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

Abstract

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.

Keywords: Abuab; Manila hemp; Musa spp.; Musa textilis Née; NGS; de novo assembly; fiber crop; whole genome sequencing.

Figure 1

K-mer graph of abaca var. Abuab genome assembly.

Figure 2

Unigenes annotated in several databases.

Figure 3

Number distribution of eggNOG annotation of Unigenes related to A–Z. A—RNA processing and modification; B—Chromatin structure and dynamics; C—Energy production and conversion; D—Cell cycle control, cell division, chromosome partitioning; E—Amino acid transport and metabolism; F—Nucleotide transport and metabolism; G—Carbohydrate transport and metabolism; H—Coenzyme transport and metabolism; I—Lipid transport and metabolism; J—Translation, ribosomal structure and biogenesis; K—Transcription, L—Replication, recombination and repair; M—Cell wall/membrane/envelope biogenesis; N—Cell motility; O—Posttranslational modification, protein turnover, chaperones; P—Inorganic ion transport and metabolism; Q—Secondary metabolites biosynthesis, transport and catabolism; R—General function prediction only; S—Function unknown; T—Signal transduction mechanisms; U—Intracellular trafficking, secretion, and vesicular transport; V—Defense mechanisms; W—Extracellular structures; Y—Nuclear structure; Z—Cytoskeleton.

Figure 4

Venn diagram showing the number of orthologous groups. (A) The common and unique orthologous groups among M. textilis, G. raimondii, A. thaliana and O. sativa. (B) The common and unique orthologous groups among M. textilis, M. acuminata, M. balbisiana and M. schizocarpa.

Figure 5

Phylogenetic tree of Musa textilis var. Abuab, four other Musa spp., Oryza sativa, and two outgroup species, Arabidopsis thaliana and Gossypium raimondii using OrthoFinder 2.5.2 Multiple Sequence Alignment, set to use MAFFT 7.475 and RAxML.