scholarly journals Molecular Phylogenetics and Evolutionary Analysis of a Highly Recombinant Begomovirus, Cotton Leaf Curl Multan Virus and Associated Satellites

2021 ◽  
Author(s):  
Tahir Farooq ◽  
Muhammad Umar ◽  
Xiaoman She ◽  
Yafei Tang ◽  
Zifu He
Keyword(s):  
Molecular Phylogenetics ◽  
Management Strategies ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Cotton Leaf ◽  
Evolutionary Analysis ◽  
Cotton Production ◽  
Evolutionary Patterns ◽  
Satellite Sequences ◽  
Leaf Curl

Abstract Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite’s virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite (CLCuMuA) and Cotton leaf curl Multan betasatellite (CLCuMuB) populations arising from distinct regions exhibit high mutation rates. Though evolutionary linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

Cotton leaf curl Gezira virus (African cotton leaf curl Begomovirus).

2021 ◽  
Author(s):  
Judith K Brown
Keyword(s):  
Bemisia Tabaci ◽  
Yield Loss ◽  
Growing Season ◽  
Cotton Leaf ◽  
Cotton Production ◽  
Natural Spread ◽  
Sahel Region ◽  
Whitefly Vector ◽  
African Sahel ◽  
Leaf Curl

Abstract Cotton leaf curl Gezira virus (CLCuGV) is endemic to the African Sahel region (Idris et al., 2000). It is an economically important cotton-infecting begomovirus, and poses a serious threat to cotton production. It causes yield loss in all affected cotton-growing areas in Africa. Losses are difficult to assess, but estimates range up to 20% when infection occurs early in the growing season and/or with highly susceptible cultivars. Natural spread is mainly by the whitefly vector, Bemisia tabaci, which transmits the virus in a persistent, circulative manner. Viruliferous whiteflies on infested/infected plants harbouring CLCuGV imported to other countries are of concern for preventing introduction.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl  Arusha virus affecting tomato plants in Kenya

2020 ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background: Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya.Methods: Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated.Results: Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in 5 out of the 6 coding regions of the sequences.Conclusions: The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

scholarly journals Cloning and Partial Characterization of Cotton Leaf Curl Burewala Virus From Khanewal

2021 ◽  
Vol 3 (1) ◽  
pp. 28-34
Author(s):  
Fizza Akhter ◽  
Muhammad Tahir
Keyword(s):  
Coat Protein ◽  
Complete Characterization ◽  
Universal Primers ◽  
Ammonium Bromide ◽  
Cotton Leaf ◽  
Cotton Production ◽  
Leaf Sample ◽  
Coat Protein Region ◽  
Leaf Curl

Begomoviruses are a serious threat to cotton production throughout the world. In Pakistan, enormous crop losses occur as a result of cotton leaf curl disease (CLCuD) caused by begomoviruses. Molecular characterization of begomoviruses has made possible the identification and analysis of begomoviruses prevalent in a host plant. Infected cotton leaf sample (C-59) was obtained from area around Khanewal during 2011. The total DNA was isolated from the infected sample by Cetyl trimethyl ammonium bromide (CTAB) method. An expected size band of approximately 1100bp, covering coat protein region of the virus, was amplified using universal primers. The amplified product was T/A cloned and sequenced to its entirety. DNA sequence showed 99% nucleotide sequence identity to each of Cotton leaf curl Burewala virus ((CLCuBuV; Accession No HF549Begomoviruses are a serious threat to cotton production throughout the world. In Pakistan, enormous crop losses occur as a result of cotton leaf curl disease (CLCuD) caused by begomoviruses. Molecular characterization of begomoviruses has made possible the identification and analysis of begomoviruses prevalent in a host plant. Infected cotton leaf sample (C-59) was obtained from area around Khanewal during 2011. The total DNA was isolated from the infected sample by Cetyl trimethyl ammonium bromide (CTAB) method. An expected size band of approximately 1100bp, covering coat protein region of the virus, was amplified using universal primers. The amplified product was T/A cloned and sequenced to its entirety. DNA sequence showed 99% nucleotide sequence identity to each of Cotton leaf curl Burewala virus ((CLCuBuV; Accession No HF549184)) and Cotton leaf curl Kokhran virus (CLCuKV; Accession No AJ002449)). Since CLCuBuV is a recombinant of CLCuKV and Cotton leaf curl Multan virus and the coat protein region of CLCuBuV was derived from CLCuKV that is most probable reason that the available sequence showed identity with CLCuBuV as well as CLCuKV. A complete characterization of full length virus will determine whether isolate C-59 is CLCuBuV or CLCuKV. Literature indicates that there is no existence of CLCuKV within the region and CLCuBuV is dominating within Indo-Pak184)) and Cotton leaf curl Kokhran virus (CLCuKV; Accession No AJ002449)). Since CLCuBuV is a recombinant of CLCuKV and Cotton leaf curl Multan virus and the coat protein region of CLCuBuV was derived from CLCuKV that is most probable reason that the available sequence showed identity with CLCuBuV as well as CLCuKV. A complete characterization of full length virus will determine whether isolate C-59 is CLCuBuV or CLCuKV. Literature indicates that there is no existence of CLCuKV within the region and CLCuBuV is dominating within Indo-Pak

scholarly journals Cotton leaf curl disease – an emerging threat to cotton production worldwide

2013 ◽  
Vol 94 (4) ◽  
pp. 695-710 ◽  
Author(s):  
M. Naeem Sattar ◽  
Anders Kvarnheden ◽  
Muhammad Saeed ◽  
Rob W. Briddon
Keyword(s):  
Host Plant ◽  
Distinct Group ◽  
Cotton Leaf ◽  
Western India ◽  
Plant Tolerance ◽  
Cotton Production ◽  
Specific Symptom ◽  
Cotton Leaf Curl Disease ◽  
Leaf Curl Disease ◽  
Leaf Curl

Cotton leaf curl disease (CLCuD) is a serious disease of cotton which has characteristic symptoms, the most unusual of which is the formation of leaf-like enations on the undersides of leaves. The disease is caused by whitefly-transmitted geminiviruses (family Geminiviridae, genus Begomovirus) in association with specific, symptom-modulating satellites (betasatellites) and an evolutionarily distinct group of satellite-like molecules known as alphasatellites. CLCuD occurs across Africa as well as in Pakistan and north-western India. Over the past 25 years, Pakistan and India have experienced two epidemics of the disease, the most recent of which involved a virus and satellite that are resistance breaking. Loss of this conventional host–plant resistance, which saved the cotton growers from ruin in the late 1990s, leaves farmers with only relatively poor host plant tolerance to counter the extensive losses the disease causes. There has always been the fear that CLCuD could spread from the relatively limited geographical range it encompasses at present to other cotton-growing areas of the world where, although the disease is not present, the environmental conditions are suitable for its establishment and the whitefly vector occurs. Unfortunately recent events have shown this fear to be well founded, with CLCuD making its first appearance in China. Here, we outline recent advances made in understanding the molecular biology of the components of the disease complex, their interactions with host plants, as well as efforts being made to control CLCuD.

scholarly journals First Detection of Cotton leaf curl Burewala virus and Cognate Cotton leaf curl Multan betasatellite and Gossypium darwinii symptomless alphasatellite in Symptomatic Luffa cylindrica in Pakistan

Plant Disease ◽  
2013 ◽  
Vol 97 (8) ◽  
pp. 1122-1122 ◽  
Author(s):  
M. Zia-Ur-Rehman ◽  
H.-W. Herrmann ◽  
U. Hameed ◽  
M. S. Haider ◽  
J. K. Brown
Keyword(s):  
Plasmid Vector ◽  
Cotton Leaf ◽  
Cotton Production ◽  
Alpha Satellite ◽  
Luffa Cylindrica ◽  
First Report ◽  
Cotton Leaf Curl Disease ◽  
Total Dna ◽  
Leaf Curl Disease ◽  
Leaf Curl

Cotton leaf curl disease (CLCuD) is the major plant viral constraint to cotton production on the Indian subcontinent (2). CLCuD is primarily caused by begomovirus, Cotton leaf curl Burewala virus (CLCuBuV), and Cotton leaf curl Multan betasatellite (CLCuMB). During 2011 in Burewala, Pakistan, plants in a production field of Luffa cylindrica (Ghia tori) were infested with the whitefly Bemisia tabaci (Genn.), and ~60% of the plants exhibited leaf curling and stunting symptoms, reminiscent of those caused by begomoviruses (Geminiviridae). Total DNA was extracted from five different symptomatic leaf samples using the CTAB method (1), and extracts were analyzed by Southern blot hybridization. As a probe, we used a 1.1-kbp fragment of CLCuBuV and a positive signal was obtained from all five samples. Total DNA was used as template for rolling circle amplification (RCA) using the TempliPhi DNA Amplification Kit (GE Healthcare, Little Chalfont, United Kingdom). The amplified RCA products were digested with EcoRI, and the resulting ~2.7-kbp fragments from each isolate were directionally cloned into the EcoRI digested, pGEM-3Zf+ (Promega, Madison, WI) plasmid vector. PCR was used to amplify the prospective, associated betasatellite and alphasatellite molecules using the primers BetaF5′-GGTACCGCCGGAGCTTAGCWCKCC-3′ and BetaR5′-GGTACCGTAGCTAAGGCTGCTGCG-3′, and AlphaF5′-AAGCTTAGAGGAAACTAGGGTTTC-3′ and AlphaR5′-AAGCTTTTCATACARTARTCNCRDG-3′, respectively. The putative satellite amplicons, at ~1.4 kbp each were cloned in the plasmid vector pGEMT-Easy (Promega, Madison, WI) and sequenced. BLASTn comparisons of the apparently full-length begomoviral genomes, at 2,753 nt, against the NCBI database revealed that all five isolates were most closely related to CLCuBuV (FR750321). In addition, one each of beta- and alpha-satellite were amplified from all five samples at 1,393 and 1,378 bases, respectively. The beta- and alpha-satellites were most closely related to CLCuMB (HE985228) and the Gossypium darwinii symptomless alphasatellite (GDaSA) (FR877533), respectively. Pairwise sequence comparisons of the top 10 BLASTn hits using MEGA5 indicated that the helper begomovirus shared 99.9% identity with CLCuBuV (FR750321), the most prevalent helper virus currently associated with the leaf curl complex in Pakistan. Based on the ICTV demarcation for begomoviral species at <89%, it is considered a variant of CLCuBuV. The resultant beta- and alpha-satellite sequences were 98.1% and 97.8% identical to CLCuMB (HE985228) and GDaSA (FR877533), respectively, and are the most prevalent satellites associated with the CLCuD complex in Pakistan and India (2). To our knowledge, this is first report of the CLCuBuV-CLCuMB-GDaSA complex infecting a cucurbitaceous species, and the first report of L. cylindrica as a host of the CLCuD complex. This discovery of CLCuBuV and associated satellites in a cucurbitaceous host that is widely grown in Pakistan and India where this complex infects cotton indicates that the host range of CLCuBuV is broader than expected. This new information will aid in better understanding of cotton leaf curl disease epidemiology in the current epidemic areas. References: (1) J. J. Doyle and J. L. Doyle. Focus 12:13, 1990. (2) S. Mansoor et al. Trends Plant Sci. 11:209, 2006.

scholarly journals Cotton leaf curl Gezira virus.

2021 ◽  
Author(s):  
Judith K. Brown
Keyword(s):  
Yield Loss ◽  
Growing Season ◽  
Cotton Leaf ◽  
Cotton Production ◽  
Sahel Region ◽  
African Sahel ◽  
Leaf Curl

Abstract Cotton leaf curl Gezira virus (CLCuGV) is endemic to the African Sahel region (Idris et al., 2000). It is an economically important cotton-infecting begomovirus, and poses a serious threat to cotton production. It causes yield loss in all affected cotton-growing areas in Africa. Losses are difficult to assess, but estimates range up to 20% when infection occurs early in the growing season and/or with highly susceptible cultivars.

scholarly journals Using Multiplexed CRISPR/Cas9 for Suppression of Cotton Leaf Curl Virus

2021 ◽  
Vol 22 (22) ◽  
pp. 12543
Author(s):  
Barkha Binyameen ◽  
Zulqurnain Khan ◽  
Sultan Habibullah Khan ◽  
Aftab Ahmad ◽  
Nayla Munawar ◽  
...  
Keyword(s):  
Genome Editing ◽  
Insect Pests ◽  
Restriction Analysis ◽  
Cotton Leaf ◽  
Cotton Production ◽  
Colony Pcr ◽  
Guide Rna ◽  
Cotton Leaf Curl Virus ◽  
Leaf Curl Virus ◽  
Leaf Curl

In recent decades, Pakistan has suffered a decline in cotton production due to several factors, including insect pests, cotton leaf curl disease (CLCuD), and multiple abiotic stresses. CLCuD is a highly damaging plant disease that seriously limits cotton production in Pakistan. Recently, genome editing through CRISPR/Cas9 has revolutionized plant biology, especially to develop immunity in plants against viral diseases. Here we demonstrate multiplex CRISPR/Cas-mediated genome editing against CLCuD using transient transformation in N. benthamiana plants and cotton seedlings. The genomic sequences of cotton leaf curl viruses (CLCuVs) were obtained from NCBI and the guide RNA (gRNA) were designed to target three regions in the viral genome using CRISPR MultiTargeter. The gRNAs were cloned in pHSE401/pKSE401 containing Cas9 and confirmed through colony PCR, restriction analysis, and sequencing. Confirmed constructs were moved into Agrobacterium and subsequently used for transformation. Agroinfilteration in N. benthamiana revealed delayed symptoms (3–5 days) with improved resistance against CLCuD. In addition, viral titer was also low (20–40%) in infected plants co-infiltrated with Cas9-gRNA, compared to control plants (infected with virus only). Similar results were obtained in cotton seedlings. The results of transient expression in N. benthamiana and cotton seedlings demonstrate the potential of multiplex CRISPR/Cas to develop resistance against CLCuD. Five transgenic plants developed from three experiments showed resistance (60−70%) to CLCuV, out of which two were selected best during evaluation and screening. The technology will help breeding CLCuD-resistant cotton varieties for sustainable cotton production.

scholarly journals Gene expression in response to Cotton Leaf Curl Virus infection in Gossypium hirsutum under variable environmental conditions

Genetika ◽  
2017 ◽  
Vol 49 (3) ◽  
pp. 1115-1126
Author(s):  
Iqra Rehman ◽  
Beenish Aftab ◽  
Sarwar Bilal ◽  
Bushra Rashid ◽  
Qurban Ali ◽  
...  
Keyword(s):  
Relative Humidity ◽  
Gossypium Hirsutum ◽  
Pcr Amplification ◽  
Defense Responses ◽  
Cotton Leaf ◽  
Cotton Production ◽  
Cotton Leaf Curl Virus ◽  
Temperature And Humidity ◽  
Leaf Curl Virus ◽  
Leaf Curl

Cotton Leaf Curl Disease (CLCuD) is one of the threatening constrains of cotton production in Pakistan for which no adequate remedy is available until now. Local variety of Gossypium hirsutum (FH-142) was grown in field and infected naturally by CLCuV under variable range of temperature and humidity. Plants showed thickening of veins in lower leaf surface at 34?C and 60% relative humidity at 15days post infection (dpi) and curling of leaf margins at 33?C with 58% relative humidity at 30dpi. Remarkable leaf darkening was observed with reduced boll formation at 45dpi at 26?C and 41% relative humidity. Enation developed, severe thickening and curling of leaves intensified and plants showed dwarf growth at 60dpi at 24?C with 52% relative humidity. PCR amplification of Rep associated gene confirmed the presence of CLCuD-associated begomovirus in the infected samples. Quantitative RT-PCR confirmed the amplification and differential expression of a number of pathogen stress responsive genes at different levels of temperature and humidity. This observation predicts that Cotton Leaf Curl Virus (CLCuV) interacts with several host genes that are upregulated to make plants susceptible or suppress other genes to overcome host defense responses.

scholarly journals Leaf cuticular wax content is involved in cotton leaf curl virus disease resistance in cotton (Gossypium hirsutum L.)

2019 ◽  
Vol 16 (4) ◽  
pp. e0705
Author(s):  
Muhammad Saeed ◽  
Song Xianliang ◽  
Sun Xuezhen ◽  
Muhammad Riaz
Keyword(s):  
Virus Disease ◽  
Cuticular Wax ◽  
Yield Potential ◽  
Cotton Leaf ◽  
Cotton Production ◽  
Cotton Leaf Curl Virus ◽  
Cotton Genotypes ◽  
Wax Content ◽  
Leaf Curl Virus ◽  
Leaf Curl

Cotton leaf curl virus disease (CLCuVD) limits cotton production in many cotton growing countries of the world, including Pakistan. In the past, efforts were made to combat this disease by different approaches. Cuticular wax is reported to confer resistance to plants against various biotic and abiotic stresses. Present study was designed to assess the role of cuticular wax content (WC) to resist CLCuVD infestation. The WC of 42 cotton genotypes, originating from various countries (Pakistan, USA, China, etc.), was quantified during two culture periods (2015 & 2016). Cotton germplasm was also scored for % disease index (%DI), seed cotton yield (SCY), number of bolls/plant (NB), and plant height (PHt) for the same culture periods. Significant negative correlation between WC and %DI was found during the two years of experimentation. WC was found positively correlated with SCY and NB. Six cotton genotypes (A-7233, B-557, A-162, BLANCO-3363, CIM-473, and SLH-2010-11) did not show any signs of CLCuVD infestation during both 2015 and 2016. These cotton genotypes contained relatively higher WC. The results from analysis of variance (ANOVA) demonstrated that there were significant differences among genotypes for %DI, WC, SCY, NB, and PHt. These results indicated that WC was involved in resisting CLCuVD and it also had positive effect on plant growth and yield potential. On the basis of these findings, it was concluded that cuticular wax could be used as an indirect criterion for distinguishing and selecting resistant/susceptible cotton genotypes.

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