Identification and analysis of expressed sequence tags present in xylem tissues of kelampayan (Neolamarckia cadamba (Roxb.) Bosser)

Abstract

The large-scale genomic resource for kelampayan was generated from a developing xylem cDNA library. A total of 6,622 high quality expressed sequence tags (ESTs) were generated through high-throughput 5' EST sequencing of cDNA clones. The ESTs were analyzed and assembled to generate 4,728 xylogenesis unigenes distributed in 2,100 contigs and 2,628 singletons. About 59.3 % of the ESTs were assigned with putative identifications whereas 40.7 % of the sequences showed no significant similarity to any sequences in GenBank. Interestingly, most genes involved in lignin biosynthesis and several other cell wall biosynthesis genes were identified in the kelampayan EST database. The identified genes in this study will be candidates for functional genomics and association genetic studies in kelampayan aiming at the production of high value forests.

<i>In Silico</i> Analysis of Cellulose Synthase Gene (NcCesA1) in Developing Xylem Tissues of <i>Neolamarckia Cadamba</i>

“…Singletons of CesA gene were selected from the kelampayan tree transcriptome database (NcdbEST) (Ho et al, 2014). These singletons were blast again NCBI database to search for sequence homology and binding position on the respective gene.…”

“…A total of 13 CesA singletons were obtained from NcdbEST (Ho et al, 2014). These singletons showed high maximum identity value scores of more than 80% as shown in Table 1.…”

“…N. cadamba or locally known as kelampayan belongs to the family of Rubiaceae. It has been selected as one of the fast growing plantation species for planted forest development in Sarawak (Tchin et al, 2012;Lai et al, 2013;Tiong et al, 2014a;2014b;Ho et al, 2014;Phui et al, 2014). The state government of Sarawak has introduced the Forest (Planted Forest) Rules (1997) to encourage the development of commercial planted forests and has set a target of 1.0 million hectares for forest plantations to be established by 2020.…”

Bioinformatics Analysis of Xyloglucan Endotransglycosylase/Hydrolase (XTH) Gene from Developing Xylem of a Tropical Timber Tree <i>Neolamarckia Cadamba</i>

“…Singletons of XTH gene were selected from the Kelampayan tree transcriptome database (NcdbEST) (Ho et al, 2014). The XTH singletons were blast again NCBI database to search for sequence homology and binding position on the respective gene.…”

“…N. cadamba or locally known as kelampayan belongs to the family of Rubiaceae. It has been selected as one of the fast growing plantation species for planted forest development in Sarawak (Tchin et al, 2012;Lai et al, 2013;Tiong et al, 2014a;2014b;Ho et al, 2014). The state government of Sarawak has introduced the Forest (Planted Forest) Rules (1997) to encourage the development of commercial planted forests and has set a target of 1.0 million hectares for forest plantations to be established by 2020.…”