Deciphering extrachromosomal circular DNA in Arabidopsis

Keyi Wang; Hui Tian; Lequn Wang; Lin Wang; Yacong Tan; Ziting Zhang; Kai Sun; Meng Yin; Qinggong Wei; Baohua Guo; Jinyu Han; Peiru Zhang; Han Li; Yulong Liu; Hongwei Zhao; Xiaoyong Sun

doi:10.1016/j.csbj.2021.01.043

Deciphering extrachromosomal circular DNA in Arabidopsis

Comput Struct Biotechnol J. 2021 Feb 9:19:1176-1183. doi: 10.1016/j.csbj.2021.01.043. eCollection 2021.

Authors

Keyi Wang¹, Hui Tian², Lequn Wang¹, Lin Wang³, Yacong Tan¹, Ziting Zhang¹, Kai Sun¹, Meng Yin¹, Qinggong Wei¹, Baohua Guo³, Jinyu Han¹, Peiru Zhang¹, Han Li¹, Yulong Liu¹, Hongwei Zhao³, Xiaoyong Sun¹

Affiliations

¹ Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China.
² Shanghai ERA Medicine, Shanghai, China.
³ Department of Plant Pathology, Nanjing Agricultural University, 210095, China.

Abstract

Extrachromosomal circular DNA (eccDNA) is independent of the chromosome and exists in many eukaryotes. However, the nature and origin of eccDNA in plants remains unclear. In this study, we sequenced 12 samples from four tissues (leaf, flower, stem and root) with three biological replicates. In total, we found 743 eccDNAs found in at least two samples. Most of eccDNA have inverted repeats ranging from 4 to 12 bp in the boundaries. Interestingly, eccDNA is not only related to transposon activity, but also hosts tRNA genes, suggesting that the eccDNAs may be associated with tRNA abundance which controls protein synthesis under conditions of stress. Our results provide an unprecedented view of eccDNA, which is still naïve in scope.

Keywords: Arabidopsis; Extrachromosomal circular DNA; High-throughput sequencing; Transposon; tRNA.