Genome Sequences of Three Apple chlorotic leaf spot virus Isolates from Hawthorns in China.

Wei Guo,Hongyan Dai,Xiaohong Li,Yue Ma,Mei Wang,Wenyan Zheng,Yuepeng Han

doi:10.1371/journal.pone.0161099

Wei Guo, Hongyan Dai + Show 5 more

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https://doi.org/10.1371/journal.pone.0161099

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Abstract

The genome sequences of Apple chlorotic leaf spot virus (ACLSV) isolates from three accessions of hawthorns (Crataegus pinnatifida) grown at Shenyang Agricultural University were determined using Illumina RNA-seq. To confirm the assembly data from the de novo sequencing, two ACLSV genomic sequences (SY01 and SY02) were sequenced using the Sanger method. The SY01 and SY02 sequences obtained with the Sanger method showed 99.5% and 99.7% nucleotide identity with the transcriptome data, respectively. The genome sequences of the hawthorn isolates SY01, SY02 and SY03 (GenBank accession nos. KM207212, KU870524 and KU870525, respectively) consisted of 7,543, 7,561 and 7,545 nucleotides, respectively, excluding poly-adenylated tails. Sequence analysis revealed that these hawthorn isolates shared an overall nucleotide identity of 82.8–92.1% and showed the highest identity of 90.3% for isolate YH (GenBank accession no. KC935955) from pear and the lowest identity of 67.7% for isolate TaTao5 (GenBank accession no. EU223295) from peach. Hawthorn isolate sequences were similar to those of ‘B6 type’ ACLSV. The relationship between ACLSV isolates largely depends upon the host species. This represents the first comparative study of the genome sequences of ACLSV isolates from hawthorns.

Highlights

Apple chlorotic leaf spot virus (ACLSV), a representative species of genus Trichovirus in family Betaflexiviridae [1], is distributed worldwide and can infect most fruit tree species of family Rosaceae, including apple, pear, peach, plum, almond, apricot, cherry and hawthorn [2]
The reassembled full-length sequences of SY01 and SY02 showed 99.5% and 99.7% nucleotide identities, respectively, with the transcriptome data, which confirmed the reliability of our transcriptome data
Viral RNA was extracted from purified virus [6] and first- and second-strand cDNA were obtained by generating cDNA libraries [20]

Summary

Introduction

Apple chlorotic leaf spot virus (ACLSV), a representative species of genus Trichovirus in family Betaflexiviridae [1], is distributed worldwide and can infect most fruit tree species of family Rosaceae, including apple, pear, peach, plum, almond, apricot, cherry and hawthorn [2]. ACLSV is a latent virus that usually cannot cause obvious symptoms in cultivars of apples and pears. The severity of the symptoms caused by ACLSV shows a strong association with plant species and virus strains [2,3]. The virus can cause severe symptoms in many pomes and stone fruit trees, including plant dysplasia and less robust plant growth. The main disease agent of apples and pears grafted onto susceptible rootstocks can be attributed to co-infection of ACLSV with Apple stem grooving virus and/or Apple stem pitting virus [4].

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