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A Populus EST resource for plant functional genomics
KTH, Superseded Departments, Biotechnology.ORCID iD: 0000-0003-3281-8088
KTH, Superseded Departments, Biotechnology.
KTH, Superseded Departments, Biotechnology.
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2004 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 38, 13951-13956 p.Article in journal (Refereed) Published
Abstract [en]

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

Place, publisher, year, edition, pages
2004. Vol. 101, no 38, 13951-13956 p.
Keyword [en]
gene-expression, draft sequence, arabidopsis, poplar, evolution, biology
National Category
Biological Sciences
URN: urn:nbn:se:kth:diva-23752DOI: 10.1073/pnas.0401641101ISI: 000224069800046ScopusID: 2-s2.0-4644282569OAI: diva2:342451
QC 20100525 QC 20110916Available from: 2010-08-10 Created: 2010-08-10 Last updated: 2011-09-16Bibliographically approved
In thesis
1. Computational approaches for in-depth analysis of cDNA sequence tags
Open this publication in new window or tab >>Computational approaches for in-depth analysis of cDNA sequence tags
2004 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Major recent improvements in biotechnology have led to an accelerated production of DNA sequences. The completion of the human genome sequence, along with the genomes of more than two hundred other species, has marked the arrival of the genome era. The ultimate goal is to understand the structure and function of genomes and their genes. This thesis has focused on the computational analysis of complementary DNA (cDNA) sequences. These are copies of mRNA transcripts that correspond to the coding regions of genomes.

Studying the expression patterns of genes is essential for understanding gene function. Many gene expression profiling techniques generate short sequence tags that derive from transcripts. A pilot study was performed to assess the feasibility of using the pyrosequencing platform for gene expression analysis. The sequences generated by pyrosequencing in most cases (≈ 85%) were long enough (> 18 nucleotides) to uniquely identify the corresponding transcripts through database searches. Aspects of transcript identification by short sequence tags were further investigated in a number of public databases, revealing that a tag length 16-17 nucleotides was sufficient for unique identifi- cation.

Longer transcript representations are obtained from expressed sequence tag (EST) sequencing. Method development for the analysis and maintenance of large EST data sets has been performed on data from poplar, which is a tree of commercial interest to the forest biotechnology industry. In 2003 a large ESTsequencing project reached > 100 000 reads, providing a unique resource for tree biology research. ESTs have been grouped into clusters and singletons that represent potential genes. Preliminary analyses have estimated gene content in Populus to be very similar to that of model organism Arabidopsis thaliana.

EST data collections provide a rich source for mining polymorphisms. A software application was developed and applied to EST data from two Populus species, and candidate single nucleotide polymorphisms (SNPs) were recorded. A study of genetic variation between the species revealed a striking similarity, with orthologous pairs being > 98% identical on the protein level.

Keywords: cDNA, EST, gene expression, SNP, SAGE, polymorphism, assembly, clustering, DNA sequencing, pyrosequencing, mRNA transcript, orthology, tree biotechnology, restriction enzyme

Place, publisher, year, edition, pages
Bioteknologi, 2004
Biotechnology, cDNA, EST, gene expression, SNP, SAGE, polymorphism, Bioteknik
National Category
Industrial Biotechnology
urn:nbn:se:kth:diva-23 (URN)91-7283-837-X (ISBN)
Public defence
2004-10-08, E1, KTH, Lindstedsvägen 3, Stockholm, 13:00
Available from: 2004-10-08 Created: 2004-10-08 Last updated: 2012-03-21Bibliographically approved

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Sterky, FredrikBhalerao, Rupali R.Unneberg, PerNilsson, PeterUhlén, MathiasLundeberg, Joakim
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