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

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 se...

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Autores principales: Galvez, Leny Calano, Koh, Rhosener Bhea Lu, Barbosa, Cris Francis Cortez, Asunto, Jayson Calundre, Catalla, Jose Leonido, Atienza, Robert Gomez, Costales, Kennedy Trinidad, Aquino, Vermando Masinsin, Zhang, Dapeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8392402/
https://www.ncbi.nlm.nih.gov/pubmed/34440376
http://dx.doi.org/10.3390/genes12081202
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author Galvez, Leny Calano
Koh, Rhosener Bhea Lu
Barbosa, Cris Francis Cortez
Asunto, Jayson Calundre
Catalla, Jose Leonido
Atienza, Robert Gomez
Costales, Kennedy Trinidad
Aquino, Vermando Masinsin
Zhang, Dapeng
author_facet Galvez, Leny Calano
Koh, Rhosener Bhea Lu
Barbosa, Cris Francis Cortez
Asunto, Jayson Calundre
Catalla, Jose Leonido
Atienza, Robert Gomez
Costales, Kennedy Trinidad
Aquino, Vermando Masinsin
Zhang, Dapeng
author_sort Galvez, Leny Calano
collection PubMed
description 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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spelling pubmed-83924022021-08-28 Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome Galvez, Leny Calano Koh, Rhosener Bhea Lu Barbosa, Cris Francis Cortez Asunto, Jayson Calundre Catalla, Jose Leonido Atienza, Robert Gomez Costales, Kennedy Trinidad Aquino, Vermando Masinsin Zhang, Dapeng Genes (Basel) Article 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. MDPI 2021-08-02 /pmc/articles/PMC8392402/ /pubmed/34440376 http://dx.doi.org/10.3390/genes12081202 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Galvez, Leny Calano
Koh, Rhosener Bhea Lu
Barbosa, Cris Francis Cortez
Asunto, Jayson Calundre
Catalla, Jose Leonido
Atienza, Robert Gomez
Costales, Kennedy Trinidad
Aquino, Vermando Masinsin
Zhang, Dapeng
Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome
title Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome
title_full Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome
title_fullStr Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome
title_full_unstemmed Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome
title_short Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome
title_sort sequencing and de novo assembly of abaca (musa textilis née) var. abuab genome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8392402/
https://www.ncbi.nlm.nih.gov/pubmed/34440376
http://dx.doi.org/10.3390/genes12081202
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