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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The raw genome data from Illumina sequencing, raw transcriptome data from Illumina sequencing, and raw transcriptome data from PacBio sequencing were deposited in the NCBI Short Read Archive (accession Nos.: SRR9983189 and SRR9983190; SRR8735277-SRR8735279, SRR8712975-SRR8712976, and SRR8712978-SRR8712991; and SRR9203584, SRR9185089, and SRR9185090, respectively).
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (31702334, 31730098, U19A2040 and 31430088), the Key Research and Development Program of Hunan Province (2018NK2072 and 2017NK1031), the Earmarked Fund for China Agriculture Research System (CARS-45), 111 Project (D20007), High-Level Talent Agglomeration Program of Hunan, China (2019RS1044), the Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486). We thank Mallory Eckstut, PhD, from Liwen Bianji, Edanz Editing China (https://www.liwenbianji.cn/ac), for editing the English text of a draught of this manuscript.
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Ren, L., Zhang, X., Li, J. et al. Diverse transcriptional patterns of homoeologous recombinant transcripts in triploid fish (Cyprinidae). Sci. China Life Sci. 64, 1491–1501 (2021). https://doi.org/10.1007/s11427-020-1749-9
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DOI: https://doi.org/10.1007/s11427-020-1749-9