Transcriptome analysis of banana (Musa balbisiana) basedon next-generation sequencing technology

Abstract

Banana (Musa spp.) is an important tropical fruit with high commercial potential. Musa balbisiana (B genome) is a progenitor of one of the most cultivated banana species and exhibits unique traits, including resistance or tolerance to many biotic and abiotic stresses. RNA sequencing of the Musa B genome would provide a vast array of transcriptomic information that could lead to the development of trait-specific markers and the discovery of new genes and regulatory sequences involved in resistance mechanisms. Thus, transcriptome sequencing was performed in Musa B genome accession Attikol using the Ion Torrent platform. This led to the generation of about 4.5 million paired-end reads, which were assembled using the MIRA assembler. The assembly produced 82,413 unique transcripts with a mean length of approximately 113 bp. The sequence similarity search against the Swiss-Prot database resulted in the identification of 35,783 unique transcripts (62.18%). Out of these, 193,826 gene ontology terms were assigned to unique transcripts. Functional annotation against PlantCYC pathway database identified 20,696 unique transcripts, which were mapped to 455 pathways. About 4780 simple sequence repeats (SSRs) were obtained from 82,413 unique transcripts. Primers could be designed for only 2628 SSRs, out of which 30 primers were randomly selected from defense-related genes to confirm their efficiency. This information will make the improvement of banana cultivars easier by facilitating the selection of resistance genes as well as the development of trait-specific markers.

Biological Control Agents Against Fusarium Wilt of Banana

“…Furthermore, transcriptomics has been implemented in studies on Musa spp. (e.g., Backiyarani et al, 2015) enhancing our knowledge on physiological processes such as the fruit ripening (Asif et al, 2014) and the responses to abiotic stresses such as low-temperature (Yang Q. S. et al, 2015). This “-omics” has been largely used to study the interaction between BCAs, plant and/or microbiome, but no studies are available on the banana/ Foc pathosystem.…”

Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein-protein interaction network

“…Identi cation of candidate gene/s responsible for the trait parthenocarpy in Musa spp. is a prerequisitefor the commercial exploitation of accessions with B genome that exhibit resistance against biotic or abiotic stresses 41 . It was reported that the trait parthenocarpy in banana is governed by three independent complementary geneswhere seediness could result even with the loss of one dominant gene 29,30 .…”

Transcriptome Analysis in Banana

“…Recently, a whole transcriptome from different tissues like leaf, root, sheath, flower bud, flower bract, pulp, and rhizome was performed by Backiyarani [12]. The identification of rapid activation and selective induction of cold tolerance genes ICE1 and MYBS3 and their pathways in plantain and banana, along with expression of other cold-specific genes provided useful information on the expression patterns using comparative transcriptomics [13].…”

“…Its application in Musa could improve our understanding of the molecular mechanisms involved in defence [14], biosynthesis, and other biochemical processes [12,13,15] providing a potential resource for future genetic or genomic studies on this important food crop. It can also be expected to bridge a critical gap that exists in the Musa comparative genomics and could ultimately contribute to the evolutionary and functional studies of its genes and genomes.…”