Sequencing and de Novo Assembly of Abaca (<i>Musa textilis</i> Née) var. Abuab Genome
Abaca (<i>Musa textilis</i> 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 abac...
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| Format: | Article |
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MDPI AG
2021-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/8/1202 |
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| author | Leny Calano Galvez Rhosener Bhea Lu Koh Cris Francis Cortez Barbosa Jayson Calundre Asunto Jose Leonido Catalla Robert Gomez Atienza Kennedy Trinidad Costales Vermando Masinsin Aquino Dapeng Zhang |
| author_facet | Leny Calano Galvez Rhosener Bhea Lu Koh Cris Francis Cortez Barbosa Jayson Calundre Asunto Jose Leonido Catalla Robert Gomez Atienza Kennedy Trinidad Costales Vermando Masinsin Aquino Dapeng Zhang |
| author_sort | Leny Calano Galvez |
| collection | DOAJ |
| description | Abaca (<i>Musa textilis</i> 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. |
| first_indexed | 2024-03-10T08:48:06Z |
| format | Article |
| id | doaj.art-c55b0b56d5f148e1a09765613269f4ad |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T08:48:06Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-c55b0b56d5f148e1a09765613269f4ad2023-11-22T07:46:00ZengMDPI AGGenes2073-44252021-08-01128120210.3390/genes12081202Sequencing and de Novo Assembly of Abaca (<i>Musa textilis</i> Née) var. Abuab GenomeLeny Calano Galvez0Rhosener Bhea Lu Koh1Cris Francis Cortez Barbosa2Jayson Calundre Asunto3Jose Leonido Catalla4Robert Gomez Atienza5Kennedy Trinidad Costales6Vermando Masinsin Aquino7Dapeng Zhang8Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, PhilippinesNational Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, PhilippinesPhilippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, PhilippinesPhilippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, PhilippinesPhilippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, PhilippinesPhilippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, PhilippinesPhilippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, PhilippinesNational Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, PhilippinesSustainable Perennial Crops Laboratory, USDA-ARS, Beltsville, MD 20705, USAAbaca (<i>Musa textilis</i> 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.https://www.mdpi.com/2073-4425/12/8/1202<i>Musa textilis</i> Néefiber cropManila hempAbuabNGSwhole genome sequencing |
| spellingShingle | Leny Calano Galvez Rhosener Bhea Lu Koh Cris Francis Cortez Barbosa Jayson Calundre Asunto Jose Leonido Catalla Robert Gomez Atienza Kennedy Trinidad Costales Vermando Masinsin Aquino Dapeng Zhang Sequencing and de Novo Assembly of Abaca (<i>Musa textilis</i> Née) var. Abuab Genome Genes <i>Musa textilis</i> Née fiber crop Manila hemp Abuab NGS whole genome sequencing |
| title | Sequencing and de Novo Assembly of Abaca (<i>Musa textilis</i> Née) var. Abuab Genome |
| title_full | Sequencing and de Novo Assembly of Abaca (<i>Musa textilis</i> Née) var. Abuab Genome |
| title_fullStr | Sequencing and de Novo Assembly of Abaca (<i>Musa textilis</i> Née) var. Abuab Genome |
| title_full_unstemmed | Sequencing and de Novo Assembly of Abaca (<i>Musa textilis</i> Née) var. Abuab Genome |
| title_short | Sequencing and de Novo Assembly of Abaca (<i>Musa textilis</i> Née) var. Abuab Genome |
| title_sort | sequencing and de novo assembly of abaca i musa textilis i nee var abuab genome |
| topic | <i>Musa textilis</i> Née fiber crop Manila hemp Abuab NGS whole genome sequencing |
| url | https://www.mdpi.com/2073-4425/12/8/1202 |
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