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Transcriptome sequencing reveals novel Citrus bark cracking viroid (CBCVd) variants from citrus and their molecular characterization

Yafei Wang: Citrus Research Institute, Southwest University

<div><em>Citrus bark cracking viroid</em> (CBCVd) has been identified as an important causative agent on citrus and hop. In this study, we obtained the full-length genomes of different variants of citrus viroids from Pakistan through transcriptome sequencing. CBCVd variants were first found in Pakistan. These newly discovered Pakistani CBCVd variants were provisionally named as ‘CBCVd-LSS’ for their low sequence similarity (80.9%-88.9%) with the CBCVd RefSeq sequence (NC_003539). Two most predominant CBCVd sequences from Pakistan had the highest, 91% and 88% identity with two CBCVd sequences isolated from hop, respectively. Identification and molecular characterization of CBCVd from citrus in Pakistan and China were also reported. The length of CBCVd from China ranged from 282 to 286 nucleotides, while from Pakistan it ranged from 273 to 277 nucleotides. Based on genetic diversity and phylogenetic analysis, two main CBCVd clades were identified. CBCVd sequences were further divided into six sub-clades. Sequence alignment revealed some nucleotide changes between these sub-clades, and analysis indicated that several mutations could significantly affect the primary and secondary structure of the viroid. Our results indicated that the CBCVd sequences from Pakistan and China were significantly different and Pakistan might be one of the independent geographical origins of CBCVd worldwide.</p> <p>Funding:Chongqing Research Program of Basic Research and Frontier Technology (cstc2017jcyjBX0016)</div>

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