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

Authors: GALVEZ, LENY - Philippine Fiber Industry Development Authority; KOH, RHOSENER - University Of The Philippines; BARBOSA, CRIS FRANCIS - Philippine Fiber Industry Development Authority; ASUNTO, JAYSON - Philippine Fiber Industry Development Authority; CATALLA, JOSE - Philippine Fiber Industry Development Authority; ATIENZA, ROBERT - Philippine Fiber Industry Development Authority; COSTALESA, KENNEDY - Philippine Fiber Industry Development Authority; AQUINO, VERMANDO - University Of The Philippines; Zhang, Dapeng

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2021
Publication Date: 8/2/2021
Citation: Galvez, L.C., Koh, R.B., Barbosa, C.C., Asunto, J.C., Catalla, J.L., Atienza, R.G., Costalesa, K.T., Aquino, V.M., Zhang, D. 2021. Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome. Genes. 12:1202. https://doi.org/10.3390/genes12081202.
DOI: https://doi.org/10.3390/genes12081202

Interpretive Summary: The abaca plant (Musa textilis), a close relative of banana, is native to the Philippines and widely distributed in the humid tropics. This crop is used to produce abaca fibers (also called manila hemp), extracted from the leaf sheath of the plant. Abaca is a popular eco-friendly product around the world and a major source of livelihood for nearly 1.5 million Filipinos. Cutting edge genetic tools are needed to support the conservation and use of Abaca genetic resources. This study aims to develop the first draft genome of abaca plant. The result significantly increased the capacity for understanding the genetic factors influencing growth and development of abaca plants. It’s an indispensable resource for breeding new varieties with improved yield, fiber quality and disease-resistance. In addition, the abaca draft genome is highly useful for studying genetic diversity in other Musa species, including banana and plantain. This information will be used by researchers, plant breeders, and collection curators, around the world, to study and improve abaca and other Musa species and advance their production and utilization.

Technical Abstract: The physical properties of the abaca plant (Musa textilis Née) fiber render abaca indispensable for the Philippine economy and global green industry. The occurrence of biotic and abiotic stress factors such as virus diseases and extreme environmental conditions, however, negatively affects its potential productivity. The field of genomics offers impactful solutions to mitigate these problems, in which commencing steps involve elucidation of the abaca draft genome. 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 and assembled using the generated reads, wherein the data of the latter was used for assembly improvement through scaffolding and gap-filling. The genome size of Abuab was estimated to be 616 Mbp based on total k-mer number and volume peak. The genome sequence of Abuab was assembled at 65X depth, respectively, mapping 95.28% of the estimated genome size. The assembled genome consists of 48,495 scaffolds and possesses an N50 value of 47,921. Moreover, BUSCO analysis recovered 78.2% complete BUSCO genes, indicating a comparable level of assembly completeness upon comparison with assembled genomes of other Musa spp. A total of 330 Mbp repetitive elements were also mined, accounting to 53.6% of the genome length. Here we report a genome sequence assembly of abaca. The draft genome shall facilitate in gene discovery for crop improvement and disease resistance, marker-assisted breeding, as well as serve as an indispensable source for genetic diversity studies in Musa.