Identification and sequence analysis of five allexiviruses species infecting garlic crops in Brazil

Oliveira, M. L.; Marchi, Bruno Rossitto De; Mituti, Tatiana; Pavan, Marcelo Agenor; Krause‐Sakate, Renate

doi:10.1590/s1982-56762014000600011

Cited by 10 publications

(4 citation statements)

References 9 publications

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“…One of the most important fungal diseases occurring in garlic (Allium sativum) and onion (Allium cepa) is white rot, caused by the sclerotium-forming fungus Sclerotium cepivorum, often causing severe losses in garlic and onion production worldwide [1]. In Brazil, the states of Paraná, Minas Gerais, São Paulo and Goiás produce 64% of the national Allium crop (mostly garlic and onion) [2]. Despite recent advances in Allium production in Brazil, production is not sufficient to fulfil internal demand, due to low productivity [3].…”

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confidence: 99%

Trichoderma from Brazilian garlic and onion crop soils and description of two new species: Trichoderma azevedoi and Trichoderma peberdyi

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Fifty four Trichoderma strains were isolated from soil samples collected from garlic and onion crops in eight different sites in Brazil and were identified using phylogenetic analysis based on combined ITS region, tef1-α, cal, act and rpb2 sequences. The genetic variability of the recovered Trichoderma species was analysed by AFLP and their phenotypic variability determined using MALDI-TOF. The strain clusters from both typing techniques coincided with the taxonomic determinations made from phylogenetic analysis. The phylogenetic analysis showed the occurrence of Trichoderma asperellum, Trichoderma asperelloides, Trichoderma afroharzianum, Trichoderma hamatum, Trichoderma lentiforme, Trichoderma koningiopsis, Trichoderma longibrachiatum and Trichoderma erinaceum, in the soil samples. We also identified and describe two new Trichoderma species, both in the harzianum clade of section Pachybasium, which we have named Trichoderma azevedoi sp. nov. and Trichoderma peberdyi sp. nov. The examined strains of both T. azevedoi (three strains) and T. peberdyi (12 strains) display significant genotypic and phenotypic variability, but form monophyletic clades with strong bootstrap and posterior probability support and are morphologically distinct from their respective most closely related species.

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Section: Introductionmentioning

confidence: 99%

Trichoderma from Brazilian garlic and onion crop soils and description of two new species: Trichoderma azevedoi and Trichoderma peberdyi

et al. 2020

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“…GarMbFV was not previously identified from Poland, and the other allexivirus species were identified from Poland only recently (Chodorska et al 2012(Chodorska et al , 2013. According to our knowledge, GarMbFV had been detected in Argentina (Helguera et al 1997), South Korea (Kang et al 2007) and Brazil (Oliveira et al 2014). ShVX was not detected in any of the samples tested.…”

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confidence: 84%

Occurrence and phylogenetic analysis of allexiviruses identified on garlic from China, Spain and Poland commercially available on the polish retail market

2017

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“…A species complex of Onion yellow dwarf virus (OYDV) and Leek yellow stripe virus (LYSV) were the most crucial viruses in Italy, Greek, and Brazil [9,[16][17][18]. Whereas Garlic virus A (Gar-VA), Garlic virus B (Gar-VB), Garlic virus C (Gar-VC), Garlic virus D (Gar-VD), Garlic virus E (Gar-VE) and Garlic virus X (Gar-VX) were the most prevalent species from Allexivirus [7,19]. It is not uncommon to see viral species complex from the three genera as reported by different authors [5,[20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of the coat protein gene revealed considerable diversity of viral species complex in Garlic (Allium sativum L.)

Mitiku

Degefu

Abraham

et al. 2020

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Garlic is one of the most crucial Allium vegetables used as seasoning of foods. It has a lot of benefits from the medicinal and nutritional point of view; however, its production is highly constrained by both biotic and abiotic challenges. Among these, viral infections are the most prevalent factors affecting crop productivity around the globe. This experiment was conducted on eleven selected garlic accessions and three improved varieties collected from different garlic growing agro-climatic regions of Ethiopia. This study aimed to identify and characterize the isolated garlic virus using the coat protein (CP) gene and further determine their phylogenetic relatedness. RNA was extracted from fresh young leaves, thirteen days old seedlings, which showed yellowing, mosaic, and stunting symptoms. Pairwise molecular diversity for CP nucleotide and amino acid sequences were calculated using MEGA5. Maximum Likelihood tree of CP nucleotide sequence data of Allexivirus and Potyvirus were conducted using PhyML, while a neighbor-joining tree was constructed for the amino acid sequence data using MEGA5. From the result, five garlic viruses were identified viz. Garlic virus C (78.6 %), Garlic virus D (64.3 %), Garlic virus X (78.6 %), Onion yellow dwarf virus (OYDV) (100%), and Leek yellow stripe virus (LYSV) (78.6 %). The study revealed the presence of complex mixtures of viruses with 42.9 % of the samples had co-infected with a species complex of Garlic virus C, Garlic virus D, Garlic virus X, OYDV, and LYSV. Pairwise comparisons of the isolated Potyviruses and Allexiviruses species revealed high identity with that of the known members of their respected species. As an exception, less within species identity was observed among Garlic virus C isolates as compared with that of the known members of the species. Finally, our results highlighted the need for stepping up a working framework to establish virus-free garlic planting material exchange in the country which could result in the reduction of viral gene flow across the country.Author SummaryGarlic viruses are the most devastating disease since garlic is the most vulnerable crop due to their vegetative nature of propagation. Currently, the garlic viruses are the aforementioned production constraint in Ethiopia. However, so far very little is known on the identification, diversity, and dissemination of garlic infecting viruses in the country. Here we explore the prevalence, genetic diversity, and the presence of mixed infection of garlic viruses in Ethiopia using next generation sequencing platform. Analysis of nucleotide and amino acid sequences of coat protein genes from infected samples revealed the association of three species from Allexivirus and two species from Potyvirus in a complex mixture. Ultimately the article concludes there is high time to set up a working framework to establish garlic free planting material exchange platform which could result in a reduction of viral gene flow across the country.

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Identification and sequence analysis of five allexiviruses species infecting garlic crops in Brazil

Cited by 10 publications

References 9 publications

Trichoderma from Brazilian garlic and onion crop soils and description of two new species: Trichoderma azevedoi and Trichoderma peberdyi

Trichoderma from Brazilian garlic and onion crop soils and description of two new species: Trichoderma azevedoi and Trichoderma peberdyi

Occurrence and phylogenetic analysis of allexiviruses identified on garlic from China, Spain and Poland commercially available on the polish retail market

Molecular characterization of the coat protein gene revealed considerable diversity of viral species complex in Garlic (Allium sativum L.)

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