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Protocols

PGDD specifications

Information


Unique identifier OMICS_03239
Name PGDD
Alternative name Plant Genome Duplication Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Cicer arietinum
    • Glycine max
    • Hordeum vulgare
    • Medicago truncatula
    • Oryza sativa
    • Populus trichocarpa
    • Vitis vinifera
    • Zea mays

Maintainers


  • person_outline Tae-Ho Lee
  • person_outline Jon Robertson
  • person_outline Xiyin Wang
  • person_outline Hui Guo

Publications for Plant Genome Duplication Database

PGDD citations

 (95)
library_books

Genome wide identification of the auxin response factor gene family in Cicer arietinum

2018
BMC Genomics
PMCID: 5921756
PMID: 29703137
DOI: 10.1186/s12864-018-4695-9

[…] alignment and phylogenetic tree construction were performed using MUSCLE and MEGA, respectively. Exon-intron distributions were analyzed using GSDS server. Gene duplications were determined using the PGDD database and the orthologous relationships were visualized using Circoletto. Amino acid content of the MR domain was calculated using the ‘Biostrings’ Bioconductor package. The putative cis-actin […]

library_books

Molecular Characterization, Evolution, and Expression Profiling of the Dirigent (DIR) Family Genes in Chinese White Pear (Pyrus bretschneideri)

2018
Front Genet
PMCID: 5911567
PMID: 29713336
DOI: 10.3389/fgene.2018.00136

[…] Collinearity analysis was completed using Plant Genome Duplication Database (PGDD) () and circos software. […]

library_books

The Sequenced Angiosperm Genomes and Genome Databases

2018
Front Plant Sci
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] third of all sequenced angiosperms are included by Phytozome, suggesting the presence of a major gap in the availability of most angiosperm genomes at Phytozome.The Plant Genome Duplication Database (PGDD) (chibba.agtec.uga.edu/duplication/) is a database currently hosting 43 angiosperm genomes, with tools to identify the intragenome and cross-genome synteny relationships. Synonymous substitutions […]

library_books

Duplication and diversification of lectin receptor like kinases (LecRLK) genes in soybean

2018
Sci Rep
PMCID: 5897391
PMID: 29651041
DOI: 10.1038/s41598-018-24266-6

[…] n 200 kb,,. Furthermore, genes within a tandem duplication cluster should show a close relationship in a phylogenetic tree. The segmental duplicated GmLecRLK genes were characterized according to the plant genome duplication database (PGDD) (http://chibba.agtec.uga.edu/duplication/). The list of genes in duplicated genomic regions and Ka/Ks values of each gene pairs were retrieved from PGDD. The r […]

library_books

The mining and evolutionary investigation of AP2/ERF genes in pear (Pyrus)

2018
BMC Plant Biol
PMCID: 5859658
PMID: 29558898
DOI: 10.1186/s12870-018-1265-x

[…] We used a method distinct from that used in the Genome Duplication Database (PGDD) (http://chibba.agtec.uga.edu/duplication/) [] to perform the synteny analysis. First, to identify the candidate homologous gene pairs (E < 1e-5, top 5 matches), a BLASTP alignment was carried ou […]

library_books

Genome wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress

2018
BMC Genomics
PMCID: 5774091
PMID: 29347912
DOI: 10.1186/s12864-018-4443-1

[…] in 100-kb chromosome fragment were considered as tandem duplicated genes []. The segmental duplicated genes of StHsp20 were identified by searching the segmental genome duplications of potato at the Plant Genome Duplication Database (PGDD, http://chibba.agtec.uga.edu/duplication/). […]

Citations

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PGDD institution(s)
Genomics Division, Department of Agricultural Bio-resource, National Academy of Agricultural Science, Rural Development Administration (RDA), Jeonju, South Korea; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
PGDD funding source(s)
Supported by National Science Foundation (DBI-0849896).

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