Inoue Komaki, Takahagi Kotaro, Kouzai Yusuke, Koda Satoru, Shimizu Minami, Uehara-Yamaguchi Yukiko, Nakayama Risa, Kita Toshie, Onda Yoshihiko, Nomura Toshihisa, Matsui Hidetoshi, Nagaki Kiyotaka, Nishii Ryuei, Mochida Keiichi
RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan.
Graduate School of Mathematics, Kyushu University, Fukuoka, 819-0395, Japan.
NAR Genom Bioinform. 2020 Sep 22;2(3):lqaa067. doi: 10.1093/nargab/lqaa067. eCollection 2020 Sep.
Polyploidy is a widespread phenomenon in eukaryotes that can lead to phenotypic novelty and has important implications for evolution and diversification. The modification of phenotypes in polyploids relative to their diploid progenitors may be associated with altered gene expression. However, it is largely unknown how interactions between duplicated genes affect their diurnal expression in allopolyploid species. In this study, we explored parental legacy and hybrid novelty in the transcriptomes of an allopolyploid species and its diploid progenitors. We compared the diurnal transcriptomes of representative cytotypes, including the allotetraploid and its diploid progenitors and . We also artificially induced an autotetraploid . We identified patterns of homoeolog expression bias (HEB) across cytotypes and time-dependent gain and loss of HEB in . Furthermore, we established that many genes with diurnal expression experienced HEB, while their expression patterns and peak times were correlated between homoeologs in relative to and , suggesting diurnal synchronization of homoeolog expression in . Our findings provide insight into the parental legacy and hybrid novelty associated with polyploidy in , and highlight the evolutionary consequences of diurnal transcriptional regulation that accompanied allopolyploidy.
多倍体是真核生物中一种普遍存在的现象，它能够导致表型新奇性，并且对进化和多样化具有重要意义。相对于其二倍体祖先，多倍体中表型的改变可能与基因表达的变化有关。然而，在异源多倍体物种中，重复基因之间的相互作用如何影响它们的昼夜表达，在很大程度上尚不清楚。在本研究中，我们在一个异源多倍体物种及其二倍体祖先的转录组中探索了亲本遗传和杂种新奇性。我们比较了代表性细胞型的昼夜转录组，包括异源四倍体及其二倍体祖先和。我们还人工诱导了一个同源四倍体。我们确定了不同细胞型间同源基因表达偏向（HEB）的模式，以及中HEB随时间的增减情况。此外，我们证实许多具有昼夜表达的基因经历了HEB，而相对于和，它们在中的同源基因的表达模式和峰值时间是相关的，这表明中同源基因表达的昼夜同步性。我们的研究结果为中与多倍体相关的亲本遗传和杂种新奇性提供了见解，并突出了伴随异源多倍体的昼夜转录调控的进化后果。
