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About PMDBase

Microsatellite DNAs are important genomic components in organisms, which are also known as simple sequence repeats (SSRs, often defined as 1–6 bp). In past decades, Microsatellite DNAs have extensively been exploited as molecular markers for diverse applications including genome characterization and mapping. Further, their roles in gene regulation and genome evolution have been studied widely. Microsatellite markers are co-dominant, multi-allelic, easily detected, hyper variable, highly reproducible and abundant in organisms, which can be used to study variety identification, genetic diversity evaluation, genetic map construction, linkage/association mapping of gene /QTL, marker-assisted selection and comparative mapping. With the development of genome sequencing technology, more and more plant genome sequences have been released. The availability of complete genome sequences of plant species provides an important opportunity for scientists to characterize and study microsatellite DNA and marker development in corresponding plants.

PMDBase (plant microsatellite DNAs database) is a comprehensive database to study microsatellite DNAs and marker development in a wide range of plant species and genome evolution. In this database, 26,230,099 microsatellite DNA entries were identified among 110 genome sequenced plant species. Most microsatellite DNAs primers were provided no more than three pairs of primers using Primer3 software. PMDBase supplied user-friendly interface, which can help scientists to extract useful microsatellite DNA information quickly. In PMDBase, 6 functional units were developed to cover all content of microsatellite DNAs among 110 plant species including 'Home', 'Browse', 'Tools', 'Document', 'Help' and 'Community' functional units. Out of 6 functional units, 'Browse' and 'Tools' were main functional modules in PMDBase. For 'Browse', all microsatellite DNAs can be browsed by alphabetical order and taxonomy. In 'Tools', PMDBase have embedded several customized open resource software, such as BLAST, GBrowse and Primers3web. Moreover, PMDBase have developed user-friendly MISAweb, which can help users to identify microsatellite DNAs in genomic sequences online. The MISAweb will be more convenient for scientists, which are not familiar with Perl language programming. All datasets of microsatellite DNAs among 110 different plant species can be downloaded online very conveniently. PMDBase will be updated constantly.

Genome Resources
Release date Latin name Ploidy Genome size Journal
2000.12 Arabidopsis thaliana  2n=10 125M Nature 
2002.04 Oryza sativa L. ssp.japonica 2n=24 466M Science 
2002.04 Oryza sativa L. ssp.indica 2n=24 466M Science 
2006.09 Populus trichocarpa 2n=38 480M Science 
2007.01 Chlamydomonas reinhardtii —— 130M Science
2007.09 Vitis vinifera 2n=38 490M Nature 
2008.01 Physcomitrella pattens —— 480M Science 
2008.04 Carica papaya 2n=18 370M Nature 
2008.05 Lotus japonicus 2n=12 472Mb DNA Research
2008.11 Phaeodactylum tricornutum —— 27.4M Nature
2009.01 Sorghum bicolor 2n=20 730M Nature 
2009.11 Cucumis sativus L. 2n=14 350M Nature Genetics 
2009.11 Zea mays ssp. mays L. 2n=20 2300M Science
2010.01 Glycine max 2n=40 1100M Nature

more >>>

2010.02 Brachypodium distachyon 2n=10 260M Nature 
2010.06 Ectocarpus siliculosus   2n=36 196M Nature 
2010.07 Volvox carteri —— 138M Science
2010.08 Ricinus communis 2n=20 350M Nature Biotechnology
2010.09 Chlorella variabilis NC64A 2n=24 46M Plant Cell
2010.09 Malus × domestica Borkh. 2n=34 742M Nature Genetics 
2010.12 Fragaria vesca 2n=14 240M Nature Genetics 
2010.12 Glycine soja 2n=40 915.4Mb PNAS
2010.12 Jatropha curcas L. —— 410M DNA Research
2010.12 Theobroma cacao 2n=20 430Mb Nature Genetics 
2011.02 Aureococcus anophagefferens —— 57M PNAS 
2011.05 Arabidopsis lyrata 2n=16 206.7Mb Nature Genetics 
2011.05 Phoenix dactylifera 2n=36 685M Nature biotechnology
2011.05 Selaginella moellendorffii  —— 212M Science 
2011.07 Solanum tuberosum 2n=4X=48 844M Nature
2011.08 Brassica rapa 2n=20 485M Nature Genetics 
2011.08 Thellugiella parvula 2n=14 140M Nature Genetics 
2011.10 Cannabis sativa 2n=20 534M Genome biology
2011.11 Cajanus cajan 2n=22 833M Nature biotechnology
2011.11 Medicago truncatula  2n=16 500M Nature
2012.02 Cyanophora paradoxa —— 70M Science
2012.05 Setaria italica 2n=18 490M Nature biotechnology
2012.05 Solanum lycopersicum 2n=24 900Mb Nature
2012.07 Cucumis melo L. 2n=24 450Mb PNAS
2012.07 Linum usitatissimum 2n=30 373Mb Plant Journal
2012.07 Musa acuminata 2n=22 523Mb Nature
2012.07 Thellungiella salsuginea 2n=14 260Mb PNAS
2012.10 Hordeum vulgare L. 2n=14 5.1Gb Nature
2012.11 Bigelowiella natans —— 95Mb Nature
2012.11 Citrullus lanatus 2n=22 425Mb Nature Genetics 
2012.11 Citrus sinensis 2n=18 367Mb Nature Genetics 
2012.11 Guillardia theta —— 87Mb Nature
2012.11 Pyrus bretschneideri 2n=34 527Mb Genome Research
2012.12 Gossypium raimondii  2n=26 761.4Mb Nature
2012.12 Prunus mume 2n=16 280M Nature Communication
2013.01 Cicer arietinum 2n=2x=16 738Mb Nature biotechnology
2013.02 Hevea brasiliensis 2n=36 2.15Gb BMC Genomics
2013.02 Phyllostachys heterocycla 2n=48 2.075Gb Nature Genetics 
2013.03 Aegilops tauschii 2n=14 4.36Gb Nature
2013.03 Oryza brachyantha —— 342Mb-362Mb Nature Communications
2013.03 Prunus persica 2n=2x=16 265Mb Nature Genetics 
2013.03 Triticum urartu 2n=14 4.94Gb Nature
2013.05 Nelumbo nucifera Gaertn —— 929Mb Genome biology
2013.05 Picea abies 2n=24 19.6G Nature
2013.05 Utricularia gibba —— 82Mb Nature
2013.06 Betula nana —— 450Mb Molecular Ecology
2013.06 Emiliania huxleyi —— 141.7Mb Nature
2013.07 Elaeis guineensis 2n=32 1.8G Nature
2013.07 Symbiodinium minutum —— 1.5G Current Biology
2013.08 Tarenaya hassleriana 2n=20 290Mb Plant Cell
2013.09 Morus notabilis 2n=14 357Mb Nature Communications
2013.10 Actinidia chinensis 2n=58 758Mb Nature Communications
2013.11 Fragaria x ananassa 2n=8x=56 692Mb DNA Research
2013.11 Populus euphratica —— 593Mb Nature Communications
2013.12 Amborella trichopoda 2n=26 748Mb Science
2013.12 Beta vulgaris ssp. vulgaris 2n=18 731Mb Nature
2013.12 Dianthus caryophyllus L. 2n=30 622Mb DNA Research
2014.02 Spirodela polyrhiza n=20 158Mb Nature Communications
2014.03 Capsicum annuum var. glabriusculum —— 3.48Gb PNAS
2014.03 Capsicum annuum var.Zunla-1 —— 3.35Gb PNAS
2014.03 Pinus taeda —— 22Gb Genome Biology
2014.03 Sesamum indicum L. —— 274Mb Genome Biology
2014.05 Brassica oleracea 2n=18 630Mb Nature Communication
2014.05 Gossypium arboretum 2n=26 1.75Gb Nature Genetics 
2014.05 Nicotiana tabacum var.TN90 2n=4x=48 4.41Gb Nature Communications
2014.05 Nicotiana tabacum var.K326 2n=4x=48 4.60Gb Nature Communications
2014.05 Nicotiana tabacum var.Basma 2n=4x=48 4.57Gb Nature Communications
2014.06 Citrus clementina —— 301.4Mb Nature Biotechnology
2014.06 Eucalyptus grandis —— 640Mb Nature
2014.07 Oryza glaberrima 2n=24 316Mb Nature Genetics 
2014.07 Salix suchowensis 2n=38 303Mb Cell Research
2014.07 Solanum pennellii 2n=24 1.2Gb Nature Genetics
2014.07 Triticum aestivum —— 6.274Gb Science
2014.08 Brassica napus 2n=38 1.130Gb Science
2014.09 Coffea canephora 2n=2x=22 710Mb Science
2014.09 Solanum melongena —— 1.09Gb DNA Research
2014.10 Ziziphus jujuba Mill. 2n=2x=24 444Mb Nature Communications
2014.11 Humulus lupulus 2n=30 2.57Gb Plant and Cell Physiology
2014.11 Phalaenopsis equestris 2n=2x=38 1.16Gb Nature Genetics 
2014.11 Vigna radiata 2n=2x=22 543Mb Nature Communications
2015.01 Primula veris —— 479.22Mb Genome Biology
2015.03 Boea hygrometrica —— 1.5Gb PNAS
2015.03 Saccharina japonica —— 545Mb Nature Communications
2015.04 Gossypium hirsutum 2n=4x=52 2,173M Nature Biotechnology
2015.06 Dendrobium officinale —— 1.35Gb Molecular Plant
2015.06 Zizania latifolia —— 604.1Mb Plant Journal
2015.10 Vigna angularis 2n=22 542Mb PNAS
2015.11 Ananas comosus (Linn.) Merr. —— 526Mb Nature Genetics
2015.11 Oropetium thomaeum. —— 245Mb Nature
2015.11 Trifolium pratense L. 2n=2x=14 420Mb SCIENTIFIC REPORTS
2016.01 Zostera marina —— 202.3Mb Nature
2016.02 Arachis duranensis 2n=2x=20 1.25Gb Nature Genetics
2016.02 Arachis ipaensis 2n=2x=20 1.56Gb Nature Genetics
2016.02 Dendrobium catenatum 2N=2X=38 1.01Gb SCIENTIFIC REPORTS
2016.03 Phaseolus vulgaris L —— 549MBb Genome Biology
News
  • (2016-06-26) PMDBase was online.
  • (2016-05-25) Modifying and adding user-friendly interfare.
  • (2016-03-13) Adding the distribution of microsatellite DNA on pseudo-moleculas or chromosomes.
  • (2016-02-20) Developing plant microsatellite DNA database.
  • (2015-12-25) Starting marker development based on the identified microsatellite.
  • (2015-10-01) Preparing genomic data from genome sequencing plant species for identifying microsatellite DNA.
  • (2015-08-30) Constructing pipeline for extrieving microsatellite DNA.
  • (2015-06-12) Launching Plant microsatellite DNA project.
How to cite

Jingyin Yu, Komivi Dossa, Linhai Wang, Yanxin Zhang, Xin Wei, Boshou Liao, Xiurong Zhang. PMDBase: a database for studying microsatellite DNA and marker development in plants. Nucleic Acids Research 2016, doi: 10.1093/nar/gkw906. <Link>

Acknowledgements

This work was supported by the Oil Crops Research Institute, CAAS, China on behalf of National High Technology Research and Development Program of China (2013AA102602) and National Key Basic Research Program of China (2011CB109300). Funding for open access charge: Oil Crops Research Institute, CAAS, China.

Contact

Principal Investigators: Xiurong Zhang, Boshou Liao.

Database Development: Jingyin Yu.

Data Integration: Jingyin Yu, Komivi Dossa, Yanxin Zhang, Linhai Wang, Xin Wei.

֍ Resource Links

  NCBI

  EMBL-EBI

  DDBJ

  JGI

  Phytozome

  TAIR

  PTGBase

  Bolbasse

  Sinbase

  ocsESTdb

......

֍ Useful Tools

  KEGG

  InterProScan

  CPAN

  MySQL

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