PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

2017/10/27

Web Site: http://pgdbj.jp/pages/index.html?dir=;page=mk;ln=en
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/pgdbj-dna-marker-linkage-map/

The database of general information, DNA markers, QTLs, DB links and genome analysis methods of plants including model plants.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Registered plant list
  3. Marker list
  4. QTL list
  5. Plant DB link
  6. Genome analysis methods
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods" data.
File README_e.html (English)
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2.2 Registered plant list

Data name Registered plant list
Description of data contents

The list of organisms handled in this database. It includes that basic explanation of the organism, links to the DNA marker list, the QTL list, the list of related databases and/or the genomic analysis information.
File pgdbj_dna_marker_linkage_map_plant_species_list_en.zip (30.1 KB)

Data items are the following:
Data itemDescription
Scientific name Scientific name
Scientific name authority Scientific name authority
Taxonomy ID NCBI Taxonomy ID
Phylum division Phylum division(Japanese)
Family Family
Genus Genus
Species Species
Variety Variety
Common name Common name
Synonym Synonym
Links (DFCI) Links to DFCI Gene Index
Resource info Resource information
Reference Reference
Sequencing method Sequencing method
Reads count Reads count
Assembly method Assembly method
Sequencing depth Sequencing depth
Gene annotation method Gene annotation method
Contig count Contig count
Scaffold count Scaffold count
Gene count Gene count
Chromosome count Chromosome count
Covered region Covered region
Genome size Genome size
ORF count ORF count
GC content GC content
Contact Contact
Country Country
Links (GOLD) Links to JGI GOLD
Links (NCBI Genome) Links to NCBI Genome
Description Description
Links (Marker list) Presence or absence of Marker list in this DB (link to the Marker list in simple search page)
Links (QTL list) Presence or absence of QTL list in this DB (link to the QTL list in simple search page)
Links (KNApSAcK Core) Presence or absence of KNApSAcK Core in this DB (link to the KNApSAcK Core site in simple search page)
Links (Skewered KNApSAcK) Presence or absence of Skewered KNApSAcK in this DB (link to the Skewered KNApSAcK site in simple search page)
Links (Mass Base) Presence or absence of Mass Base in this DB (link to the Mass Base site in simple search page)
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2.3 Marker list

Data name Marker list
Description of data contents

The list of DNA markers, including following information: marker name, organism name, type of marker, sequence of marker and related papers.
File pgdbj_dna_marker_linkage_map_plant_marker_list.zip (6.7 MB)

Data items are the following:
Data itemDescription
ID Marker ID
Scientific name Scientific name
Family Family name
Marker Marker name
Source Marker source:
  • 1: Kazusa Marker DB
  • 2: PGDBj Culated Marker DB
Marker type Marker type
Forward primer Forward primer
Reverse primer Reverse primer
Population Population
LG Linkage group
Chr Chromosome
Linked trait Linked trait
Trait type Trait type:
  • 1:anatomy and morphology trait
  • 2:stature or vigor trait
  • 3:stress trait
  • 4:biochemical trait
  • 5:growth and development trait
  • 6:yield trait
  • 7:sterility or fertility trait
  • 8:quality trait
  • 9:other miscellaneous trait
DOI DOI of reference
PMID PMID of reference
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2.4 QTL list

Data name QTL list
Description of data contents

The list of QTLs, including following information: organism name, papers and trait.
File pgdbj_dna_marker_linkage_map_plant_qtl_list.zip (292 KB)

Data items are the following:
Data itemDescription
QTL ID QTL ID
Scientific name Scientific name
Family Family name
QTL QTL name
Trait name Trait name
Description Description
Trait type Trait type:
  • 1:anatomy and morphology trait
  • 2:stature or vigor trait
  • 3:stress trait
  • 4:biochemical trait
  • 5:growth and development trait
  • 6:yield trait
  • 7:sterility or fertility trait
  • 8:quality trait
  • 9:other miscellaneous trait
Significant marker Significant marker
LG Linkage group
Chr Chromosome
LOD peak (cM) Position of LOD peak (cM)
LOD score LOD score
P value/-log10(p) etc. P value or -log10(p) etc.
DOI DOI of reference
PMID PMID of reference
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2.5 Plant DB link

Data name Plant DB link
Description of data contents

The list of Databases related in Plant Science, which includes databases of DNA markers, QTLs, and information of organisms.
File pgdbj_dna_marker_linkage_map_plant_db_link_en.zip (36.3 KB)

Data items are the following:
Data itemDescription
Database ID Database ID
Database name Database name
Species Species mentioned in the Database
Family name Family name
Common name Common name
Country Country
Institute Institute
URL URL of database
Research/General Distinction between Research and General
Class Class of database
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2.6 Genome analysis methods

Data name Genome analysis methods
Description of data contents The current status and related information of the genomic analysis about each organism (March, 2014). In the case of organisms carried out genomic analysis, the details of analytical method, references and information of genomic database are shown in this list.
File pgdbj_dna_marker_linkage_map_genome_analysis_methods_en.zip (5.8 KB)

Data items are the following:
Data itemDescription
Scientific name Scientific name
Status Status of genome analysis
Chromosome number Chromosome number
Genome size Genome size
Year Year of genome analysis
Sequencing method Sequencing method
Read counts Read counts
Covered genome region Covered genome region
Sequencing depth Sequencing depth
Assembly method Assembly method
Number of scaffolds Number of scaffolds
Contig counts Contig counts
Gene annotation method Gene annotation method
Number of predicted genes Number of predicted genes
Genome database Genome database information
Assembly release Assembly release
Annotation release Annotation release
Reference1 (DOI) Reference1 (DOI)
Reference1 (PMID) Reference1 (PMID)
Reference2 (DOI) Reference2 (DOI)
Other reference (DOI) Other reference (DOI)
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3. License

Last updated : 2017/10/27

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

 

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods © Satoshi Tabata (Kazusa DNA Research Institute) licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

Satoshi Tabata
Kazusa DNA Research Institute
2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 JAPAN
pgdbj[at]kazusa[dot]or[dot]jp

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

DateUpdate contents
2017/10/27 Archive version V2 Released.
These data are updated.
  • 「Registered plant list」
  • 「Marker list」
  • 「QTL list」
2016/07/29 Database Description page is updated.
  • The URL of The original website information
2014/10/10 PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods English archive site is opened.
2012/08/08 PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods is opened.
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5. Literature

Erika Asamizu, Hisako Ichihara, Akihiro Nakaya, Yasukazu Nakamura, Hideki Hirakawa, Takahiro Ishii, Takuro Tamura, Kaoru Fukami-Kobayashi, Yukari Nakajima and Satoshi Tabata
Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
Plant Cell Physiol (2014) 55 (1): e8
PMID: 24363285

Akihiro Nakaya, Hisako Ichihara, Erika Asamizu, Shirasawa Sachiko, Yasukazu Nakamura, Satoshi Tabata and Hideki Hirakawa
Plant Genome DataBase Japan (PGDBj)
Methods Mol Biol (2017) 1533: 45-77.
PMID: 27987164

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6. Contact address

When you have any question about "PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods", contact the following:

Kazusa DNA Research Institute
2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 JAPAN
pgdbj[at]kazusa[dot]or[dot]jp

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