期刊名称：Computational and Structural Biotechnology Journal
印刷版ISSN：2001-0370
出版年度：2021
卷号：19
页码：600-611
DOI：10.1016/j.csbj.2020.12.046
出版社：Computational and Structural Biotechnology Journal
摘要：Retroduplication variation (RDV), a type of retrocopy polymorphism, is considered to have essential biological significance, but its effect on gene function and species phenotype is still poorly understood. To this end, we analyzed the retrocopies and RDVs in 3,010 rice genomes. We calculated the RDV frequencies in the genome of each rice population; detected the mutated, ancestral and expressed retrogenes in rice genomes; and analyzed their RDV influence on rice phenotypic traits. Collectively, 73 RDVs were identified, and 14 RDVs in ancestral retrogenes can significantly affect rice phenotypes. Our research reveals that RDV plays an important role in rice migration, domestication and evolution. We think that RDV is a good molecular breeding marker candidate. To our knowledge, this is the first study on the relationship between retrogene function, expression, RDV and species phenotype.
关键词：Retrocopy ; Retrogene ; Rice ; Retroposition ; RDV ; RDV Retroduplication variation ; Indel Insertion-deletion ; ORF Open reading frame ; FPKM Fragments per kilobase per million mapped reads ; GO Gene ontology ; MF Molecular function ; CC Cellular component ; BP Biological process ; MST monosaccharide transporter
