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Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome
Author(s) -
Jin GuiHua,
Zhou YanLi,
Yang Hong,
Hu YanTing,
Shi Yong,
Li Ling,
Siddique Abu N.,
Liu ChangNing,
Zhu AnDan,
Zhang ChengJun,
Li DeZhu
Publication year - 2021
Publication title -
journal of systematics and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.249
H-Index - 46
eISSN - 1759-6831
pISSN - 1674-4918
DOI - 10.1111/jse.12548
Subject(s) - transposable element , genome , biology , gene , genetics , transposition (logic) , oryza sativa , intron , retrotransposon , group ii intron , rna splicing , rna , linguistics , philosophy
Orphan genes are genetic innovations that lack homologs in other lineages. Orphan genes can rapidly originate and become substantially functional, yet the mechanisms underlying their origins are still largely unknown in plants. Here, we investigated the origin of orphan genes in the Oryza sativa ssp. japonica “Nipponbare” genome using genome‐wide comparisons with 10 closely related Oryza species. We identified a total of 37 orphan genes in the Nipponbare genome that show short sequence lengths, elevated GC content, and absence of introns. Interestingly, half of the identified orphan genes originated by way of a distinctive mechanism that involved the generation of new coding sequences through independent and rapid divergence within the inserted transposable element. Our results provide valuable insight into genetic innovations in the model rice genome that formed on a very short timescale.