De novo transcriptome analysis and identification of defensive genes in garlic (Allium sativum L.) using high-throughput sequencing

Abstract Background: Garlic (Allium sativum L.) is the second most widely cultivated Allium which is mainly grown in temperate regions and used as a flavouring agent in wide variety of foods. Garlic contains various bioactive compounds whose metabolic pathways, plant pathogen interactions, defensive genes, identify interaction networks and functional genomics was not previously predicted in the garlic at genomic level. To address this issue, we constructed two garlic Illumina 2000 libraries from tissues of garlic clove and leaf. Results: Approximately 43 million 125 bp paired-end reads were obtained in the two libraries. A total of 239,973 contigs were generated by de novo assembly of both samples and were compared with the sequences in NCBI non-redundant protein database. In total, 42% of contigs were matched to known proteins in public databases including Nr, GO and COG and then contigs were mapped to 138 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, a number of regulatory genes including CCHC(Zn) family, followed by WD40, bromodomain, bZIP, AP2-EREBP, BED-type (Zn) proteins and defense response proteins related different conserved domains, such as RGA3, NBS-LRR, TIR-NBS-LRR, LRR, NBS-ARC, and CC-NBS-LRR. were discovered based on transcriptome dataset. We compared the ortholog gene family of the A. sativum transcriptome to A. thaliana, O. sativa and Z. mays and found that 12,077 orthologous gene families are specific to A. sativum L. Furthermore, we identified genes involved in plant defense mechanism, their protein-protein interaction network and plant pathogen interaction pathways. Conclusions: Our study contains an extensive sequencing and functional gene-annotation analysis of A. sativum L. The findings provide insights into molecular basis of TFs, defensive gene and a reference for future studies on the genetics and breeding of A. sativum L.