The genetic structure and recombination analyses of Sweetpotato leaf curl virus (SPLCV) population in China
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ORIGINAL ARTICLE
The genetic structure and recombination analyses of Sweetpotato leaf curl virus (SPLCV) population in China Chengling Zhang1 · Houjun Sun1 · Yiping Xie1 · Dongjing Yang1 · Mei Zhang1 · Jukui Ma1 Received: 17 September 2019 / Accepted: 14 June 2020 © Deutsche Phytomedizinische Gesellschaft 2020
Abstract Sweetpotato leaf curl virus (SPLCV) is a species of virus that causes substantial yield losses in sweetpotato. In this study, twenty-four complete genomic sequences of SPLCV which identified from the sweetpotato samples collected from China, were calculated into four strains. A total of 11.9% isolates were recombinants, and ten recombination patterns were detected. In addition to C3, V1, IR and C1 genes, the both ends of the V2 gene were also identified as recombination hot spots for SPLCV. Negative (purifying) selection was identified among all six SPLCV genes, except for C4 gene was under the variety of choices (positive selection) for adaptive protein evolution. The mismatch distribution of SPLCV in all subgroups and groups was multiple peaked or ragged, indicating SPLCV population has existed for a long time. The gene flows between Shandong, Hebei and Jiangsu Provinces in China were frequent, which was also observed between the groups of China, Brazil, South Korea. Recombination, selection pressure and gene flow promote the evolution of the SPLCV in China. Keywords Sweetpotato · Sweetpotato leaf curl virus · Gene flow · Genetic diversity · Recombination
Introduction Sweetpotato (Ipomoea batatas) is a creepy herbaceous plant and widely cultivated staple crop among the world (Clark et al. 2012). China is considered as the largest producer of sweetpotato in the world, and it produces about 75% of world production (Gao et al. 2000). However, production of sweetpotato is affected by several serious diseases that still not effectively controlled in China (Gao et al. 2000; Clark et al. 2002; Xie et al. 2013). More than thirty different viruses have been found in sweetpotato, including RNA and DNA viruses. Sweetpotato leaf curl virus (SPLCV), a member of begomoviruses that belongs to the large family Geminiviridae, Electronic supplementary material The online version of this article (https://doi.org/10.1007/s41348-020-00348-4) contains supplementary material, which is available to authorized users. * Chengling Zhang [email protected] 1
Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou 221131, Jiangsu, China
has been detected in countries where sweetpotato was cultivated, such as China (Luan et al. 2007), USA (Lotrakul et al. 1998), Spain (Albuquerque et al. 2012), Peru (Fuentes and Salazar 2003), Italy (Briddon et al. 2006), Kenya (Maina et al. 2017), Korea (Park et al. 2011), Argentina (Pardina et al. 2012) and Sudan (Mohammed et al. 2017). Symptoms induced by SPLCV are leaf curling, yellowing or vein swelling, darkening of tuber sk
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