Chlorotic fleck disease of ginger, the causal virus of which was unknown so far is an important production constraint of ginger in India and other parts of the world. In the present study, two new RNA viruses were discovered in chlorotic fleck affected plant by the virome analysis using high‐throughput sequencing (HTS) of small RNA and transcriptome. The HTS results were verified through reverse transcriptase polymerase chain reaction (RT‐PCR) using total RNA from infected plants and primers designed from the contigs. Cloning and sequencing of the RT‐PCR products of one of the viruses resulted in a sequence of 4,143 bases that showed similarities to panicoviruses and machlomoviruses. The complete genome of this virus contained six open reading frames (ORFs) that potentially encode proteins of 43, 104, 8, 7, 15 and 27 kDa. Based on the genomic and phylogenetic analysis, this virus is predicted to be a new member of the family Tombusviridae for which the name ginger chlorotic fleck‐associated virus 1 is proposed. Similarly, cloning and sequencing of the RT‐PCR products of the other virus resulted in a sequence of 5,514 bases that showed similarities to ampeloviruses. Based on the genomic and phylogenetic analysis, this virus is predicted to be a new member of the genus Ampelovirus for which the name ginger chlorotic fleck‐associated virus 2 is proposed. Reliable RT‐PCR and SYBR Green‐based quantitative RT‐PCR assays were developed for the detection of both viruses in plants that would aid in the identification and propagation of virus‐free ginger plants. Additional investigations are required to elucidate the relationship between the symptoms and viral infections.

中文翻译：

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两种新型病毒与姜黄萎病病的关系

在印度和世界其他地区，生姜的致黄性斑点病（目前尚不清楚其致病病毒）是生姜的重要生产限制。在本研究中，通过使用小RNA和转录组的高通量测序（HTS）进行的病毒分析，在受黄萎病斑点影响的植物中发现了两种新的RNA病毒。HTS结果通过逆转录酶聚合酶链反应（RT-PCR）使用受感染植物的总RNA和重叠群设计的引物进行验证。其中一种病毒的RT-PCR产物的克隆和测序产生了4,143个碱基的序列，该序列显示出与Panicoviruses和machlomoviruses的相似性。该病毒的完整基因组包含六个开放阅读框（ORF），它们可能编码43、104、8、7、15和27 kDa的蛋白质。有人建议将其命名为姜黄褪色斑点相关病毒1的Tombusviridae。类似地，另一种病毒的RT-PCR产物的克隆和测序产生了5,514个碱基的序列，显示了与两栖病毒的相似性。根据基因组和系统发育分析，该病毒预计是两栖病毒属的一个新成员，为此提出了姜黄化斑点相关病毒2的名称。开发了可靠的RT-PCR和SYBR Green定量RT-PCR分析方法，用于检测植物中的两种病毒，这有助于鉴定和繁殖无病毒的生姜植物。需要进行进一步的研究以阐明症状与病毒感染之间的关系。