Limits...
Gramene: a growing plant comparative genomics resource.

Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L - Nucleic Acids Res. (2007)

Bottom Line: Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them.Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose).We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.

ABSTRACT
Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

Show MeSH
The rice bhlh90 gene tree (partial) showing the orthologous genes between rice, maize, A. thaliana and poplar. The full tree can be viewed at http://tinyurl.com/3clrjv. Note the bhlh90 gene is mapped in the region shown in Figure 2, but its maize gene ortholog is a predicted gene and has not been studied functionally. The solid box on the right shows the aligned regions in the proteins. It is expected that there are more maize orthologs to be identified after the maize genome sequence becomes complete.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238951&req=5

Figure 3: The rice bhlh90 gene tree (partial) showing the orthologous genes between rice, maize, A. thaliana and poplar. The full tree can be viewed at http://tinyurl.com/3clrjv. Note the bhlh90 gene is mapped in the region shown in Figure 2, but its maize gene ortholog is a predicted gene and has not been studied functionally. The solid box on the right shows the aligned regions in the proteins. It is expected that there are more maize orthologs to be identified after the maize genome sequence becomes complete.

Mentions: A gene tree that shows orthologs and paralogs of each gene (if available) is a new addition, and can be reached through the link on the left-side bar on the gene detailed page (see a gene tree example in Figure 3). The gene trees were built using Ensembl gene tree pipeline where maximum-likelihood trees were reconciled with their species tree to infer gene orthology and paralogy relations (16). For Gramene release 26, the gene trees were computed for four plant genomes: O. sativa ssp. japonica, O. sativa ssp. indica, A. thaliana and poplar, as well as four model metazoan species Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae. For example, from 41 908 genes of O. sativa ssp. japonica, we identified the following number of orthologs: 18 520 in A. thaliana, 19 684 in poplar, 5324 in S. cerevisiae, 7175 in C. elegans, 7449 in D. melanogaster and 8313 in Homo sapiens. The homologous gene set and gene tree can significantly add to users’ understanding of the rice gene functions, since many genes from A. thaliana and the animal species are better annotated than their homologs in rice.Figure 3.


Gramene: a growing plant comparative genomics resource.

Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L - Nucleic Acids Res. (2007)

The rice bhlh90 gene tree (partial) showing the orthologous genes between rice, maize, A. thaliana and poplar. The full tree can be viewed at http://tinyurl.com/3clrjv. Note the bhlh90 gene is mapped in the region shown in Figure 2, but its maize gene ortholog is a predicted gene and has not been studied functionally. The solid box on the right shows the aligned regions in the proteins. It is expected that there are more maize orthologs to be identified after the maize genome sequence becomes complete.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238951&req=5

Figure 3: The rice bhlh90 gene tree (partial) showing the orthologous genes between rice, maize, A. thaliana and poplar. The full tree can be viewed at http://tinyurl.com/3clrjv. Note the bhlh90 gene is mapped in the region shown in Figure 2, but its maize gene ortholog is a predicted gene and has not been studied functionally. The solid box on the right shows the aligned regions in the proteins. It is expected that there are more maize orthologs to be identified after the maize genome sequence becomes complete.
Mentions: A gene tree that shows orthologs and paralogs of each gene (if available) is a new addition, and can be reached through the link on the left-side bar on the gene detailed page (see a gene tree example in Figure 3). The gene trees were built using Ensembl gene tree pipeline where maximum-likelihood trees were reconciled with their species tree to infer gene orthology and paralogy relations (16). For Gramene release 26, the gene trees were computed for four plant genomes: O. sativa ssp. japonica, O. sativa ssp. indica, A. thaliana and poplar, as well as four model metazoan species Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae. For example, from 41 908 genes of O. sativa ssp. japonica, we identified the following number of orthologs: 18 520 in A. thaliana, 19 684 in poplar, 5324 in S. cerevisiae, 7175 in C. elegans, 7449 in D. melanogaster and 8313 in Homo sapiens. The homologous gene set and gene tree can significantly add to users’ understanding of the rice gene functions, since many genes from A. thaliana and the animal species are better annotated than their homologs in rice.Figure 3.

Bottom Line: Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them.Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose).We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.

ABSTRACT
Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.

Show MeSH