Journal
JOURNAL OF SYSTEMATICS AND EVOLUTION
Volume 59, Issue 2, Pages 341-351Publisher
WILEY
DOI: 10.1111/jse.12548
Keywords
comparative genomics; origin; orphan gene; transposable element
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Funding
- National Natural Science Foundation of China [31571311]
- Pioneer Hundred Talents Program of the Chinese Academy of Sciences [29Y127E71]
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In this study, the origin of orphan genes in the Oryza sativa ssp. japonica Nipponbare genome was investigated through genome-wide comparisons with 10 closely related Oryza species. A total of 37 orphan genes were identified, with half of them originating through a distinctive mechanism involving the generation of new coding sequences within inserted transposable elements. These results provide valuable insight into genetic innovations in the model rice genome that formed on a very short timescale.
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.
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