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Abstract
Apple (Malus domestica) fruits exhibiting bright stripe symptoms were identified in Weihai City, Shandong Province, China. To investigate the virome in the apple samples, the method of high throughput sequencing (HTS) was used to identify the viruses. It was found that the sequence of citrus concave gum-associated virus (CCGaV) was involved in the apple transcriptome dataset. The full-length genome of the CCGaV-Weihai isolate contained two segments, the RNA1 was 6674 nt in size containing a conserved RNA-dependent RNA polymerase (RdRp), and the RNA2 was ambisense, 2706 nt in length, encoding a movement protein (MP) and a coat protein (CP). Sequence alignment and phylogenetic analyses indicated that CCGaV-Weihai was more closely related to CCGaV-H2799 isolated from the apple host in the United States and distantly related to CCGaV-CGW2 from Citrus sinensis in Italy, indicating a possibly geographical and host differentiation of CCGaV isolates. This was the first identification and characterization of CCGaV infecting apples in China. Additionally, a rapid and sensitive reverse transcription recombinase polymerase amplification (RT-RPA) assay technique was established for CCGaV detection in apple plants. The RT-RPA of CCGaV was not affected by other common viruses in apple plants and is about 10-fold more sensitive than the conventional reverse transcription polymerase chain reaction method, which can be used in large-scale testing.
Highlights
Identification of Virome Using High Throughput Sequencing In October 2020, apple fruits showing obvious bright stripe symptoms were observed in Weihai City, Shandong Province, China
To identify the viruses in the apple samples, total RNAs were isolated from the sample which was subjected to high throughput sequencing (HTS)
This study is the first report on the characterization of the concave gum-associated virus (CCGaV)-Weihai isolate, offering preliminary investigation of local incidences in China and a novel isothermal amplification technique for the detection of CCGaV-infected apple trees
Summary
Apple (Malus domestica) is an economically important fruit crop in many areas of the world. China was the largest producer of apples in 2019, with approximately 38.1% of the world cultivating area and 51.1% of total crop production (FAOSTAT, http://faostat.fao.org, accessed on 30 August 2021). The yield and quality of apples have been affected by the incidence and severity of various diseases, and viral diseases are one of the most common constraints. Apple decline has increased in incidence, and several pathogens have been proposed to be associated with this disease, including apple chlorotic leafspot virus (ACLSV) and apple stem grooving virus (ASGV), while no one or group of pathogens have been totally determined [1,2]
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