Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan)

Abstract

A complementary DNA (cDNA) library was con- structed from the developing xylem tissues of Neolamarckia cadamba. A total of 10,368 single-pass sequences was gener- ated through high-throughput 5'-expressed sequence tag (EST) sequencing of the cDNA clones, and 6622 high- quality ESTs were obtained after removing the low-quality sequences; this gave approximately 3.17 Mb of data. Clustering of the high-quality ESTs revealed 4728 unigenes, consisting of 2100 consensus and 2628 singletons. A total of 2405 ESTs were successfully annotated with 7753 gene on- tology (GO) terms that distributed among three main GO cat- egories, which were biological processes (2333), molecular function (3056) and cellular component (2364). Simple se- quence repeat (SSR) mining revealed that the frequency of SSR in the N. cadamba EST database (NcbdEST) was 3.3 %, with the GCT/AGC motif being the most abundant repeat motif. The most abundant transcript with known func- tion found in this database was 60S ribosomal protein follow- ed by 40S ribosomal protein. Some of the important genes involved in xylogenesis and lignin biosynthesis were found in NcdbEST; these include tubulin genes, cellulose synthase (CesA), xyloglucan endotransglycosylase (XET), arabinogalactan, cinnamate 4-hydroxylase (C4H), caffeoyl- coenzyme A O-methyltransferase (CCoAOMT) and peroxi- dase. The data obtained from this study will provide a power- ful means for identifying mechanisms controlling wood for- mationpathwaysofkelampayanandsupplymanynew cloned genes for future endeavours to modify wood and fibre properties.