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Sequencing of genes and genomes
KTH, Superseded Departments, Biotechnology.ORCID iD: 0000-0003-3281-8088
1998 (English)Doctoral thesis, comprehensive summary (Other scientific)
Place, publisher, year, edition, pages
Stockholm: KTH , 1998. , 63 p.
Keyword [en]
DNA sequencing, genome analysis, expressed sequence tag, expression analysis, complementary DNA, biotin-capture, solid-phase technology, automation, poplar
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-2714ISBN: 91-7170-315-2 (print)OAI: oai:DiVA.org:kth-2714DiVA: diva2:8418
Public defence
1998-11-01, 00:00
Note
QC 20100813Available from: 2000-01-01 Created: 2000-01-01 Last updated: 2010-08-13Bibliographically approved
List of papers
1. The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes
Open this publication in new window or tab >>The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes
1996 (English)In: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 12, no 10B, 1091-1095 p.Article in journal (Refereed) Published
Abstract [en]

We report the sequence of a 30 469 bp long DNA fragment on the left arm of chromosome XV of Saccharomyces cerevisiae. The fragment contains 15 open reading frames (ORFs) of al least 300 bp. Five previously sequenced yeast genes, PHO80, TIR2, SLG1, the gene encoding the subtilisin-like protease III precursor and the gene coding for ATP-dependent permease, are found among these ORFs. By DNA sequence comparison, two ORFs identified previously reported expressed sequence tags from yeast. Of the proteins encoded by the remaining eight ORFs, six show similarities to proteins from different organisms and two lack detectable similarity with any amino acid sequence described in public data banks. The DNA sequence has been deposited in GenBank under Accession Number U43491.

Keyword
Saccharomyces cerevisiae, chromosome XV, genome sequencing, PH080, TIR2, SLG1, ATP-dependent permease, subtilisin-like protease III
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-24090 (URN)A1996VL43200014 ()
Note
QC 20100813Available from: 2010-08-13 Created: 2010-08-13 Last updated: 2017-12-12Bibliographically approved
2. The nucleotide sequence of Saccharomyces cerevisiae chromosome XV
Open this publication in new window or tab >>The nucleotide sequence of Saccharomyces cerevisiae chromosome XV
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1997 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 387, no 6632, 98-102 p.Article in journal (Refereed) Published
Abstract [en]

Chromosome XV was one of the last two chromosomes of Saccharomyces cerevisiae to be discovered(1). It is the third-largest yeast chromosome after chromosomes XII and IV, and is very similar in size to chromosome VII. It alone represents 9% of the yeast genome (8% if ribosomal DNA is included). When systematic sequencing of chromosome XV was started, 93 genes or markers were identified, and most of them were mapped(2). However, very little else was known about chromosome XV which, in contrast to shorter chromosomes, had not been the object of comprehensive genetic or molecular analysis. It was therefore decided to start sequencing chromosome XV only in the third phase of the European Yeast Genome Sequencing Programme, after experience was gained on chromosomes III, XI and II (refs 3-5). The sequence of chromosome XV has been determined from a set of partly overlapping cosmid clones derived from a unique yeast strain, and physically mapped at 3.3-kilobase resolution before sequencing. As well as numerous new open reading frames (ORFs) and genes encoding tRNA or small RNA molecules, the sequence of 1,091,283 base pairs confirms the high proportion of orphan genes and reveals a number of ancestral and successive duplications with other yeast chromosomes.

Keyword
OPEN READING FRAMES; COMPLETE DNA-SEQUENCE; LEFT ARM; FRAGMENT; GENE; CONTAINS; SEGMENT
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-24072 (URN)A1997XB54600014 ()
Note
QC 20100812Available from: 2010-08-12 Created: 2010-08-12 Last updated: 2017-12-12Bibliographically approved
3. Direct sequencing of bacterial artificial chromosomes (BACs) and prokaryotic genomes by biotin-capture PCR
Open this publication in new window or tab >>Direct sequencing of bacterial artificial chromosomes (BACs) and prokaryotic genomes by biotin-capture PCR
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1998 (English)In: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 60, no 1-2, 119-129 p.Article in journal (Refereed) Published
Abstract [en]

Determination of unknown DNA sequences adjacent to known segments is an important task in genome-related research. We have applied the methodology of biotin-capture PCR for direct sequencing of bacterial artificial chromosomes (BACs) and bacterial genomes. The strategy involves extension of a biotinylated primer from a known locus into unknown regions of the template to yield single-stranded DNA, which is immobilised onto paramagnetic beads. An arbitrary primer initiates extension from the unknown region and back towards the known locus. The arbitrary primer contains a universal primer 'handle', which is utilised for subsequent amplification. The PCR products are then directly sequenced by solid-phase or cycle sequencing. The fact that BACs or bacterial chromosomes can be sequenced without prior purification or subcloning might be useful in numerous applications, such as gap-filling, sequencing of regulatory regions upstream known genes and determination of intron/exon-boundaries.

Keyword
genome sequencing, biotin capture, solid-phase technology, PCF
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-24088 (URN)000073047100012 ()
Note
QC 20100813Available from: 2010-08-13 Created: 2010-08-13 Last updated: 2017-12-12Bibliographically approved
4. Chromosomal sequencing using a PCR-based biotin-capture method allowed isolation of the complete gene for the outer membrane protein A of Klebsiella pneumoniae
Open this publication in new window or tab >>Chromosomal sequencing using a PCR-based biotin-capture method allowed isolation of the complete gene for the outer membrane protein A of Klebsiella pneumoniae
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1998 (English)In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 210, no 1, 93-101 p.Article in journal (Refereed) Published
Abstract [en]

By employing a novel biotin-and PCR-assisted capture method, which allows determination of unknown sequences on chromosomal DNA. the gene for the outer membrane protein A (OmpA) of Klebsiella pneumoniae has been isolated and sequenced to completion. The method involves linear amplification of DNA from a biotinylated primer annealing to a region with known sequence. After capture of the amplified single-stranded DNA on to paramagnetic beads, unspecifically annealing primers, i.e. arbitrary primers, were used to generate fragments with only partly determined nt sequences. The homology of the sequenced gene to ompAs of related bacteria is discussed. The ompA gene was assembled for intracellular expression in Escherichia coli, and two different fusion proteins were produced and recovered with good yields. The importance of the novel chromosomal sequencing method for gene isolation in general and the potential use of the OmpA fusion proteins are discussed. (C) 1998 Elsevier Science B.V.

Keyword
solid-phase technology, biotin-assisted capture, outer membrane protein A, Klebsiella pneumoniae, fusion protein
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-24089 (URN)000073075300012 ()
Note
QC 20100813Available from: 2010-08-13 Created: 2010-08-13 Last updated: 2017-12-12Bibliographically approved
5. Gene discovery in the wood-forming tissues of poplar: Analysis of 5,692 expressed sequence tags
Open this publication in new window or tab >>Gene discovery in the wood-forming tissues of poplar: Analysis of 5,692 expressed sequence tags
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1998 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 95, no 22, 13330-13335 p.Article in journal (Refereed) Published
Abstract [en]

A rapidly growing area of genome research is the generation of expressed sequence tags (ESTs) in which large numbers of randomly selected cDNA clones are partially sequenced. The collection of ESTs reflects the level and complexity of gene expression in the sampled tissue, To date, the majority of plant ESTs are from nonwoody plants such as Arabidopsis, Brassica, maize, and rice. Here, we present a large-scale production of ESTs from the wood-forming tissues of two poplars, Populus tremula L, x tremuloides Michx, and Populus trichocarpa 'Trichobel.' The 5,692 ESTs analyzed represented a total of 3,719 unique transcripts for the two cDNA libraries, Putative functions could be assigned to 2,245 of these transcripts that corresponded to 820 protein functions. Of specific interest to forest biotechnology are the 4% of ESTs involved in various processes of cell wall formation, such as lignin and cellulose synthesis, 5% similar to developmental regulators and members of known signal transduction pathways, and 2% involved in hormone biosynthesis. An additional 12% of the ESTs show ed no significant similarity to any other DNA or protein sequences in existing databases. The absence of these sequences from public databases may indicate a specific role for these proteins in wood formation. The cDNA libraries and the accompanying database are valuable resources for forest research directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.

Keyword
cambium, forestry, functional genomics, xylem, xylogenesis
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-24087 (URN)000076757300110 ()
Note
QC 20100813Available from: 2010-08-13 Created: 2010-08-13 Last updated: 2017-12-12Bibliographically approved
6. Molecular cloning of a cDNA encoding a cytosolic form of phosphoglucomutase from cambium of poplar (Populus tremula x tremuloides)
Open this publication in new window or tab >>Molecular cloning of a cDNA encoding a cytosolic form of phosphoglucomutase from cambium of poplar (Populus tremula x tremuloides)
1998 (English)Article in journal (Other academic) Submitted
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-24091 (URN)
Note
QC 20100813Available from: 2010-08-13 Created: 2010-08-13 Last updated: 2010-08-13Bibliographically approved
7. Molecular cloning of UPD-glucose dehydrogenase from cambium of poplar (Populus tremula x tremuloides)
Open this publication in new window or tab >>Molecular cloning of UPD-glucose dehydrogenase from cambium of poplar (Populus tremula x tremuloides)
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(English)Article in journal (Other academic) Submitted
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-24092 (URN)
Note
QS 20120327Available from: 2010-08-13 Created: 2010-08-13 Last updated: 2012-03-27Bibliographically approved

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