New Approaches in Begomovirus Classification and their Geographic Distribution

Abstract

Begomoviruses (family Geminiviridae) are group of plant viruses that have circular single stranded (ss) DNA genome(s), transmitted by a single species of whitefly (Bemisia tabaci) and infect dicotyledonous plants only. Begomoviruses are infecting wide range of economically important plants including crops, vegetable, ornamental plants and weeds. Weeds and ornamental plants serve as alternate hosts, source of inoculum and recombination sites for economically important begomoviruses. Due to revision in taxonomy those viruses which were once the member of x species of begomovirus are now the member of another species of begomovirus, but their names remain unchanged. The present study was aimed at to analyze species demarcation, geographic distribution over the years, and alternate hosts plants of begomoviruses present in Pakistan. host range, year of collection and geographic distribution of Begomoviruses. FASTA and GenBank sequences of full-length genome of begomoviruses available in the databases were retrieved and tabulated the given parameters. The sequences were aligned using Muscle alignments and species were identified through species demarcation tool (SDT) and verified by sequence distances Phylogenetic tree was developed using maximum likelihood method of Mega X. Graphs and maps were generated through MS Excel. There were 307 species of begomoviruses and ~5043 isolates to date in the World. In Pakistan, 28 species (~451 isolates) of begomoviruses are present. However, the total number of isolates of respective species are ~1657 found in Pakistan and neighbouring countries, infecting one hundred and fifty-six (156) different host plants including twenty-two (22) crops, fourty (40) ornamental plants, sixty-seven (67) vegetables and twenty-seven (27) weeds. In Pakistan and neighbouring countries, ACMV is predominant in terms of isolates (303) number among respective 28 begomovirus species. While, the maimum number of alternate hosts are infected by TLCuNDV (38), followed by PaLCV (24) and AEV (18) respectively. In Pakistan, these 28 begomovirus species infect seventy-five (75) different host plants including sixteen (16) crops, fifteen (15) ornamental plants, thirty (30) vegetables and fourteen (14) weeds. Cotton leaf curl Kokhran virus (CLCuKoV) was found predominant (142 isolates) among cotton infecting begomoviruses and infects eight (8) different alternate host plants while ToLCNDV is predominant in non-malvaceous hosts in Pakistan infecting fifteen (15) alternate hosts followed by Pedilanthus leaf curl virus (PedLCV) and Papaya leaf curl virus infecting 13 and 12 alternate host plants, respectively. Cotton belongs to family Malvaceae. Malvaceous viruses were known to infect malvaceous hosts but present data showed that viruses of malvaceous plants are also infecting non-malvaceous hosts and vice versa. Number of isolates of 28 virus species were determined and renamed them. Since the number of 2 | P a g e species increased from previous classification, number of virus isolates are sharing different species of viruses. Number of isolates are increased, and they are moving from one region to another, and not restricted to geographical boundaries. There are several begomoviruses (CLCMuV, ChiLCV, ChiLCPKV, PeLCV, HoLCV, RhYMV, RoLCV, PaLCV, RaLCV) having Pakistani origin, moved towards other countries while many viruses came from other regions and infected several plants in Pakistan. The capability of existing Begomoviruses in Pakistan to infect a variety of hosts and spread across a broad and ecologically variable geographical range was understood to illuminate the potential economic threats associated with begomoviral invasions. Cotton leaf curl Multan virus was found first in Pakistan during 1992 and then it was reported from India, China, Philippines and Thailand during 1996, 2007, 2012 and 2015 respectively. Begomoviruses have increased their host range and they have several alternate hosts as well. A single virus species has capability to infect members of multiple plant families. Moreover, single plant is a home of several begomovirus species. The number of isolates is increased which demands renaming and they are moving from one country to another.