Transcriptome analysis of root development in bottle gourd (Lagenaria siceraria)

Bottle gourd is widely used as rootstock because of its highly resistant efficiency on Fusarium wilt. Previous work mainly focused on its resistance to Fusarium wilt and/or its effects on gene expression patterns in scions. However, little is known about its own metabolism, especially the early stage of the root development after Fusarium oxysporum inoculation. In this study, a cDNA library generated from root RNA sampled from bottle gourd seedling at 0 days after inoculation (DAI) and 10 DAI were sequenced using Illumina highseq 2000 platform. More than 41,831,589 high quality reads were generated and was assembled into 56,905 unigenes with an average sequence length of 735.11 base pairs. A total of 38,515 (67.7%) unigenes were annotated and of which 8,171 were assigned to specific metabolic pathways by the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Of all unigenes, 2,469 genes were differentially expressed, including 1,294 up-regulated genes and 1,175 down-regulated genes. With Clusters of Orthologous Groups of Proteins (COG) and Gene Ontology (GO) functional classifications, all differentially expressed-transcripts were grouped into 23 and 55 categories, respectively, which includes many functional categories, such as energy metabolism, signalling, transcription regulation and defence reactions. Genes involving the defence biosynthesis were analysed. 37 gene sequences encoding the defence metabolites were discovered in the transcriptome. Our study has provided a dataset that documents the dynamics of the root transcriptome at the early development stage. The transcriptome data also provides an important resource for understanding the formation of defence constituents in the root extract from bottle gourd.