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Small RNA sequencing studies of populations of plant virus families in tropical rainforest of Xishuangbanna |
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| รหัสดีโอไอ | |
| Creator | Yue Liu |
| Title | Small RNA sequencing studies of populations of plant virus families in tropical rainforest of Xishuangbanna |
| Contributor | Xu Shan Shan, Wang Kan, Baohua Kong, Hongxiang Li, Chongde Wang, Taiyuan Yang, Chengyun Li, Yuanhua Tan, Hao Qu, Dexi Wu, Lianchun Wang, Hairu Chen |
| Publisher | Faculty of Science and Agricultural Technology |
| Publication Year | 2563 |
| Journal Title | Journal of Science and Agricultural Technology |
| Journal Vol. | 1 |
| Journal No. | 2 |
| Page no. | 21-28 |
| Keyword | virus, family, population, tropic forest, Xishuangbanna |
| URL Website | https://ph02.tci-thaijo.org/index.php/JSAT/index |
| Website title | JSAT |
| ISSN | 2730-1524 |
| Abstract | To explore the populations of plant virus families in Xishuangbanna tropical rainforests, fifteen pools ofplant samples from different forest locations were collected and used for small RNA analyses by high throughputsequencing. All contigs were classified and annotated with the NCBI Nt database to determine the speciesdistributions, and comparisons were conducted using the Blast algorithm. The viral sequences in the Clean Readswere compared with the relevant sequences, using the Kraken software system, to infer their possible classificationand to analyze the abundance of each species statistically. The number of Clean reads of every pool sample wasfrom 1573897 to 26878598, and the average number of Clean reads was 20322116. The average number of cleanreads is taken as 0.0036% from the average number of Raw reads. The results from a total of 3703 viral sequenceswere annotated, and these represented a total of 16 plant virus families. Among these, 1952 Geminiviridae sequencescomprised the dominant annotated virus proportion. 732 sequences belonged to the Potyviridae, and 192 sequenceswere characteristic of members of the Caulimoviridae. The viral sequences primarily originated from dicots andmonocotyledonous plants, including herbaceous and woody plants. Generally, the total viral sequences fromherbaceous plants represented 66.7 %, and 33.3 % were from woody plants, and amongst these, 57.1% dicotsrepresented the plant hosts, whereas 42.9 % were derived from monocotyledonous families. The presumptiveGeminiviridae and Potyviridae viruses have broad host ranges, and different families were annotated from eachsample site in Xishuangbanna. This study lays a foundation for future research on the evolution and utilization ofviruses within tropical rainforests and those of cultivated agricultural areas. |
