First genome survey and repeatome analysis of Chrysopogon zizanioides based on next-generation sequencing
| Autor: | Jiafei Liu, Debao Cai, Jingjing Yu, Jun Zhang, Shuqiong Yang, Pengfei Duan, Lunguang Yao, Jibao Chen |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine biology food and beverages Retrotransposon Cell Biology Plant Science biology.organism_classification 01 natural sciences Biochemistry Genome DNA sequencing Chrysopogon zizanioides Loss of heterozygosity 03 medical and health sciences 030104 developmental biology Evolutionary biology Genetics Coding region Animal Science and Zoology Molecular Biology Genome size Ecology Evolution Behavior and Systematics GC-content 010606 plant biology & botany |
| Zdroj: | Biologia. 75:1273-1282 |
| ISSN: | 1336-9563 0006-3088 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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