First genome survey and repeatome analysis of Chrysopogon zizanioides based on next-generation sequencing
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ORIGINAL ARTICLE
First genome survey and repeatome analysis of Chrysopogon zizanioides based on next-generation sequencing Shuqiong Yang 1 & Jibao Chen 1 & Jun Zhang 1 & Jiafei Liu 2 & Jingjing Yu 1 & Debao Cai 1 & Lunguang Yao 1 & Pengfei Duan 1 Received: 23 January 2020 / Revised: 6 May 2020 / Accepted: 7 May 2020 # Plant Science and Biodiversity Centre, Slovak Academy of Sciences 2020
Abstract Chrysopogon zizanioides is a perennial C4 grass that has been widely utilized for soil erosion control and ecological restoration. Nevertheless, genomic information of C. zizanioides is currently unavailable. Here, we firstly conducted a genome survey of C. zizanioides to obtain its repeatome information through next generation sequencing (NGS) and RepeatExplorer analysis. As a result, the estimated genome size of C. zizanioides was about 880 Mb, the heterozygosity rate was calculated to be 0.80%, the repeat content was 62.08%, and the GC content was 44.71%. Nine different repeat families were identified in the C. zizanioides genome, Ty3/Gypsy retrotransposons represented the dominant family and demonstrated greater diversity than Ty1/Copia retrotransposons, and two C. zizanioides rDNAs displayed high conservation in the genic coding regions and high polymorphism in the intergenic spacer regions. Overall, these results enhanced our understanding of the C. zizanioides genome, and provided a large amount of genomic resources for further excavation and utilization of C. zizanioides. Keywords Chrysopogon zizanioides . Genome survey . Next-generation sequencing . Repeatome
Introduction Chrysopogon zizanioides (L.) Roberty is a perennial C4 grass of the Poaceae, which growing in the tropics and sub-tropics and is native to India (Lavania 2000). C. zizanioides is a miracle grass that can tolerate wide range of climatic and soil conditions, ranging from dry to submerged conditions (Chakrabarty et al. 2015). This grass has been globally and widely used as a source of essential oil extracted from the root, a natural and inexpensive resource for multifarious environmental applications, including conservation and detoxification Shuqiong Yang and Jibao Chen contributed equally to this work. * Jibao Chen [email protected] 1
Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Henan Provincal Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-NorthDiversion Project, Henan Provincal Academician Workstation of Water Security, Nanyang Normal University, Nanyang 473061, China
2
Henan Provincial Key Laboratory of Funiu Mountain Insect Biology, School of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China
of degraded soil and water and also for mitigation of flood and landslide disasters (Kemper 1993; Adams et al. 2003, 2004). However, no genome survey sequences on C. zizanioides have been reported, the narrow genetic and genomic resources obviously limited our understanding of this important
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