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

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...

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Main Authors: Shek-Ling, Pang, Wei-Seng, Ho, M.N., Mat Isa, Julaihi, Abdullah
Format: Article
Language:English
Published: Springer-Verlag Berlin Heidelberg 2015
Subjects:
GE Environmental Sciences
SD Forestry
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
id unimas-12989
recordtype eprints
spelling unimas-129892017-02-06T07:23:22Z http://ir.unimas.my/12989/ Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan) Shek-Ling, Pang Wei-Seng, Ho M.N., Mat Isa Julaihi, Abdullah GE Environmental Sciences SD Forestry 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. Springer-Verlag Berlin Heidelberg 2015 Article PeerReviewed text en http://ir.unimas.my/12989/1/NO%2059%20Gene%20discovery%20in%20the%20developing%20xylem%20tissue%20of%20a%20tropical%20timber%20tree%20species%20-%20abstrak.pdf Shek-Ling, Pang and Wei-Seng, Ho and M.N., Mat Isa and Julaihi, Abdullah (2015) Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan). Tree Genetics & Genomes, 11 (47). ISSN 1614-2950 http://link.springer.com/article/10.1007/s11295-015-0873-y DOI 10.1007/s11295-015-0873-y
repository_type Digital Repository
institution_category Local University
institution Universiti Malaysia Sarawak
building UNIMAS Institutional Repository
collection Online Access
language English
topic GE Environmental Sciences
SD Forestry
spellingShingle GE Environmental Sciences
SD Forestry
Shek-Ling, Pang
Wei-Seng, Ho
M.N., Mat Isa
Julaihi, Abdullah
Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan)
description 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.
format Article
author Shek-Ling, Pang
Wei-Seng, Ho
M.N., Mat Isa
Julaihi, Abdullah
author_facet Shek-Ling, Pang
Wei-Seng, Ho
M.N., Mat Isa
Julaihi, Abdullah
author_sort Shek-Ling, Pang
title Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan)
title_short Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan)
title_full Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan)
title_fullStr Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan)
title_full_unstemmed Gene discovery in the developing xylem tissue of a tropical timber tree species: Neolamarckia cadamba (Roxb.) Bosser (kelampayan)
title_sort gene discovery in the developing xylem tissue of a tropical timber tree species: neolamarckia cadamba (roxb.) bosser (kelampayan)
publisher Springer-Verlag Berlin Heidelberg
publishDate 2015
url 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
first_indexed 2018-09-06T16:04:10Z
last_indexed 2018-09-06T16:04:10Z
_version_ 1610874723512614912

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