Gramene database in 2010: updates and extensions

Youens‐Clark, Ken; Buckler, Edward S.; Casstevens, Terry M.; Chen, Charles; DeClerck, Genevieve; Derwent, Paul S.; Dharmawardhana, Palitha; Jaiswal, Pankaj; Kersey, Paul J.; Karthikeyan, Athikkattuvalasu S.; Lu, Jerry; McCouch, Susan R.; Ren, Liya; Spooner, William; Stein, Joshua C.; Thomason, Jim; Wei, Sharon; Ware, Doreen

doi:10.1093/nar/gkq1148

Cited by 158 publications

(146 citation statements)

References 36 publications

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“…We used DAGchainer 119 to identify collinear gene pairs within syntenic blocks, with parameters requiring neighboring genes to be no more than ten genes apart and a minimum chain length of five collinear genes. As this method is strict, we additionally identified 'in-range' syntenies of orthologs that mapped no more than five genes distant from the expected collinear position 120 . Clustered sets of syntenic genes encompassing all species were identified by single-linkage clustering over the pairwise relationships.…”

Section: Synteny Maps and Screen For Chromosomal Inversionsmentioning

confidence: 99%

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

et al. 2018

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Section: Synteny Maps and Screen For Chromosomal Inversionsmentioning

confidence: 99%

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

et al. 2018

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“…The peptide sequences used were from Arabidopsis lyrata, Arabidopsis thaliana, Brachypodium distachyon, Caenorhabditis elegans, Chlamydomonas reinhardtii, Danio rerio, Ectocarpus siliculosus, Escherichia coli, Eucalyptus grandis, Fragaria vesca, Glycine max, Homo sapiens, Jatropha curcas, Mus musculus, Neurospora crassa, Nostoc punctiforme, Oryza sativa, Phoenix dactylifera, Physcomitrella patens, Populus trichocarpa, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Selaginella moellendorffii, Solanum tuberosum, Sorghum bicolor, Synechocystis pcc6803, Theobroma cacao, Vitis vinifera and Zea mays. The sequences were downloaded from Gramene 53,54 , Phytozome (http://www.phytozome. net) and Ensembl (http://www.ensembl.org).…”

Section: Research Article Methodsmentioning

confidence: 99%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

761

750

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Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled .94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.A major opportunity for a sustainable energy and biomaterials economy in many parts of the world lies in a better understanding of the molecular basis of superior growth and adaptation in woody plants. Part of this opportunity involves species of Eucalyptus L'Hér, a genus of woody perennials native to Australia 1 . The remarkable adaptability of eucalypts coupled with their fast growth and superior wood properties has driven their rapid adoption for plantation forestry in more than 100 countries across six continents (.20 million ha) 2 , making eucalypts the most widely planted hardwood forest trees in the world. The subtropical E. grandis and the temperate E. globulus stand out as targets of breeding programmes worldwide. Planted eucalypts provide key renewable resources for the production of pulp, paper, biomaterials and bioenergy, while mitigating human pressures on native forests 3 . Eucalypts also have a large diversity and high concentration of essential oils (mixtures of mono-and sesquiterpenes), many of which have ecological functions as well as medicinal and industrial uses. Predominantly outcrossers 1 with hermaphroditic animal-pollinated flowers, eucalypts are highly heterozygous and display pre-and postzygotic barriers to selfing to reduce inbreeding depression for fitness and survival 4 .To mitigate the challenge of assembling a highly heterozygous genome, we sequenced the genome of 'BRASUZ1', a 17-year-old E. grandis genotype derived from one generation of selfing. The availability of annotated forest tree genomes from two separately evolving rosid lineages, Eucalyptus (order Myrtales) and Populus (order Malpighiales 5 ), in combination with genomes from domesticated woody plants (for example, Vitis, Prunus, Citrus), provides a comparative foundation for addressing

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“…The Ensembl method identifies ortholog and paralog relationships between genes using phylogenetic inference (Vilella, et al, 2009; see also http://useast.ensembl.org/info/genome/ compara/homology_method.html). The Gramene project subsequently maps collinear and near-collinear orthologous genes between related species (Youens-Clark et al, 2011), adapting a protocol originally developed for the analysis of synteny in maize (Schnable et al, 2009; for details, see supporting online materials: http://www.sciencemag.org/content/suppl/2009/11/18/ 326.5956.1112.DC1/Schnable.SOM.pdf), which uses DAGChainer (Haas et al, 2004). The Compara Gene Trees in Gramene release 39 incorporated gene sets for 25 plant and five nonplant species.…”

Section: Classification Of the 5b+ Annotation Set Using Comparative Gmentioning

confidence: 99%

“…These sequences would be labeled Phase 1 HTGS_IMPROVED at GenBank, and the GenBank record for each BAC was to include information on the improved regions as well as order and orientation, where available, as comments. The Maize Genome Sequencing Consortium planned to release all data via MaizeSequence.org, a project database, with a plan to transition all data into MaizeGDB (Sen et al, 2009) and Gramene (Monaco et al, 2014), a comparative resource for plant genomics (Youens-Clark et al, 2011), at project close.…”

mentioning

confidence: 99%

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes

Law

Childs²,

Campbell

et al. 2014

Plant Physiology

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The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, wellsupported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes.Plant genomes, especially grass genomes, are difficult substrates for genome annotation due to regional and whole-genome duplication events and often contain large numbers of pseudogenes. These factors impact every aspect of gene structure annotation, from revision of existing annotations in light of new data to annotation of newly sequenced plant genomes. These aspects of plant genomes also dramatically lengthen compute times, because the many repeated genes and other sequences result in commensurately more sequence alignments and gene predictions. In many ways, annotation of the maize genome epitomizes these problems.In 2005, the National Science Foundation, U.S. Department of Agriculture, and Department of Energy announced that the approximately 2.3-Gb genome of the maize (Zea mays) inbred line B73, a major contributor to much of the germplasm used for U.S. grain production, would be sequenced using a bacterial artificial chromosome (BAC)-by-BAC approach. The plan was to sequence BACs from a minimal tiling path to approximately 63 coverage and to further improve only the unique genic regions. These sequences would be labeled Phase

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Gramene database in 2010: updates and extensions

Cited by 158 publications

References 36 publications

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

The genome of Eucalyptus grandis

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes

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