PlantGDB, plant genome database and analysis tools

Dong, Qunfeng; Schlueter, Shannon D.; Brendel, Volker

doi:10.1093/nar/gkh046

Cited by 195 publications

(109 citation statements)

References 24 publications

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“…Both uncharacterized genes lack homologs and one lacks expression evidence (Dong et al 2004;Sen et al 2010). However, the genic content of the region may differ in Tx303.…”

Section: Discussionmentioning

confidence: 99%

Unraveling Genomic Complexity at a Quantitative Disease Resistance Locus in Maize

et al. 2014

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Multiple disease resistance has important implications for plant fitness, given the selection pressure that many pathogens exert directly on natural plant populations and indirectly via crop improvement programs. Evidence of a locus conditioning resistance to multiple pathogens was found in bin 1.06 of the maize genome with the allele from inbred line "Tx303" conditioning quantitative resistance to northern leaf blight (NLB) and qualitative resistance to Stewart's wilt. To dissect the genetic basis of resistance in this region and to refine candidate gene hypotheses, we mapped resistance to the two diseases. Both resistance phenotypes were localized to overlapping regions, with the Stewart's wilt interval refined to a 95.9-kb segment containing three genes and the NLB interval to a 3.60-Mb segment containing 117 genes. Regions of the introgression showed little to no recombination, suggesting structural differences between the inbred lines Tx303 and "B73," the parents of the fine-mapping population. We examined copy number variation across the region using next-generation sequencing data, and found large variation in read depth in Tx303 across the region relative to the reference genome of B73. In the fine-mapping region, association mapping for NLB implicated candidate genes, including a putative zinc finger and pan1. We tested mutant alleles and found that pan1 is a susceptibility gene for NLB and Stewart's wilt. Our data strongly suggest that structural variation plays an important role in resistance conditioned by this region, and pan1, a gene conditioning susceptibility for NLB, may underlie the QTL.T HE genes and loci that influence host-pathogen interactions vary in allele effects, specificities, and linkage relationships. While disease resistance can be conditioned by single genes with large effect (Bent 1996;Jones and Dangl 2006), the emerging model of resistance for many plant diseases is complex in nature, with many genes and loci functioning in concert and each contributing a small proportion of the total phenotypic variation Poland et al. 2011;Cook et al. 2012b). Each locus has a unique profile, with some loci contributing broadspectrum protection against diverse pathogen species and strains. Investigating these intricacies offers the opportunity to understand the diverse ways in which plants defend themselves against microbial assault.Correlated responses to multiple diseases have been observed in various germplasm panels, implying that there are loci and genes that condition broad-spectrum resistance (Rossi et al. 2006;Gurung et al. 2009;Wisser et al. 2011). At the chromosomal segment level, disease and insect resistance loci colocalize in a nonrandom fashion (McMullen and Simcox 1995;Williams 2003;Wisser et al. 2005) and loci have been identified that confer resistance to diverse pathogen isolates and taxa (Zwonitzer et al. 2010;Chung et al. 2011;Belcher et al. 2012). There is evidence to suggest that gene clusters can confer resistance to more than one disease. A cluster of germin-like ...

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“…Both uncharacterized genes lack homologs and one lacks expression evidence (Dong et al 2004;Sen et al 2010). However, the genic content of the region may differ in Tx303.…”

Section: Discussionmentioning

confidence: 99%

Unraveling Genomic Complexity at a Quantitative Disease Resistance Locus in Maize

et al. 2014

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“…Tannins and their compounds are also known to be responsible for preventing and treating urinary tract infections and other bacterial infections (Dong et al, 2004;Morton, 1981;Arbonnier, 2004). The presence of tannins in the leaves of C. cujete Linn.…”

Section: Phytochemical Screeningmentioning

confidence: 99%

Phytochemical screening, cytotoxicity, mutagenicity, antimutagenicity, and protective potentials of the different solvent extracts from the air-dried leaves of Crescentia cujete Linn.

Billacura

Pangcoga

2017

Int. j. adv. appl. sci

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Crescentia cujete Linn. is a fast-growing evergreen tree in the Philippines. Folklore says C. cujete Linn. has been used as an alternative medicine to treat ailments such as hematoma and tumors. In this study, air-dried leaves of C. cujete Linn. was prepared and partitioned using hexane, and ethyl acetate as solvents and was qualitatively assessed for the presence of phytochemical constituents. Secondary metabolites like flavonoids, tannins, reducing sugar, and steroids were observed in the preliminary phytochemical screening of hexane, ethyl acetate and aqueous extracts. Cytotoxicity of the different extracts were determined using brine shrimp lethality test (BSLT). Median lethal concentration (LC50) of the hexane, aqueous, and crude ethanolic extracts were determined after 6 hours of exposure showing 572, 3048 and 220 ppm, respectively. Moreover, LC50 of the hexane, aqueous, and crude ethanolic extract, after 24 hours of exposure, were also determined showing 0, 0.184, and 6.47 ppm, respectively. The hexane, aqueous, and crude ethanolic extracts of C. cujete Linn. were also tested for its mutagenicity, antimutagenicity, and protective potentials using peripheral blood micronucleus test. The number of micronucleated polychromatic erythrocyte (MNPCE) observed from the mutagenicity test of hexane, aqueous, and crude ethanolic extract administered at a dose of 50mg/kg and 100mg/kg showed an average mean of 16.7,14.6 and 14.7, respectively, are lower compared to that of the positive control, methyl methanesulfonate (MMS), showing 49.5 number of MNPCE. Also, results for the antimutagenicity and protective potentials of hexane, aqueous, and crude ethanolic extract administered at a dose of 50mg/kg and 100mg reduced the number of MNPCEs produced by the MMS.

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“…For rare species, a tBLASTn was first performed against the NCBI whole database using limited queries for the date and for the organism. The Plant Genome Project (http://www.pgn.cornell.edu, 2004), Plant GDB (Dong et al, 2004) and Sputnik (Rudd, 2005) were used to complete the short sequences obtained from TIGR and to find new ones.…”

Section: Construction Of the Databasementioning

confidence: 99%

PeroxiBase: A class III plant peroxidase database

et al. 2006

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Class III plant peroxidases (EC 1.11.1.7), which are encoded by multigenic families in land plants, are involved in several important physiological and developmental processes. Their varied functions are not yet clearly determined, but their characterization will certainly lead to a better understanding of plant growth, differentiation and interaction with the environment, and hence to many exciting applications. Since there is currently no central database for plant peroxidase sequences and many plant sequences are not deposited in the EMBL/GenBank/DDBJ repository or the UniProt KnowledgeBase, this prevents researchers from easily accessing all peroxidase sequences. Furthermore, gene expression data are poorly covered and annotations are inconsistent. In this rapidly moving field, there is a need for continual updating and correction of the peroxidase superfamily in plants. Moreover, consolidating information about peroxidases will allow for comparison of peroxidases between species and thus significantly help making correlations of function, structure or phylogeny. We report a new database (PeroxiBase) accessible through a web server (http://peroxidase.isb-sib.ch) with specific tools dedicated to facilitate query, classification and submission of peroxidase sequences. Recent developments in the field of plant peroxidase are also mentioned.

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PlantGDB, plant genome database and analysis tools

Cited by 195 publications

References 24 publications

Unraveling Genomic Complexity at a Quantitative Disease Resistance Locus in Maize

Unraveling Genomic Complexity at a Quantitative Disease Resistance Locus in Maize

Phytochemical screening, cytotoxicity, mutagenicity, antimutagenicity, and protective potentials of the different solvent extracts from the air-dried leaves of Crescentia cujete Linn.

PeroxiBase: A class III plant peroxidase database

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