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Complete Genome Sequences and Evolutionary Analysis of Cucurbit aphid-borne yellows virus Isolates from Melon in Korea

  • Kwak, Hae-Ryun (Crop Protection Division, National Institute of Agricultural Science) ;
  • Lee, Hee Ju (Vegetable Research Division, National Institute of Horticultural and Herbal Science) ;
  • Kim, Eun-A (Crop Protection Division, National Institute of Agricultural Science) ;
  • Seo, Jang-Kyun (Graduate school of International Agricultural Technology, Seoul National University) ;
  • Kim, Chang-Seok (Crop Protection Division, National Institute of Agricultural Science) ;
  • Lee, Sang Gyu (Vegetable Research Division, National Institute of Horticultural and Herbal Science) ;
  • Kim, Jeong-Soo (Department of Plant Medicine, Andong National University) ;
  • Choi, Hong-Soo (Crop Protection Division, National Institute of Agricultural Science) ;
  • Kim, Mikyeong (Crop Protection Division, National Institute of Agricultural Science)
  • Received : 2018.03.19
  • Accepted : 2018.07.24
  • Published : 2018.12.01

Abstract

Complete genome sequences of 22 isolates of Cucurbit aphid-borne yellows virus (CABYV), collected from melon plants showing yellowing symptom in Korea during the years 2013-2014, were determined and compared with previously reported CABYV genome sequences. The complete genomes were found to be 5,680-5,684 nucleotides in length and to encode six open reading frames (ORFs) that are separated into two regions by a non-coding internal region (IR) of 199 nucleotides. Their genomic organization is typical of the genus Polerovirus. Based on phylogenetic analyses of complete nucleotide (nt) sequences, CABYV isolates were divided into four groups: Asian, Mediterranean, Taiwanese, and R groups. The Korean CABYV isolates clustered with the Asian group with > 94% nt sequence identity. In contrast, the Korean CABYV isolates shared 87-89% sequence identities with the Mediterranean group, 88% with the Taiwanese group, 81-84% with the CABYV-R group, and 72% with another polerovirus, M.. Recombination analyses identified 24 recombination events (12 different recombination types) in the analyzed CABYV population. In the Korean CABYV isolates, four recombination types were detected from eight isolates. Two recombination types were detected in the IR and P3-P5 regions, respectively, which have been reported as hotspots for recombination of CABYV. This result suggests that recombination is an important evolutionary force in the genetic diversification of CABYV populations.

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Fig. 1. Geographical locations in Korea at which the CABYV isolates were collected.

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Fig. 3. Genome organization of Korean CABYV isolates (A). The six proteins are separated by IR into two regions: 5’ proximal and 3’ proximal proteins. A ribosomal frame shift (-1) in the P1-P2 protein is indicated at nt 1,488 and readthrough of the P3-P5 protein occurs at nt 4,110. Nucleotide (B) and deduced amino acid (C) sequence similarities in the CABYV population. Full-length sequences of 33 CABYV isolates were aligned by ClustalX2 and analyzed using AlignX by setting window site to estimate similarities. ‘+1’ on y-axis means that sequences are perfectly conserved.

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Fig. 4. Phylogenetic trees reconstructed using the complete nucleotide sequences of the CABYV isolates. Phylogenetic trees were reconstructed using maximum likelihood in MEGA 6.

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Fig. 5. Split decomposition network of the CABYV population. Phylogenetic network analysis was performed using SplitsTree v. 4.1 program.

Table 1. Survey and detection of CABYV from melon in seven areas in Korea

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Table 2. Primer pairs used for detection and full-length sequencing of the CABYV genome

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Table 3. Database of the complete nucleotide sequences of CABYV genomes

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Fig. 2. Symptoms induced by CABYV on naturally infected melon plants in Korea. Yellowing (A), leaf mosaic (B), and informal net on melon fruits (C)

Table 4. Nucleotide diversity for different genomic regions of the CABYV population

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Table 5. Nucleotide and amino acid sequence identities (%) between the Korean CABYV isolate CY3 and other CABYV isolates

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Table 6. Recombination in Korean CABYV populations

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Acknowledgement

Supported by : Rural Development Administration of Korea

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