Abstract
BackgroundBananas and plantains (Musa spp.) are among the most important crops in the world due to their nutritional and export value. However, banana production has been devastated by fungal infestations caused by Fusarium oxysporum f. sp. cubense (Foc), which cannot be effectively prevented or controlled. Since there is very little known about the molecular mechanism of Foc infections; therefore, we aimed to investigate the transcriptional changes induced by Foc in banana roots.ResultsWe generated a cDNA library from total RNA isolated from banana roots infected with Foc Tropical Race 4 (Foc TR 4) at days 0, 2, 4, and 6. We generated over 26 million high-quality reads from the cDNA library using deep sequencing and assembled 25,158 distinct gene sequences by de novo assembly and gap-filling. The average distinct gene sequence length was 1,439 base pairs. A total of 21,622 (85.94%) unique sequences were annotated and 11,611 were assigned to specific metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes database. We used digital gene expression (DGE) profiling to investigate the transcriptional changes in the banana root upon Foc TR4 infection. The expression of genes in the Phenylalanine metabolism, phenylpropanoid biosynthesis and alpha-linolenic acid metabolism pathways was affected by Foc TR4 infection.ConclusionThe combination of RNA-Seq and DGE analysis provides a powerful method for analyzing the banana root transcriptome and investigating the transcriptional changes during the response of banana genes to Foc TR4 infection. The assembled banana transcriptome provides an important resource for future investigations about the banana crop as well as the diseases that plague this valuable staple food.
Highlights
Bananas and plantains (Musa spp.) are among the most important crops in the world due to their nutritional and export value
To obtain an overview of the expression profile of banana roots under Foc TR4 stress, a cDNA sample was prepared from the total RNA of an equal mixture of roots not infected and infected with Foc TR4 for 2, 4, and 6 days to acquire the genes whose expression is altered when the plant is infected by Foc TR4
Deep-sequencing of this cDNA sample produced 26,662,006 sequence reads with a length of 90 bp each, which corresponded to approximately 2.39 gigabase pairs (Gbp) of raw data
Summary
Bananas and plantains (Musa spp.) are among the most important crops in the world due to their nutritional and export value. Banana production has been devastated by fungal infestations caused by Fusarium oxysporum f. Bananas and plantains (Musa spp.), which are staple foods due to their high protein content and nutrition value as well as the main income source in many developing countries, are among the most important crops in the world. Foc has devastated banana production and continues to threaten crops [4]. An extremely virulent form of Foc, called ‘Tropical Race 4’ (Foc TR4), is capable of attacking the susceptible Cavendish variety, causing large losses in banana production in recent years [5]
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