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Population structure and selection pressure analysis among Sugarcane yellow leaf virus isolates based on P0 and P1 sequences

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Abstract

Yellow leaf of sugarcane is caused by Sugarcane yellow leaf virus (SCYLV) and has been a threat to global sugar industry. Understanding the diversity and genetic structure of plant virus populations may help to develop strategies to control virus-induced diseases. In this study, demography, genetic differentiation and selection pressure were assessed based on 57 nucleotide sequences of the P0 (567 nt) and 54 nucleotide sequences of the P1 (1413 nt) genes of SCYLV isolates. Phylogenetic analysis revealed three phylogeographical groups: African (Clade I), Chinese/American (Clade II), and Asian (Clade III). Genetic distance values between groups (0.034–0.250) were higher than within-group values (0.011–0.033). The African group was in a state of expansion, with lower nucleotide sequence diversity. Except for those isolates within the Asian group, SCYLV showed infrequent gene flow within or between phylogenetic groups. Analysis of selection pressure suggested that these two genes have been subjected to negative (purifying) selection. However, some sites, especially in the P0 coding region of the Chinese/American group, have undergone positive selection. Overall, aside from recombination and founder effects, gene flow and purifying selection are two important factors driving SCYLV evolution.

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Acknowledgments

This research was supported by a grant from the National Natural Science Foundation of China (31170345), an Earmarked Fund from the China Agriculture Research System (CARS-20-2-4), and the Major Science and Technology Project of Fujian Province (2015NZ0002-2) in China.

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    Authors and Affiliations

    1. Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

      Chun-Hui Zhao, Hua-Ying Fu, Ru-Kai Chen & San-Ji Gao

    2. Fujian Institute of Tropical Crops, Zhangzhou, Fujian, 363000, China

      Yi-Hua Lin

    3. Sugarcane Research Unit, Houma, USDA-ARS, Louisiana, LA, 70360, USA

      Yong-Bao Pan & Michael Paul Grisham

    4. College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

      Yu Li

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    1. Chun-Hui Zhao
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    Correspondence to Yu Li or San-Ji Gao.

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    Section Editor: Alice Inoue-Nagata

    Chun-Hui Zhao and Yi-Hua Lin contributed equally to this work.

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    Zhao, CH., Lin, YH., Pan, YB. et al. Population structure and selection pressure analysis among Sugarcane yellow leaf virus isolates based on P0 and P1 sequences. Trop. plant pathol. 41, 237–245 (2016). https://doi.org/10.1007/s40858-016-0096-2

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