ArticleNucleic acids research2021
Recurrent mutations promote widespread structural and functional divergence of MULE-derived genes in plants.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 20 citations in OpenAlex.
- ThePlants (Basel, Switzerland) · 2026Review
- Identification and expression analyses of B3 genes reveal lineage-specific evolution and potential roles of REM genes in pepper.BMC plant biology · 2024Article
- Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes.Nucleic acids research · 2023Article
- Genome-wide characterization of long terminal repeat retrotransposons provides insights into trait evolution of four cucurbit species.Functional & integrative genomics · 2023Article
- Thermo-Sensitive Spikelet Defects 1 acclimatizes rice spikelet initiation and development to high temperature.Plant physiology · 2023Article
- Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae.BMC plant biology · 2023Article
- Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses.BMC plant biology · 2022Article
- Two different domain architectures generate structural and functional diversity amongFrontiers in plant science · 2022Article
- FAR1/FHY3 Transcription Factors Positively Regulate the Salt and Temperature Stress Responses inFrontiers in plant science · 2022Article
- ABA Signaling De-Repression Coordinates With Cytokinin to Drive Large Petal Formation in Brassica napus.Physiologia plantarumArticle
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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