J Syst Evol ›› 2021, Vol. 59 ›› Issue (2): 341-351.DOI: 10.1111/jse.12548

• Research Articles • Previous Articles     Next Articles

Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome

Gui-Hua Jin1,2, Yan-Li Zhou1, Hong Yang1,2, Yan-Ting Hu1,2, Yong Shi1, Ling Li1,2, Abu N. Siddique1,3, Chang-Ning Liu4, An-Dan Zhu1, Cheng-Jun Zhang1,5*, and De-Zhu Li1*   

  1. 1 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
    2 University of Chinese Academy of Sciences, Beijing 100049, China
    3 Department of Biotechnology, Bacha Khan University, Charsadda 24420, Pakistan
    4 Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China
    5 Haiyan Engineering and Technology Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
  • Received:2019-02-27 Accepted:2019-11-03 Online:2019-11-07 Published:2021-03-01

Abstract: 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.

Key words: comparative genomics, origin, orphan gene, transposable element