Short summary for the below paragraph: +Two bean plants (Phaseolus vulgaris, labelled as PV1 and PV2, both cv. Maxidor) growing in a private garden in Pezinok (western Slovakia, GPS coordinates: 48°18′11.6″N 17°16′35.6″E) were sampled in July 2021 and subjected to HTS. + +Briefly, total RNAs were extracted from leaves using the Spectrum Plant Total RNA Kit (Sigma Aldrich, St. Louis, MO, United States). Ribosomal RNA was removed using the Zymo-Seq RiboFree Universal cDNA Kit (Zymo Research, Irvine, CA, United States). The ribosomal RNA-depleted total RNA samples were used for double-stranded cDNA synthesis using the SuperScript II kit (Thermo Fisher Scientific, Waltham, MA, United States). The cDNA was then purified with the 2.2 x AMPure XP beads and quantified with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, United States). Subsequently, the samples were processed with the transposon-based chemistry library preparation kit (Nextera XT, Illumina, San Diego, CA, United States). Low-cycle PCR and mutual indexing of the fragments was carried out. Fragments were purified with 1.8 x AMPure XP beads (Beckman Coulter, Brea, CA, United States) without size selection. The fragment size structure of the DNA library was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, United States). An equimolar pool of 4 nM DNA libraries was denatured, diluted to 10 pM and sequenced (2 × 150 bp paired reads paired-end sequencing) on the Illumina MiSeq platform (Illumina, San Diego, CA, United States). High-quality trimmed reads were used for de novo assembly and contigs aligned to the viral genomes database (ftp://ftp.ncbi.nih.gov/genomes/Viruses/all.fna.tar.gz) using CLC Genomics Workbench 9.5.2 and Geneious v.8.1.9 softwares. Alternatively, the reads were mapped against selected full-length reference genome sequences of viruses identified in the previous step. Sanger sequencing of PCR products obtained by using PvEV-1-specific primers described below was used to validate two portions of the genome. + +The nearly complete nucleotide sequences reported in this paper (missing 10 and 8, and 2 and 5 nucleotides, respectively, at the 5′ and 3′extremities, for PV1 and PV2, respectively, as compared to the reference NC_039217 genome) have been deposited in the GenBank database under accession numbers OQ750683 (PV1) and OQ750684 (PV2).
Sure, here is a short summary of the paragraph you provided:
In July 2021, two bean plants (Phaseolus vulgaris, labeled as PV1 and PV2) were sampled from a private garden in Pezinok, Slovakia. Total RNA was extracted from the leaves of the plants and subjected to high-throughput sequencing (HTS). The HTS data was used to assemble the nearly complete nucleotide sequences of the plants' genomes. The sequences were deposited in the GenBank database under accession numbers OQ750683 (PV1) and OQ750684 (PV2).
Here are some additional details about the HTS procedure:
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+
- Total RNA was extracted from the leaves of the plants using a commercial kit. +
- Ribosomal RNA was removed from the total RNA using another commercial kit. +
- The ribosomal RNA-depleted total RNA samples were used to synthesize double-stranded cDNA. +
- The cDNA was then purified and quantified. +
- The samples were processed with a transposon-based chemistry library preparation kit. +
- Low-cycle PCR and mutual indexing of the fragments was carried out. +
- Fragments were purified without size selection. +
- The fragment size structure of the DNA library was assessed. +
- An equimolar pool of 4 nM DNA libraries was sequenced on the Illumina MiSeq platform. +
- High-quality trimmed reads were used for de novo assembly. +
- Contigs were aligned to the viral genomes database. +
- Sanger sequencing was used to validate two portions of the genome. +
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