Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan)
A complementary DNA (cDNA) library was constructed from the developing xylem tissues of Neolamarckia cadamba. A total of 10,368 single-pass sequences was generated through high-throughput 5′-expressed sequence tag (EST) sequencing of the cDNA clones, and 6622 highquality ESTs were obtained afte...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer-Verlag Berlin Heidelberg
2015
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| Subjects: | |
| Online Access: | http://ir.unimas.my/12989/ http://ir.unimas.my/12989/ http://ir.unimas.my/12989/ http://ir.unimas.my/12989/1/NO%2059%20Gene%20discovery%20in%20the%20developing%20xylem%20tissue%20of%20a%20tropical%20timber%20tree%20species%20-%20abstrak.pdf |
| Summary: | A complementary DNA (cDNA) library was constructed
from the developing xylem tissues of Neolamarckia
cadamba. A total of 10,368 single-pass sequences was generated
through high-throughput 5′-expressed sequence tag
(EST) sequencing of the cDNA clones, and 6622 highquality
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 ontology
(GO) terms that distributed among three main GO categories,
which were biological processes (2333), molecular
function (3056) and cellular component (2364). Simple sequence
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 function
found in this database was 60S ribosomal protein followed
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), caffeoylcoenzyme
A O-methyltransferase (CCoAOMT) and peroxidase.
The data obtained from this study will provide a powerful
means for identifying mechanisms controlling wood formation
pathways of kelampayan and supplymany new cloned
genes for future endeavours to modify wood and fibre
properties. |
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