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

Computational and Structural Biotechnology Journal (Jan 2021)

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

Affiliations

Keyi Wang: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Hui Tian: Shanghai ERA Medicine, Shanghai, China
Lequn Wang: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Lin Wang: Department of Plant Pathology, Nanjing Agricultural University, 210095, China
Yacong Tan: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Ziting Zhang: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Kai Sun: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Meng Yin: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Qinggong Wei: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Baohua Guo: Department of Plant Pathology, Nanjing Agricultural University, 210095, China
Jinyu Han: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Peiru Zhang: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Han Li: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Yulong Liu: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
Hongwei Zhao: Department of Plant Pathology, Nanjing Agricultural University, 210095, China; Corresponding authors.
Xiaoyong Sun: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China; Corresponding authors.

DOI: https://doi.org/10.1016/j.csbj.2021.01.043
Journal volume & issue: Vol. 19
pp. 1176 – 1183

Abstract

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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.

Published in Computational and Structural Biotechnology Journal

ISSN: 2001-0370 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Technology: Chemical technology: Biotechnology
Website: https://www.sciencedirect.com/journal/computational-and-structural-biotechnology-journal

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