First report of cucurbit yellow stunting disorder virus and <i>Cucumis melo alphaendornavirus</i> in <i>Cucumis melo</i> in Indonesia

Melon (Cucumis melo L.) is an economically important cucurbit crop in Indonesia, with a production of 117,793 tons cultivated on 7,039 ha (FAOSTAT, 2023). In 2023, virus-like symptoms including interveinal yellowing and chlorosis were observed in open-field melons in Kediri District, Indonesia. To identify associated viruses, two symptomatic leaf samples (IND-ME10, IND-ME11) were analyzed by high-throughput sequencing (HTS) and reverse transcription (RT)-PCR. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Germany) and sequenced on an Illumina NovaSeq 6000 platform (Macrogen, Korea). De novo assembly of 79,400,902 clean reads using Trinity (v. r20140717) generated 254,870 contigs. BLAST analyses against the GenBank viral database identified six virus-associated large contigs corresponding to cucurbit yellow stunting disorder virus (CYSDV), Cucumis melo alphaendornavirus (CmEV), and tomato leaf curl New Delhi virus (ToLCNDV). The CYSDV contig (31,881 mapped reads; 281.7× depth) comprised nearly complete RNA1 (8,594 nt) and RNA2 (7,781 nt), sharing 99% and 97% nucleotide identity (100% coverage), respectively, with CYSDV isolate GDBL from China (PV232312, PV232313). Three CmEV contigs (717–2,914 mapped reads; 32.9–114.7× depth) had a nearly complete genome of 15,073 nt, showing 96% nucleotide identity (100% coverage) with the United States CmEV isolate CL-01 (NC_029064) (Sabanadzovic et al. 2016). Two ToLCNDV contigs (DNA-A, DNA-B) shared 96% nucleotide identity with previously reported Indonesian isolates (AB613825, AB613826) (Mizutani et al. 2011). RT-PCR and PCR assays confirmed that sample IND-ME11 was positive for CYSDV and CmEV, whereas IND-ME10 was positive for CmEV and ToLCNDV. Sanger-sequenced amplicons of CYSDV and CmEV from IND-ME11 shared 99% nucleotide identity with corresponding HTS-derived sequences. The obtained sequences were deposited in GenBank under accession numbers PX959674 (9,157 nt, CYSDV_RNA1), PX959675 (7,779 nt, CYSDV_RNA2), PX959676 (15,073 nt, CmEV), and PX959677 (2,739 nt, ToLCNDV_DNA-A from IND-ME10). Because multiple viruses were detected, we compared the observed symptoms with those previously reported for the detected viruses. Sample IND-ME11, co-infected with CYSDV and CmEV, showed interveinal yellowing and chlorosis. While CmEV (genus Alphaendornavirus, family Endornaviridae) is generally regarded as asymptomatic in melon (Sabanadzovic et al. 2016; Zeng et al. 2020), CYSDV (genus Crinivirus, family Closteroviridae) characteristically induces severe foliar yellowing and chlorotic symptoms in cucurbits (Wintermantel et al. 2017). Sample IND-ME10 was infected with CmEV and ToLCNDV. Due to the mixed infections and restricted sample size, definitive symptom causality was not assessed. CYSDV isolates divide into two phylogenetic groups with 73–76% nucleotide identities. The Indonesian isolate identified in this study grouped with Asian CYSDV isolates, which have been proposed as cucurbit chlorotic virus (CuCV) (Che et al. 2023). To the best of our knowledge, this is the first report of CYSDV and CmEV in melon in Indonesia. Given the limited sample size, broad conclusions regarding regional prevalence or distribution cannot be made; further large-scale surveys are warranted to determine their economic impact on Indonesian cucurbit production.