Generation and analysis of expressed sequence tags from a normalized cDNA library of young leaf from Ma bamboo (Dendrocalamus latiflorus Munro)

Abstract

Ma bamboo (Dendrocalamus latiflorus Munro) belongs to Dendrocalamus genus, Bambusease tribe, Bambusoideae subfamily, Poaceae family. It is a representative species of clumping bamboo, and a principal commercial species for various construction purposes using mature culms and for human consumption using young shoots. A normalized cDNA library was constructed from young leaves of Ma bamboo and 9,574 high-quality ESTs were generated, from which 5,317 unigenes including 1,502 contigs and 3,815 singletons were assembled. The unigenes were assigned into different gene ontology (GO) categories and summarized into 13 broad biologically functional groups according to similar functional characteristics or cellular roles by BLAST search against public databases. Eight hundred and ninety-one unigenes were assigned by KO identifiers and mapped to six KEGG biochemical pathways. The transcripts involved in biosynthesis of secondary metabolites such as cytochrome 450, flavonol synthase/flavanone 3-hydroxylase, and dihydroflavonol-4-reductase were well represented by 14 unigenes in the unigene set. The candidate genes involved in phytohormone metabolism, signal transduction and encoding cell wall-associated receptor kinases were also identified. Sixty-seven unigenes related to plant resistance (R) genes, including RPP genes, RGAs and RDL/RF genes, were discovered. These results will provide genome-wide knowledge about the molecular physiology of Ma bamboo young leaves and tools for advanced studies of molecular mechanism underlying leaf growth and development.

De Novo Assembly and Annotation of Salvia splendens Transcriptome Using the Illumina Platform

“…A unigene database consisting of potential alternative splicing transcripts was obtained through the clustering analysis. SSR analysis of the unigenes longer than 1 kb was performed using the SSRIT software [9].…”

Discovery and Comparative Profiling of microRNAs in Representative Monopodial Bamboo (Phyllostachys edulis) and Sympodial Bamboo (Dendrocalamus latiflorus)

“…However, there were no specific PCR products from ma bamboo. In order to identify the targets of these miRNAs, we had screened the published ma bamboo data of transcriptome [42] and ESTs [43] in NCBI and bambooGDB database [44] using the targets of miR396, miR397, miR1432, and miR7748, respectively, and no matched sequences was found for them, which indicated that the target genes in moso bamboo and ma bamboo are not comparable. On the basis of these results, miR397, miR1432, and miR7748 were specific conserved in the leaf sample of moso bamboo.…”

An Efficient Plant Regeneration and Transformation System of Ma Bamboo (Dendrocalamus latiflorus Munro) Started from Young Shoot as Explant

“…For example, 10,345 ESTs library had been generated from young leaves of Ma bamboo (Gao et al, 2011), the complete nucleotide sequences of its chloroplast genome was also published (Wu et al, 2009) and transcriptomic resources are also available (Liu et al, 2012). By using next generation high-throughput sequencing technology and bioinformatics analysis, 84 conserved miRNAs have been identified in Ma bamboo (Zhao et al, 2013).…”