title: De novo characterization of the banana root transcriptome and analysis of gene expression under Fusarium oxysporum f. sp. Cubense tropical race 4 infection.
abstract: BACKGROUND
  Bananas 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China.
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Wang
authors.forename: Jianbin
authors.initials: J
authors.lastname: Zhang
authors.forename: CaiHong
authors.initials: C
authors.lastname: Jia
authors.forename: JuHua
authors.initials: J
authors.lastname: Liu
authors.forename: YanQiang
authors.initials: Y
authors.lastname: Li
authors.forename: XiaoMin
authors.initials: X
authors.lastname: Yin
authors.forename: BiYu
authors.initials: B
authors.lastname: Xu
authors.forename: ZhiQiang
authors.initials: Z
authors.lastname: Jin
mesh_terms: D030541:Databases, Genetic; D005670:Fusarium / Q000502:physiology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D028521:Musa / Q000235:genetics* / Q000382:microbiology*; D010649:Phenylalanine / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics* / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D017962:alpha-Linolenic Acid / Q000235:genetics / Q000378:metabolism
chemical_list: D017962:alpha-Linolenic Acid; D010649:Phenylalanine