Gramene: a growing plant comparative genomics resource

Liang, Chengzhi; Jaiswal, Pankaj; Hebbard, Claire; Shuly, Avraham; Buckler, Edward S.; Casstevens, Terry M.; Hurwitz, Bonnie; McCouch, Susan R.; Ni, Jian; Pujar, Anuradha; Ravenscroft, Dean; Ren, Liya; Spooner, William; Tecle, Isaak Y.; Thomason, Jim; Tung, Chih‐Wei; Wei, Xuehong; Yap, Immanuel V.; Youens‐Clark, Ken; Ware, Doreen; Stein, Lincoln

doi:10.1093/nar/gkm968

Cited by 154 publications

(125 citation statements)

References 18 publications

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“…There has been a rapid growth in the number of plant genomics databases (Table 2). A major difference between these databases is the number of organisms included: whereas the Genome Cluster Database (Horan et al, 2005) and GreenPhylDB (Conte et al, 2008) only include Arabidopsis and rice, Gramene (Liang et al, 2008), PLAZA, and CoGe (Lyons and Freeling, 2008) have the most comprehensive set of species. CoGe includes, besides fully sequenced plant genomes, a large collection of viral, bacterial, fungal, and animal genomes.…”

Section: Comparison With Other Plant Genomics Platformsmentioning

confidence: 99%

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

et al. 2009

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The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.

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Section: Comparison With Other Plant Genomics Platformsmentioning

confidence: 99%

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

et al. 2009

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“…For insight into host responses, the TreeGenes database (Wegrzyn et al, 2008), Phytozome database (http://phytozome.jgi.doe.gov) (Goodstein et al, 2012), The Plant Genome Integrative Explorer (PlantGenIE; www.plantgenie.org) (Sundell et al, 2015), and Gramene (www.gramene.org) (Liang et al, 2008) provide tools for analyses and visualization. Gramene contains the Plant Reactome database, which can be used to identify plant metabolic and regulatory pathways (Tello-Ruiz et al, 2016).…”

Section: Downstream Analysismentioning

confidence: 99%

Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel

Naidoo¹,

Visser²,

Zwart³

et al. 2018

Current Issues in Molecular Biology

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RNA-sequencing technology has been widely adopted to investigate host responses during infection with pathogens. Dual RNA-sequencing (RNA-seq) allows the simultaneous capture of pathogen-specific transcripts during infection, providing a more complete view of the interaction. In this review, we focus on the design of dual RNAseq experiments and the application of downstream data analysis to gain biological insight into both sides of the interaction. Recent literature in this area demonstrates the power of the dual RNA-seq approach and shows that it is not limited to model systems where genomic resources are available. Sequencing costs continue to decrease and single cell transcriptomics is becoming more feasible. In combination with proteomics and metabolomics studies, these technological advances are likely to contribute to our understanding of the temporal and spatial aspects of dynamic plant-pathogen interactions. A dual approach in plantaThe interaction between plants and pathogens is an active and dynamic process that can be likened to a duel. Plants have complex defence mechanisms that can be rendered ineffective when pathogens interfere with one of the various processes required for host defence. These processes include penetration resistance, recognition by Pattern Recognition Receptors (PRRs), phytohormone signalling pathways, secretory pathways, secondary metabolite production, and plant cell death (Dou and Zhou, 2012). Until recently, transcriptomic approaches have been applied in the host and pathogen separately to obtain the gene expression profile of each organism and gain insight into infection biology or host defence mechanisms.RNA sequencing (RNA-seq) is a powerful technology that does not rely on any prior knowledge of transcripts and can generate vast quantities of data with much smaller costs involved than for older techniques such as microarrays (Pareek et al., 2011;Wilhelm and Landry, 2009). An advantage of RNA-seq in the field of plant-pathogen interactions is that both plant and pathogen transcripts can be detected simultaneously and accurately in the same sample. This tactic, known as dual RNAseq, in planta RNA-seq, simultaneous RNA-seq, or comparative RNA-seq, is a relatively new technique both in the plant and medical fields. In plants, it allows for the study of plant-pathogen interactions in herbaceous crops Kunjeti et al., 2012;Lowe et al., 2014) as well as trees (Hayden et al., 2014;Liang et al., 2014;Teixeira et al., 2014). This review outlines technical considerations for dual RNA-seq experiments, summarizes recent insights drawn from such approaches in plant-pathogen interactions, and provides an

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“…The total map size of these markers was 1362 cM, with an average marker interval of 8.2 cM. The primer sequences of these SSR markers were obtained from the Gramene database (http:// www.gramene.org/) by Liang et al (2008). PCR was carried out in a 25-µl reaction, and the amplified products were electrophoresed in 4% polyacrylamide denaturing gel with 0.5× TBE buffer.…”

Section: Determination Of Marker Genotypes At Ssr Locimentioning

confidence: 99%

Development of backcross recombinant inbred lines between Oryza sativa Nipponbare and O. rufipogon and QTL detection on drought tolerance

et al. 2011

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Backcross populations at advanced generations are useful in evaluating the agronomic traits from unadapted germplasms, such as wild species. In this study, we generated 159 backcross recombinant inbred lines (BRILs) at the BC 2 F 8 generation between Oryza sativa Nipponbare (a recurrent parent) and O. rufipogon W630 (a donor parent). These BRILs were found to have nearly homozygous genome constitutions based on the marker genotypes at 180 SSR loci covering whole chromosomes. Since their selfed progenies have almost identical genotypes in each line, they were further used for QTL analysis of drought tolerance. Out of six QTLs detected, three were found to have wild alleles with favorable effects on drought tolerance. The present BRILs with known marker data can be applied to more QTL analyses of traits specific to wild species.

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Gramene: a growing plant comparative genomics resource

Cited by 154 publications

References 18 publications

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel

Development of backcross recombinant inbred lines between Oryza sativa Nipponbare and O. rufipogon and QTL detection on drought tolerance

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