Exploring distribution and genomic diversity of begomoviruses associated with yellow mosaic disease of legume crops from India, highlighting the dominance of mungbean yellow mosaic India virus

Abstract

Yellow mosaic disease (YMD) caused by several begomoviruses is one of the major constraints of over a dozen leguminous crops worldwide, particularly in Asian and Southeast Asian countries. The present study aimed to investigate the distribution, diversity and prevalence of begomoviruses associated with YMD in leguminous hosts in five agro-climatic zones of India, to assess the extent of their geographical presence and develop location and crop-specific distribution maps. One hundred and seventy-four leguminous plant samples were tested from 32 locations in India to detect YMD-causing viruses. Additionally, publicly available data were incorporated into this study to provide a comprehensive overview of their distribution in India. This resulted in 581 reports on the DNA-A component representing 119 locations, which were also utilized to depict the distribution of YMD-causing viruses on a map of India. In this study, 117 full-length DNA-A and 103 DNA-B components were successfully characterized, representing the detected mungbean yellow mosaic India virus (MYMIV), mungbean yellow mosaic virus (MYMV), and horsegram yellow mosaic virus in the collected samples. Phylogenetic analysis of isolates of these species showed no differentiation based on location in India. Diversity indices revealed the abundance (55.9%) and dominance (0.56) of MYMIV across 119 locations. These findings hold significant implications for legume researchers, offering insights into disease prevalence and geographic distribution. Furthermore, the distribution of YMD-causing viruses in different agro-climatic zones will help researchers in developing zone-specific YMD-resistant cultivars of the legume crops and would facilitate effective disease management options.

Keywords: agro-climatic zones; begomoviruses; distribution; diversity; legumoviruses; map.

Figure 1

Representative illustration showing symptoms of yellow mosaic disease observed in (A) mungbean; (B) urdbean; (C) cowpea; (D) horsegram; (E) dolichos; (F) mothbean; (G) French bean; (H) Rhynchosia minima and (I) Vigna stipulacea, collected from different locations in India.

Figure 2

(A) An outline map of India showing 119 locations across five agro-climatic zones: North Hill Zone (NHZ), North East Plain Zone (NEPZ), North West Plain Zone (NWPZ), Central Zone (CZ), and South Zone (SZ), where reports of legumovirus were made. An illustration of these five zones in India is shown as an inset at the top right corner. Each location is represented with a circular spot, colour-coded to correspond with the respective zone. The variable size of the spot denotes the detection of one to a maximum of four out of eight virus species from that location; (B) The 119 locations from where 8 legume-infecting begomoviruses were detected and reported. Different colours of spots were used to represent the 8 virus species. The variable size of the spot is proportional to the number of reports made per location. Several locations have reports of multiple virus detections and in such cases, the species with the least reports is shown at the centre of the spots shown as concentric circles at such locations. (C) A circos plot showing the frequency distribution of reports made on MYMIV, MYMV, DoYMV and HgYMV from CZ, NHZ, NEPZ, NWPZ and SZ. The zones are shown anticlockwise in descending order with respect to the total data points (DPs) from the respective zone. The width of the colored ribbon is directly proportional to the frequency of respective virus species in relation to the corresponding zones. (D) Distribution of reports on 8 legumoviruses detected in India across various hosts. There are 22 crop hosts categorized as leguminous and non-leguminous, represented by differently colored spots placed at their respective locations of detection. Additionally, 31 species of weed hosts, are considered as one category and are depicted with a single colored spot. The variable size of each spot indicates the number of reports associated with a particular host, with hosts having the least number of reports at each location depicted at the centre of concentric circles. RhYMV, Rhynchosia yellow mosaic virus; CsYMV, Cajanus scarabaeoides yellow mosaic virus; MYMV, mungbean yellow mosaic virus; HgYMV, horsegram yellow mosaic virus; VbSMV, velvet bean severe mosaic virus; RhYMIV, Rhynchosia yellow mosaic India virus; MYMIV, mungbean yellow mosaic India virus; DoYMV, dolichos yellow mosaic virus.

Figure 3

Phylogenetic tree derived from the DNA-A components of 530 begomoviruses. Legumoviruses considered in this study with only one isolate are shown with their corresponding species abbreviation, accession number, and location. Legumoviruses with multiple isolates are represented by collapsed clades, marked by colored triangles. Different colored triangles represents different species Other begomoviruses are shown in their abbreviated form followed by their RefSeq accession number, with detailed information provided in Supplementary Table S5. Bootstrap values, indicative of the reliability of each branch, are represented by the size of the blue circles at the nodes, with larger circles indicating higher confidence, as shown in the upper right.

Figure 4

Phylogenetic tree derived from the DNA-A components of 117 full-length DNA-A sequences generated in this study comprising 81, 28 and 8 isolates of MYMIV, MYMV and HgYMV, respectively. Bootstrap values, indicative of the reliability of each branch, are represented by the size of the blue circles at the nodes, with larger circles indicating higher confidence, as shown in the upper right.

Figure 5

Histogram plot showing (A) per cent abundance of 8 virus namely MYMIV (mungbean yellow mosaic India virus), MYMV (mungbean yellow mosaic virus), HgYMV (horsegram yellow mosaic virus), DoYMV (dolichos yellow mosaic virus), RhYMV (Rhynchosia yellow mosaic virus), RhYMIV (Rhynchosia yellow mosaic India virus), CsYMV (Cajanus scarabaeoides yellow mosaic virus) and VbSMV (velvet bean severe mosaic virus); (B) Berger-Parker dominance index (d) of these 8 virus species; in terms of hosts, locations and total number of reports (or DPs) per virus species in India.