基因融合作为在稻属中产生新基因的重要机制。
Gene fusion as an important mechanism to generate new genes in the genus Oryza.
机构信息
Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China.
Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.
出版信息
Genome Biol. 2022 Jun 15;23(1):130. doi: 10.1186/s13059-022-02696-w.
BACKGROUND
Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown.
RESULTS
We conduct genome-wide interrogations of four Oryza genomes by designing and implementing novel pipelines to detect fusion genes. Based on the phylogeny of ten plant species, we detect 310 fusion genes across four Oryza species. The estimated rate of origination of fusion genes in the Oryza genus is as high as 63 fusion genes per species per million years, which is fixed at 16 fusion genes per species per million years and much higher than that in flies. By RNA sequencing analysis, we find more than 44% of the fusion genes are expressed and 90% of gene pairs show strong signals of purifying selection. Further analysis of CRISPR/Cas9 knockout lines indicates that newly formed fusion genes regulate phenotype traits including seed germination, shoot length and root length, suggesting the functional significance of these genes.
CONCLUSIONS
We detect new fusion genes that may drive phenotype evolution in Oryza. This study provides novel insights into the genome evolution of Oryza.
背景
基因融合事件在几种生物中都有报道。然而，作为新基因起源的一部分，基因融合的一般作用仍然未知。
结果
我们通过设计和实施新的管道来检测融合基因，对四个水稻基因组进行了全基因组调查。基于十种植物物种的系统发育，我们在四个水稻物种中检测到 310 个融合基因。融合基因在水稻属中的起源速度估计高达每个物种每百万年 63 个融合基因，这一速度固定在每个物种每百万年 16 个融合基因，远高于果蝇中的速度。通过 RNA 测序分析，我们发现超过 44%的融合基因是表达的，90%的基因对显示出强烈的纯化选择信号。对 CRISPR/Cas9 敲除系的进一步分析表明，新形成的融合基因调节表型特征，包括种子萌发、茎长和根长，表明这些基因具有功能意义。
结论
我们检测到新的融合基因，这些基因可能驱动水稻的表型进化。本研究为水稻的基因组进化提供了新的见解。
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