Next generation sequencing and proteomics in plant virology: how is Colombia doing?

Madroñero, Johana; Rozo, Zayda Lorena Corredor; Escobar-Pérez, Javier; Velandia-Romero, Myriam L.

doi:10.15446/abc.v24n3.79486

Cited by 5 publications

(5 citation statements)

References 122 publications

(138 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In order to make more efficient use of the sequencing capacity of the NGS platforms, it will be more economical if multiple specimens are sequenced in a single run; i.e., the sequencing data generated by each platform are generally higher in quantities than required per specimen. With this strategy, the cost of sequencing one sample is around USD 500 [ 83 ]. In 2016, Oxford Nanopore Technologies has introduced its first sequencing device, MinION, into the market.…”

Section: Opportunities Obstacles and Future Trendmentioning

confidence: 99%

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Tsang

Teng

Lau

et al. 2021

JoF

View full text Add to dashboard Cite

Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.

show abstract

Section: Opportunities Obstacles and Future Trendmentioning

confidence: 99%

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Tsang

Teng

Lau

et al. 2021

JoF

View full text Add to dashboard Cite

show abstract

“…Papaya sticky disease (PSD) is a combined infection of papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2). Transcriptomics of PSD infection at pre-flowering accumulated negative regulators of SA signalling, consisting of NPR1-inhibitor ( NPR1-I/NIM1-I ), genes coding for UDP-glucosyltransferases (UGTs) and ethylene pathway, whereas post-flowering infection caused the downregulation of PR-1 gene and the induction of BSMT1 and JA metabolism related genes [ 212 ]. Transcriptome profiling of PRSV resistant transgenic papaya identified TFs such as MYB , WRKY , ERF , NAC and nitrate and zinc transporters involved in ABA, SA and ethylene signalling pathways [ 213 ].…”

Section: Biotic Stressmentioning

confidence: 99%

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

Mathiazhagan

Chidambara

Laxman

et al. 2021

Genes

View full text Add to dashboard Cite

The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.

show abstract

“…Grupo infectado con FOC Los resultados reportados en el presente estudio sirven de prueba para consolidar las bases de la validación en campo de nuevos métodos de diagnóstico y de evaluación de tratamientos de las enfermedades ocasionadas por microorganismos patógenos y condiciones ambientales desfavorables, como las altas temperaturas y la falta de agua (Ashraf & Harris, 2013;Madroñero, et al, 2019), que continúan siendo un reto en la investigación agronómica.…”

Section: Parámetrosunclassified

Monitoreo fotoacústico de plantas Musa acuminata (Musaceae) infectadas con el hongo Fusarium oxysporum (Nectriaceae)

Gordillo-Delgado

Botero-Zuluaga

2020

Rev. Acad. Colomb. Cienc. Ex. Fis. Nat.

View full text Add to dashboard Cite

La técnica fotoacústica permite evaluar el comportamiento de la razón de evolución de oxígeno de las plantas, el cual es un indicador del rendimiento fotosintético. En este estudio se monitoreó este parámetro y el crecimiento de un grupo de plantas de banano Gros Michel (Musa AAA), infectadas con Fusarium oxysporum f.sp. cubense, patógeno causante de la marchitez vascular, una enfermedad destructiva que amenaza la sostenibilidad de los cultivares sensibles a ella en las regiones productoras. La infección efectiva de las plantas y el progreso de la marchitez comúnmente se evalúan a partir de la manifestación de los primeros síntomas externos de clorosis en las hojas bajeras, a los que se asigna un valor cuantitativo según su gravedad. Aunque en el análisis de la razón de evolución de oxígeno y del crecimiento no se encontraron diferencias estadísticas significativas entre las plantas infectadas con Fusarium oxysporum f.sp. cubense y las plantas sanas, se demostró que esta técnica permite incluir caracteres fenotípicos relacionados con la actividad fotosintética en la caracterización de los cultivos. Los resultados en cuanto a la afectación de la enfermedad se pueden asociar con las condiciones de cultivo en invernadero y con la etapa asintomática de la enfermedad en la que se hizo la observación.

show abstract

Next generation sequencing and proteomics in plant virology: how is Colombia doing?

Cited by 5 publications

References 122 publications

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

Monitoreo fotoacústico de plantas Musa acuminata (Musaceae) infectadas con el hongo Fusarium oxysporum (Nectriaceae)

Contact Info

Product

Resources

About