Rapid, simple detection of banana bract mosaic virus in abaca using a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay

Koh, Rhosener Bhea L.; Barbosa, Cris Francis C.; Aquino, Vermando M.; Galvez, Leny C.

doi:10.1007/s10327-020-00949-9

Cited by 5 publications

(3 citation statements)

References 25 publications

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“…To mitigate problems in abaca virus diseases, PhilFIDA developed abaca virus detection technologies applicable in both laboratory research settings [19][20][21][22] and point-of-care diagnostics [20,23,24] for effective disease management. Moreover, one of the major undertakings of PhilFIDA is the implementation of the Abaca Disease Management Program (ADMP) that aims to eradicate and rehabilitate disease-infected abaca areas.…”

Section: Introductionmentioning

confidence: 99%

Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome

Galvez

Koh

Barbosa

et al. 2021

Genes

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Abaca (Musa textilis Née), an indigenous crop to the Philippines, is known to be the source of the strongest natural fiber. Despite its huge economic contributions, research on crop improvement is limited due to the lack of genomic data. In this study, the whole genome of the abaca var. Abuab was sequenced using Illumina Novaseq 6000 and Pacific Biosciences Single-Molecule Real-Time Sequel. The genome size of Abuab was estimated to be 616 Mbp based on total k-mer number and volume peak. Its genome was assembled at 65× depth, mapping 95.28% of the estimated genome size. BUSCO analysis recovered 78.2% complete BUSCO genes. A total of 33,277 gene structures were predicted which is comparable to the number of predicted genes from recently assembled Musa spp. genomes. A total of 330 Mbp repetitive elements were also mined, accounting to 53.6% of the genome length. Here we report the sequencing and genome assembly of the abaca var. Abuab that will facilitate gene discovery for crop improvement and an indispensable source for genetic diversity studies in Musa.

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Section: Introductionmentioning

confidence: 99%

Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome

Galvez

Koh

Barbosa

et al. 2021

Genes

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“…LAMP has been used to detect various plant pathogens which could be completed within 30-60 min after incubation at isothermal temperatures ranging from 60 to 68°C (Katoh et al 2016;Bhuvitarkorn et al 2019;Koh et al 2020;Suzaki et al 2022). However, it was dependent on the use of a LAMP master mix.…”

Section: Discussionmentioning

confidence: 99%

Journal of Plant Protection Research

Supakitthanakorn,

Vichittragoontavorn,

Kunasakdakul

et al. 2022

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Chrysanthemum stunt viroid (CSVd) is a serious pathogen infecting chrysanthemum worldwide. To improve and enhance the detection procedure, a colorimetric loop-mediated isothermal amplification (LAMP) technique was developed. Six LAMP primers were newly designed and tested to determine the optimal conditions using a recombinant plasmid of CSVd as a DNA template. The optimal conditions for colorimetric LAMP were incubation at 65°C for 45 min. Under these conditions, a ladder-like pattern of LAMP products was detected along with a change of color from pink to yellow in the positive reactions. Limits of the detection (LOD) of colorimetric LAMP were up to 1 fg • µl -1 of plasmid DNA concentration which was 10 4 times greater than that of polymerase chain reaction (PCR). The developed colorimetric LAMP was not cross reacted to other viruses and viroids. From detection of actual samples and chrysanthemum plantlets which were obtained from meristem tip culture, the colorimetric LAMP showed effective potential in detecting CSVd. Therefore, the colorimetric LAMP can be used as a main technique to detect CSVd and ensure CSVd-free chrysanthemum plantlet production due to its accuracy, rapidness and sensitivity.

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“…As LAMP is a sensitive method, hence using LAMP, Amplification Amplification 00:05:00 00:10:00 00:15:00 00:20:00 0 0:25:00 00:30:00 00:05:00 00:10:00 00:15:00 00:20:00 0 0:25:00 00:30:00 mild infections can also be detected effectively which might give false negative during detection using conventional PCR methods. Apart from BBTV, the LAMP technique is also being widely used globally for rapid and sensitive detection of several plant viruses like Odontoglossum Ring Spot Virus (ORSV) (Tsai et al, 2016), Banana Bract Mosaic Virus (BBrMV) (Koh et al, 2020), Potato Leaf Roll Virus (PLRV) (Almasi et al, 2013;Ju, 2011), Potato Virus Y (PVY) (Tredar et al, 2018) etc. In this study, the Real-Time LAMP method was standardized for detecting BBTV in North-east India as it gives us cumulative advantages over conventional diagnostic methods like ELISA or PCR.…”

Section: Reaction Mixtures and Optimal Condition For Lamp Assaysmentioning

confidence: 99%

Real-Time loop-mediated isothermal amplification assay for rapid detection of Banana bunchy top virus in North-east India

Kaushik¹,

Halabi²,

Barua³

et al. 2022

JEB

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Aim: The study aims to standardize a Real-Time LAMP assay for effective, highly sensitive, and rapid detection of BBTV in North-east India. Methodology: Forty samples of banana showing BBTV like symptoms were collected from Assam, India and subjected to conventional PCR for confirmation. Six sets of BBTV LAMP primers were designed and the PCR positive samples were subjected to Real-Time LAMP assay for detection of BBTV. Finally, a sensitivity test of BBTV LAMP assay and comparison of BBTV LAMP assay with conventional PCR was done using seven 10-fold dilutions of total genomic DNA of leaf samples with the highest dilution starting from 100 ng µl-1. Results: Initially a total of twenty six out of forty banana samples were tested positive for BBTV with conventional PCR method. The Real-Time LAMP assay for BBTV detection resulted in typical sigmoidal amplification curves with the peak values ranging between 8.00 to 12.15 min and annealing derivatives ranging between 83.3oC to 84.3oC in the tested samples. Sensitivity testing and comparison of BBTV Real-Time LAMP assay with conventional PCR revealed that the BBTV LAMP assay could efficiently detect up to 0.0001ng µl-1 of total DNA against 0.01ng µl-1 in conventional PCR. Interpretation: The findings highlight rapid, sensitive, accurate and effective diagnosis of BBTV using Real-Time LAMP method. This method can be preferred over conventional diagnostic techniques like PCR or ELISA for rapid large scale detection of BBTV in banana plants in North-east India. Key words: Banana, Banana bunchy top virus, Rapid detection, Real-Time LAMP assay

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Rapid, simple detection of banana bract mosaic virus in abaca using a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay

Cited by 5 publications

References 25 publications

Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome

Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome

Journal of Plant Protection Research

Real-Time loop-mediated isothermal amplification assay for rapid detection of Banana bunchy top virus in North-east India

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