Immunodiagnosis of bunchy top viruses in abaca with polyclonal antibodies against their recombinant coat proteins

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

doi:10.1080/03235408.2020.1727106

Cited by 3 publications

(4 citation statements)

References 27 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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“…Since the rst application of CTAB-based extraction method for plants [22], there have been variations depending on the plant species. Although currently published methods on DNA extraction of abaca has been based mostly on the CTAB method of DNA extraction [9][10][11][12], several studies on extraction of DNA from the monocot crop palm [18] and RNA from the ber crop Cannabis sativa [23] have shown the effectiveness of using lysis buffers containing SDS. The use of SDS as the main detergent in the lysis buffer of Protocol 4 was also able to extract high molecular weight DNA from abaca leaf samples (Fig.…”

Section: Dna Extraction Methods Comparisonmentioning

confidence: 99%

“…Currently used DNA extraction protocols for abaca are based on the traditional (cetyltrimethylammonium bromide) CTABbased method [9][10][11][12]. Boguero et al have supplemented additives such as polyvinylpyrrolidone (PVP) and polyethylene glycol (PEG) to contend with the phenolics found in abaca tissues [9].…”

Section: Introductionmentioning

confidence: 99%

“…However the protocol requires two rounds of water incubation at 55 o C and 65 o C which extends the processing time to more than 3 hours. The existing protocol in our laboratory [11,12] uses a modi ed CTAB-based protocol optimized for leaf tissues of bananas and sweet potato [16]. This has yielded average DNA quantities suitable for polymerase chain reaction (PCR) experiments [11,12]; however, the protocol requires half a day to complete and lacks an RNase A treatment step.…”

Section: Introductionmentioning

confidence: 99%

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Extraction of high molecular weight abaca DNA suitable for next-generation sequencing

Koh

Barbosa²,

Aquino

et al. 2020

Preprint

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Background The abaca (Musa textilis Née) is a fiber crop native to the Philippines with high economic value because of its fiber - the Manila hemp, known to be the strongest of all the natural fibers. DNA extraction in abaca is difficult due to its fibrous nature, high cellulose content and polyphenol compounds. Thus an optimized DNA extraction method is required for extracting high quality abaca DNA for next-generation sequencing applications. Results In this study, we have compared five different methods for the extraction of high molecular weight DNA from abaca leaves. The methods are the traditional CTAB method (Protocol 1), the CTAB with PVP method (Protocol 2), the CTAB with 0.3% β-mercaptoethanol method (Protocol 3), SDS-method (Protocol 4) and CTAB with Triton X-100 and PVP method (Protocol 5). Out of the five methods tested, traditional CTAB-method (Protocol 1), CTAB with 0.3% β-mercaptoethanol method (Protocol 3) and SDS-method (Protocol 4) have shown to be the most consistent in giving high molecular weight DNA with good yield and purity based on A260/A280 and A260/A230 absorption values. TissueLyserII was also utilized for homogenization for the three extraction protocols for applications in high-throughput DNA extraction. DNA from two abaca varieties were extracted using the CTAB with 0.3% β-mercaptoethanol method (Protocol 3) and were sent for NGS based on Illumina HiSeq platform having both passed the quality control for library preparation. Conclusion The CTAB with 0.3% β-mercaptoethanol method (Protocol 3) was found to be the simplest and most consistent method for extracting average yield DNA with high quality for NGS applications. The SDS-method (Protocol 4) was determined to have the shortest processing time and together with TissueLyserII is the most appropriate method for high-throughput extraction of abaca samples which will be useful for genotyping-by-sequencing (GBS) studies.

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