An ordered EST catalogue and gene expression profiles of cassava (Manihot esculenta) at key growth stages

Abstract

A cDNA library was constructed from the root tissues of cassava variety Huanan 124 at the root bulking stage. A total of 9,600 cDNA clones from the library were sequenced with single-pass from the 5'-terminus to establish a catalogue of expressed sequence tags (ESTs). Assembly of the resulting EST sequences resulted in 2,878 putative unigenes. Blastn analysis showed that 62.6% of the unigenes matched with known cassava ESTs and the rest had no 'hits' against the cassava database in the integrative PlantGDB database. Blastx analysis showed that 1,715 (59.59%) of the unigenes matched with one or more GenBank protein entries and 1,163 (40.41%) had no 'hits'. A cDNA microarray with 2,878 unigenes was developed and used to analyze gene expression profiling of Huanan 124 at key growth stages including seedling, formation of root system, root bulking, and starch maturity. Array data analysis revealed that (1) the higher ratio of up-regulated ribosome-related genes was accompanied by a high ratio of up-regulated ubiquitin, proteasome-related and protease genes in cassava roots; (2) starch formation and degradation simultaneously occur at the early stages of root development but starch degradation is declined partially due to decrease in UDP-glucose dehydrogenase activity with root maturity; (3) starch may also be synthesized in situ in roots; (4) starch synthesis, translocation, and accumulation are also associated probably with signaling pathways that parallel Wnt, LAM, TCS and ErbB signaling pathways in animals; (5) constitutive expression of stress-responsive genes may be due to the adaptation of cassava to harsh environments during long-term evolution.

Genome-wide analysis reveals phytohormone action during cassava storage root initiation

“…This observation was consistent with previous reports showing that the stress response-related genes were expressed at high levels relative to the plant's ability to grow in harsh environments (Li et al 2010).…”

Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

“…A number of excellent studies have indicated that metabolic processes were among the most regulated during developing stages of plants, and these genes were involved in many biological processes: e.g. glycan biosynthesis and metabolism, and the metabolisms of carbohydrates, lipids, amino acids and energy [26,44,45,60,61]. In developing bamboo culm in the present study, the dominant metabolic processes (27 unigenes) included glycan biosynthesis and metabolism, the metabolisms of carbohydrates, lipids, amino acids, nucleotides, energy and biosynthesis of other secondary metabolites (Additional file 12: Table S7).…”

Physiological and molecular characterization of drought responses and identification of candidate tolerance genes in cassava

“…In addition, many molecular studies on drought responses have used a single genotype without comparing the expression of genes between contrasting genotypes (Sakurai et al . 2007; Guo et al 2009; You-Zhi et al . 2010), making it difficult to separate drought-tolerance-related genes from drought-responsive genes.…”