Identification of differentially expressed transcripts from maturing stem of sugarcane by in silico analysis of stem expressed sequence tags and gene expression profiling

• Published in: Plant molecular biology Vol. 54; no. 4; pp. 503 - 517
• Main Authors: Casu, R.E, Dimmock, C.M, Chapman, S.C, Grof, C.P.L, McIntyre, C.L, Bonnett, G.D, Manners, J.M
• Format: Journal Article
• Language: English
• Published: Netherlands Springer Nature B.V 01.03.2004
• Subjects: Amino Acid Sequence; amino acid sequences; bioinformatics; Biosynthesis; Blotting, Northern; defense mechanisms; dirigent protein; DNA, Complementary - chemistry; DNA, Complementary - genetics; Expressed Sequence Tags; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene Library; Hybridization; lignification; lignin; messenger RNA; metabolism; microarray technology; Molecular Sequence Data; nucleotide sequences; plant development; plant fibers; plant proteins; Plant Stems - genetics; Plant Stems - growth & development; RNA, Plant - genetics; RNA, Plant - metabolism; Saccharum; Saccharum - genetics; Saccharum - growth & development; sequence alignment; Sequence Analysis, DNA; Sequence Homology, Amino Acid; stems; stress tolerance; Sugar; Sugarcane; Transcription, Genetic
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1023/B:PLAN.0000038255.96128.41

Sugarcane accumulates high concentrations of sucrose in the mature stem and a number of physiological processes on-going in maturing stem tissue both directly and indirectly allow this process. To identify transcripts that are associated with stem maturation, we compared patterns of gene expression in maturing and immature stem tissue by expression profiling and bioinformatic analysis of sets of stem ESTs. This study complements a previous study of gene expression associated directly with sugar metabolism in sugarcane. A survey of sequences derived from stem tissue identified an abundance of several classes of sequence that are associated with fibre biosynthesis in the maturing stem. A combination of EST analyses and microarray hybridization revealed that genes encoding homologues of the dirigent protein, a protein that assists in the stereospecificity of lignin assembly, were the most abundant and most strongly differentially expressed transcripts in maturing stem tissue. There was also evidence of coordinated expression of other categories of fibre biosynthesis and putative defence- and stress-related transcripts in the maturing stem. This study has demonstrated the utility of genomic approaches using large-scale EST acquisition and microarray hybridization techniques to highlight the very significant transcriptional investment the maturing stem of sugarcane has placed in fibre biosynthesis and stress tolerance, in addition to its already well-documented role in sugar accumulation.