Genome-wide analysis of short interspersed nuclear elements provides insight into gene and genome evolution in citrus. (3rd May 2020)

• Record Type: Journal Article
• Authors: Meng, Haijun; Feng, Jiancan; Bai, Tuanhui; Jian, Zaihai; Chen, Yanhui; Wu, Guoliang
• Is Part Of: DNA research. Volume 27:Number 1(2020)
• Publication Date: 2020-05-03
• Subjects: citrus -- evolution -- gene association -- genome -- short interspersed nuclear elements; Genes -- Periodicals; Genomes -- Periodicals; Genes -- Research -- Periodicals; Genomics -- Periodicals; DNA -- Research -- Periodicals; 572.86072
• DOI: 10.1093/dnares/dsaa004
• Languages: English
• ISSNs: 1340-2838

Abstract

Abstract: Short interspersed nuclear elements (SINEs) are non-autonomous retrotransposons that are highly abundant, but not well annotated, in plant genomes. In this study, we identified 41, 573 copies of SINEs in seven citrus genomes, including 11, 275 full-length copies. The citrus SINEs were distributed among 12 families, with an average full-length rate of 0.27, and were dispersed throughout the chromosomes, preferentially in AT-rich areas. Approximately 18.4% of citrus SINEs were found in close proximity (≤1 kb upstream) to genes, indicating a significant enrichment of SINEs in promoter regions. Citrus SINEs promote gene and genome evolution by offering exons as well as splice sites and start and stop codons, creating novel genes and forming tandem and dispersed repeat structures. Comparative analysis of unique homologous SINE-containing loci (HSCLs) revealed chromosome rearrangements in sweet orange, pummelo, and mandarin, suggesting that unique HSCLs might be valuable for understanding chromosomal abnormalities. This study of SINEs provides us with new perspectives and new avenues by which to understand the evolution of citrus genes and genomes.