Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea.
Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
Nucleic Acids Res. 2021 Nov 18;49(20):11765-11777. doi: 10.1093/nar/gkab932.
Transposable element (TE)-derived genes are increasingly recognized as major sources conferring essential traits in agriculturally important crops but underlying evolutionary mechanisms remain obscure. We updated previous annotations and constructed 18,744 FAR-RED IMPAIRED RESPONSE1 (FAR1) genes, a transcription factor family derived from Mutator-like elements (MULEs), from 80 plant species, including 15,546 genes omitted in previous annotations. In-depth sequence comparison of the updated gene repertoire revealed that FAR1 genes underwent continuous structural divergence via frameshift and nonsense mutations that caused premature translation termination or specific domain truncations. CRISPR/Cas9-based genome editing and transcriptome analysis determined a novel gene involved in fertility-regulating transcription of rice pollen, denoting the functional capacity of our re-annotated gene models especially in monocots which had the highest copy numbers. Genomic evidence showed that the functional gene adapted by obtaining a shortened form through a frameshift mutation caused by a tandem duplication of a 79-bp sequence resulting in premature translation termination. Our findings provide improved resources for comprehensive studies of FAR1 genes with beneficial agricultural traits and unveil novel evolutionary mechanisms generating structural divergence and subsequent adaptation of TE-derived genes in plants.
转座元件（TE）衍生基因越来越被认为是赋予农业重要作物重要性状的主要来源，但潜在的进化机制仍不清楚。我们更新了之前的注释，并构建了 18744 个源自 Mutator-like 元件（MULEs）的 FAR-RED IMPAIRED RESPONSE1（FAR1）转录因子家族基因，这些基因来自 80 种植物物种，包括之前注释中省略的 15546 个基因。对更新的基因库进行深入的序列比较表明，FAR1 基因通过移码和无意义突变经历了持续的结构分化，导致翻译过早终止或特定结构域截断。基于 CRISPR/Cas9 的基因组编辑和转录组分析确定了一个参与调控水稻花粉育性的转录的新基因，这表明我们重新注释的基因模型的功能能力，特别是在具有最高拷贝数的单子叶植物中。基因组证据表明，功能基因通过获得通过串联重复 79 个碱基序列引起的移码突变而获得的缩短形式来适应，导致翻译过早终止。我们的研究结果为全面研究具有有益农业性状的 FAR1 基因提供了改进的资源，并揭示了 TE 衍生基因在植物中产生结构分化和随后适应的新进化机制。
