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Joerg Bohlmann

Bio: Joerg Bohlmann is an academic researcher from University of British Columbia. The author has contributed to research in topics: Genome & Mountain pine beetle. The author has an hindex of 39, co-authored 96 publications receiving 9398 citations.


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Journal ArticleDOI
Gerald A. Tuskan1, Gerald A. Tuskan2, Stephen P. DiFazio3, Stephen P. DiFazio2, Stefan Jansson4, Joerg Bohlmann5, Igor V. Grigoriev6, Uffe Hellsten6, Nicholas H. Putnam6, Steven G. Ralph5, Stephane Rombauts7, Asaf Salamov6, Jacquie Schein, Lieven Sterck7, Andrea Aerts6, Rishikeshi Bhalerao4, Rishikesh P. Bhalerao8, Damien Blaudez9, Wout Boerjan7, Annick Brun9, Amy M. Brunner10, Victor Busov11, Malcolm M. Campbell12, John E. Carlson13, Michel Chalot9, Jarrod Chapman6, G.-L. Chen2, Dawn Cooper5, Pedro M. Coutinho14, Jérémy Couturier9, Sarah F. Covert15, Quentin C. B. Cronk5, R. Cunningham2, John M. Davis16, Sven Degroeve7, Annabelle Déjardin9, Claude W. dePamphilis13, John C. Detter6, Bill Dirks17, Inna Dubchak18, Inna Dubchak6, Sébastien Duplessis9, Jürgen Ehlting5, Brian E. Ellis5, Karla C Gendler19, David Goodstein6, Michael Gribskov20, Jane Grimwood21, Andrew Groover22, Lee E. Gunter2, Björn Hamberger5, Berthold Heinze, Yrjö Helariutta23, Yrjö Helariutta8, Yrjö Helariutta24, Bernard Henrissat14, D. Holligan15, Robert A. Holt, Wenyu Huang6, N. Islam-Faridi22, Steven J.M. Jones, M. Jones-Rhoades25, Richard A. Jorgensen19, Chandrashekhar P. Joshi11, Jaakko Kangasjärvi23, Jan Karlsson4, Colin T. Kelleher5, Robert Kirkpatrick, Matias Kirst16, Annegret Kohler9, Udaya C. Kalluri2, Frank W. Larimer2, Jim Leebens-Mack15, Jean-Charles Leplé9, Philip F. LoCascio2, Y. Lou6, Susan Lucas6, Francis Martin9, Barbara Montanini9, Carolyn A. Napoli19, David R. Nelson26, C D Nelson22, Kaisa Nieminen23, Ove Nilsson8, V. Pereda9, Gary F. Peter16, Ryan N. Philippe5, Gilles Pilate9, Alexander Poliakov18, J. Razumovskaya2, Paul G. Richardson6, Cécile Rinaldi9, Kermit Ritland5, Pierre Rouzé7, D. Ryaboy18, Jeremy Schmutz21, J. Schrader27, Bo Segerman4, H. Shin, Asim Siddiqui, Fredrik Sterky, Astrid Terry6, Chung-Jui Tsai11, Edward C. Uberbacher2, Per Unneberg, Jorma Vahala23, Kerr Wall13, Susan R. Wessler15, Guojun Yang15, T. Yin2, Carl J. Douglas5, Marco A. Marra, Göran Sandberg8, Y. Van de Peer7, Daniel S. Rokhsar17, Daniel S. Rokhsar6 
15 Sep 2006-Science
TL;DR: The draft genome of the black cottonwood tree, Populus trichocarpa, has been reported in this paper, with more than 45,000 putative protein-coding genes identified.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

4,025 citations

Journal ArticleDOI
22 May 2013-Nature
TL;DR: The draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm, is presented, revealing numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs, which opens up new genomic avenues for conifer forestry and breeding.
Abstract: Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

1,299 citations

Journal ArticleDOI
TL;DR: The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine and is provided with detailed experimental functional annotation of 39 members of this important gene family in Grapevine and comprehensive information about gene structure and phylogeny.
Abstract: Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS) were predicted by in silico analysis of the grapevine (Vitis vinifera) genome assembly [1]. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions. We present findings from the analysis of the up-dated 12-fold sequencing and assembly of the grapevine genome that place the number of predicted VvTPS genes at 69 putatively functional VvTPS, 20 partial VvTPS, and 63 VvTPS probable pseudogenes. Gene discovery and annotation included information about gene architecture and chromosomal location. A dense cluster of 45 VvTPS is localized on chromosome 18. Extensive FLcDNA cloning, gene synthesis, and protein expression enabled functional characterization of 39 VvTPS; this is the largest number of functionally characterized TPS for any species reported to date. Of these enzymes, 23 have unique functions and/or phylogenetic locations within the plant TPS gene family. Phylogenetic analyses of the TPS gene family showed that while most VvTPS form species-specific gene clusters, there are several examples of gene orthology with TPS of other plant species, representing perhaps more ancient VvTPS, which have maintained functions independent of speciation. The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine. We provide a detailed experimental functional annotation of 39 members of this important gene family in grapevine and comprehensive information about gene structure and phylogeny for the entire currently known VvTPS gene family.

368 citations

Journal ArticleDOI
TL;DR: Phylogenetic analyses highlight events in the divergence of the TPS paralogs and suggest orthologous genes and a model for the evolution of theTPS gene family.
Abstract: A family of 40 terpenoid synthase genes (AtTPS) was discovered by genome sequence analysis in Arabidopsis thaliana. This is the largest and most diverse group of TPS genes currently known for any species. AtTPS genes cluster into five phylogenetic subfamilies of the plant TPS superfamily. Surprisingly, thirty AtTPS closely resemble, in all aspects of gene architecture, sequence relatedness and phylogenetic placement, the genes for plant monoterpene synthases, sesquiterpene synthases or diterpene synthases of secondary metabolism. Rapid evolution of these AtTPS resulted from repeated gene duplication and sequence divergence with minor changes in gene architecture. In contrast, only two AtTPS genes have known functions in basic (primary) metabolism, namely gibberellin biosynthesis. This striking difference in rates of gene diversification in primary and secondary metabolism is relevant for an understanding of the evolution of terpenoid natural product diversity. Eight AtTPS genes are interrupted and are likely to be inactive pseudogenes. The localization of AtTPS genes on all five chromosomes reflects the dynamics of the Arabidopsis genome; however, several AtTPS genes are clustered and organized in tandem repeats. Furthermore, some AtTPS genes are localized with prenyltransferase genes (AtGGPPS, geranylgeranyl diphosphate synthase) in contiguous genomic clusters encoding consecutive steps in terpenoid biosynthesis. The clustered organization may have implications for TPS gene evolution and the evolution of pathway segments for the synthesis of terpenoid natural products. Phylogenetic analyses highlight events in the divergence of the TPS paralogs and suggest orthologous genes and a model for the evolution of the TPS gene family.

368 citations

01 Sep 2006
TL;DR: Analyzing the draft genome of the black cottonwood tree, Populus trichocarpa, revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

355 citations


Cited by
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Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

11,521 citations

Journal ArticleDOI
TL;DR: The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates and has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation.
Abstract: The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.cazy.org/.

6,028 citations

Journal ArticleDOI
Gerald A. Tuskan1, Gerald A. Tuskan2, Stephen P. DiFazio3, Stephen P. DiFazio2, Stefan Jansson4, Joerg Bohlmann5, Igor V. Grigoriev6, Uffe Hellsten6, Nicholas H. Putnam6, Steven G. Ralph5, Stephane Rombauts7, Asaf Salamov6, Jacquie Schein, Lieven Sterck7, Andrea Aerts6, Rishikeshi Bhalerao4, Rishikesh P. Bhalerao8, Damien Blaudez9, Wout Boerjan7, Annick Brun9, Amy M. Brunner10, Victor Busov11, Malcolm M. Campbell12, John E. Carlson13, Michel Chalot9, Jarrod Chapman6, G.-L. Chen2, Dawn Cooper5, Pedro M. Coutinho14, Jérémy Couturier9, Sarah F. Covert15, Quentin C. B. Cronk5, R. Cunningham2, John M. Davis16, Sven Degroeve7, Annabelle Déjardin9, Claude W. dePamphilis13, John C. Detter6, Bill Dirks17, Inna Dubchak18, Inna Dubchak6, Sébastien Duplessis9, Jürgen Ehlting5, Brian E. Ellis5, Karla C Gendler19, David Goodstein6, Michael Gribskov20, Jane Grimwood21, Andrew Groover22, Lee E. Gunter2, Björn Hamberger5, Berthold Heinze, Yrjö Helariutta8, Yrjö Helariutta23, Yrjö Helariutta24, Bernard Henrissat14, D. Holligan15, Robert A. Holt, Wenyu Huang6, N. Islam-Faridi22, Steven J.M. Jones, M. Jones-Rhoades25, Richard A. Jorgensen19, Chandrashekhar P. Joshi11, Jaakko Kangasjärvi23, Jan Karlsson4, Colin T. Kelleher5, Robert Kirkpatrick, Matias Kirst16, Annegret Kohler9, Udaya C. Kalluri2, Frank W. Larimer2, Jim Leebens-Mack15, Jean-Charles Leplé9, Philip F. LoCascio2, Y. Lou6, Susan Lucas6, Francis Martin9, Barbara Montanini9, Carolyn A. Napoli19, David R. Nelson26, C D Nelson22, Kaisa Nieminen23, Ove Nilsson8, V. Pereda9, Gary F. Peter16, Ryan N. Philippe5, Gilles Pilate9, Alexander Poliakov18, J. Razumovskaya2, Paul G. Richardson6, Cécile Rinaldi9, Kermit Ritland5, Pierre Rouzé7, D. Ryaboy18, Jeremy Schmutz21, J. Schrader27, Bo Segerman4, H. Shin, Asim Siddiqui, Fredrik Sterky, Astrid Terry6, Chung-Jui Tsai11, Edward C. Uberbacher2, Per Unneberg, Jorma Vahala23, Kerr Wall13, Susan R. Wessler15, Guojun Yang15, T. Yin2, Carl J. Douglas5, Marco A. Marra, Göran Sandberg8, Y. Van de Peer7, Daniel S. Rokhsar17, Daniel S. Rokhsar6 
15 Sep 2006-Science
TL;DR: The draft genome of the black cottonwood tree, Populus trichocarpa, has been reported in this paper, with more than 45,000 putative protein-coding genes identified.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

4,025 citations

Journal ArticleDOI
14 Jan 2010-Nature
TL;DR: An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
Abstract: Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

3,743 citations

Journal ArticleDOI
TL;DR: Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number of complete plant genomes.
Abstract: The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

3,728 citations