Complete genome sequence of a novel polerovirus infecting chickpea (Cicer arietinum L.)

Chiquito-Almanza, Elizabeth; Acosta-Gallegos, Jorge Alberto; Anaya-López, José Luís

doi:10.1007/s00705-022-05581-w

Cited by 3 publications

(3 citation statements)

References 24 publications

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“…Currently, one of the species demarcation criteria for the genus Polerovirus is based on differences in amino acid sequence identity of any gene product of greater than 10% [ 55 ]. This criterion has been used to propose novel member species in the genus Polerovirus [ 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 ]. Accordingly, CABYV isolates that present an amino acid identity <90% in at least one protein regarding CABYV-N (RefSeq: NC_003688, GenBank: X76931), the first isolate identified in melon plants in France [ 17 ], would be considered as members of a different virus species.…”

Section: Resultsmentioning

confidence: 99%

Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates

Vidal

Lacorte

Sanches

et al. 2023

Viruses

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High-throughput sequencing (HTS) has been an important tool for the discovery of plant viruses and their surveillance. In 2015, several virus-like symptoms were observed in passion fruit (PF) plants in Bahia state, Brazil. Using HTS technology, bioinformatics tools, RT-PCR, and Sanger sequencing, we identified the cucurbit aphid-borne yellows virus (CABYV, Polerovirus, Solemoviridae) in co-infection with cowpea aphid-borne mosaic virus (CABMV, Potyvirus, Potyviridae) in PF, in green manure, and spontaneous plants in several localities in Bahia. Complete genomes of CABYV-PF isolates were determined and analyzed with other CABYV isolates available in GenBank that have been identified in various countries. Phylogenetic analysis and pairwise identity comparison with CABYV isolates showed that CABYV-PFs are more closely related to French and Spanish isolates. Overall, analyses of all the CABYV genomes revealed that these could represent ten distinct species, and we thus proposed reclassifying these CABYV as isolates into ten species, tentatively named “Polerovirus curcubitaeprimum” to “Polerovirus curcubitaenonum”, and “Polerovirus melo”. CABYV-PF is a member of “Polerovirus curcubitaeprimum”.

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Section: Resultsmentioning

confidence: 99%

Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates

Vidal

Lacorte

Sanches

et al. 2023

Viruses

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“…We selected VirusDetect software because it is an automated bioinformatic service for plant virus discovery with a public web interface dedicated to the analysis of sRNA data [ 32 ]. It is recommended for virologists with low to moderate bioinformatic skills and has proven useful for detecting known viruses and discovering new ones [ 17 , 31 , 44 , 45 , 46 ], including persistent viruses [ 21 , 31 ]. VirusDetect has achieved 100% sensitivity between sequencing depths of 2.5 M and 250 K, without false positives [ 47 ].…”

Section: Discussionmentioning

confidence: 99%

Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding

González-Pérez,

Chiquito-Almanza,

Villalobos-Reyes

et al. 2024

Viruses

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Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world’s most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3’ UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3’ UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-22 resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties.

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“…We selected VirusDetect software because it is an automated bioinformatic service for plant virus discovery with a public web interface dedicated to the analysis of sRNA data [21]. It is recommended for virologists with low to moderate bioinformatic skills and has proven useful for detecting known viruses and discovering new ones [20,37,[44][45][46], including persistent viruses [20,41]. VirusDetect has achieved 100% sensitivity between sequencing depths of 2.5M and 250K, without false positives [47].…”

Section: Selecting the Virus Identification Strategymentioning

confidence: 99%

Diagnosis of Plant Viruses Using NGS to Support Virus Management and Tomato Breeding

González-Pérez,

Chiquito-Almanza,

Villalobos-Reyes

et al. 2024

Preprint

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Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and validation by PCR and RT-PCR were used. Single and mixed infections with Tomato mosaic virus (ToMV), Tomato golden mosaic virus (ToGMoV), and Pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR of Mexican ToMV isolates suggest the need to evaluate known resistance genes against these viral variants. The precise identification and characterization of viruses that naturally infect tomato germplasm could be used as a strategy for selecting the appropriate disease management and guiding breeding efforts.

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Complete genome sequence of a novel polerovirus infecting chickpea (Cicer arietinum L.)

Cited by 3 publications

References 24 publications

Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates

Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates

Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding

Diagnosis of Plant Viruses Using NGS to Support Virus Management and Tomato Breeding

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