◽  
Homoeologous Genes ◽  
Culter Alburnus

Abstract Background Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animal. Results Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. In a comparison of BSB and TC homoeolog expression from the two reciprocal cross hybrids, we identified 49–347 differentially expressed BSB-homoeologous genes and 54–354 TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonads, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TB F3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BT F3 homoeologous gene pairs. These results further improve AS prediction at the homoeolog level. To analyze body shape traits, bmpr2a of the bone morphogenetic protein family was selected as an AS model to investigate expression diversity. Conclusions The distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects are the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.

The fertility of the hybrid lineage derived from female Megalobrama amblycephala×male Culter alburnus

2014 ◽  
Vol 151 (1-2) ◽  
pp. 61-70 ◽  
Author(s):  
Jun Xiao ◽  
Xuewei Kang ◽  
Lihua Xie ◽  
Qinbo Qin ◽  
Zhoulin He ◽  
...  
Keyword(s):  
Megalobrama Amblycephala ◽  
Culter Alburnus

scholarly journals Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala x Culter alburnus

2020 ◽  
Author(s):  
Li Ren ◽  
Xiaojing Yan ◽  
Xin Gao ◽  
Jialin Cui ◽  
Pengcheng Yan ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Mrna Expression ◽  
Maternal Effects ◽  
Reciprocal Cross ◽  
Differentially Expressed ◽  
Megalobrama Amblycephala ◽  
Homoeologous Genes ◽  
Morphogenetic Protein ◽  
Illumina Data ◽  
Culter Alburnus

Abstract Background Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animals. Results Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. In a comparison of BSB- and TC- homoeolog expression from the two reciprocal cross hybrids, we identified 49–348 differentially expressed BSB-homoeologous genes and 54–354 differentially expressed TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonads, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TBF3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BTF3. These results further improve AS prediction at the homoeolog level. The various AS patterns in bmpr2a belonged to the bone morphogenetic protein family were selected as an AS model to investigate expression diversity and their potential effects to body shape traits.Conclusions The distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects were the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.

scholarly journals Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala x Culter alburnus

2019 ◽  
Author(s):  
Li Ren ◽  
Xiaojing Yan ◽  
Xin Gao ◽  
Jialin Cui ◽  
Wuhui Li ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Mrna Expression ◽  
Maternal Effects ◽  
Reciprocal Cross ◽  
Differentially Expressed ◽  
Megalobrama Amblycephala ◽  
Homoeologous Gene ◽  
Gene Pairs ◽  
Homoeologous Genes ◽  
Culter Alburnus

Abstract Abstract Background Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animal. Results Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. In a comparison of BSB and TC homoeolog expression from the two reciprocal cross hybrids, we identified 49–347 differentially expressed BSB-homoeologous genes and 54–354 TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonads, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TBF 3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BTF 3 homoeologous gene pairs. These results further improve AS prediction at the homoeolog level. The various AS patterns in bmpr2a with belonged to the bone morphogenetic protein family was selected as an AS model to investigate expression diversity and their potential effects to body shape traits. Conclusions The distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects are the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.

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