About PTGBase  

    Tandem duplication plays a crucial role in plant life cycle leading to clusters of repeat genes and contributes to the expansion of gene families to adopt environment. Little is known about plant tandem repeat genes database. PTGBase is a public database to collect plant genes generated by tandem duplication mechanism in the process of plant evolution. So far, PTGBase mainly focus on plants with available whole genome sequences especially for assembled pseudomolecules with ordered gene models. In this database, we have collected 39 plant species arrayed in 54,130 tandem repeat gene clusters containing 129,652 genes.
    PTGBase is freely available for download. The researchers or scientist can extract the full list of repeat genes, their coding sequences and protein sequences, as well as whole genome sets about sequenced plant species. Researchers can also employ the search function to perform a search in the database for a target gene, a tandem array name and gene numbers of tandem array in a specific species. PTGBase will be updated regularly with new sequenced plant species as they become available.

 
Genome Resources
 
Latin Name Common Name Genome Size Ploidy Release version Date Journal
Arabidopsis lyrata Lyrate rockcress 206.7 M 2n=16 Version 1.0 (Apr 2011) 2011.05 Nature Genetics
Arabidopsis thaliana Arabidopsis 125M 2n=10 TAIR 9.0 (Jun 2009) 2000.12 Nature
Aureococcus anophagefferens Heterokont algae 57M —— JGI 1.0 (Sep 2007) 2011.02 PNAS
Brachypodium distachyon Purple false brome 260M 2n=10 Phytozome v6.0 2010.02 Nature
Brassica oleracea Cabbage 630M 2n=18 Version 1.0 2014.05 Nature Communication
Brassica rapa Chinese cabbage 485M 2n=20 Version 1.1 2011.08 Nature Genetics
Cajanus cajan Pigeonpea 833M 2n=22 IIPG v1.0 2011.11 Nature biotechnology
Carica papaya Papaya 370M 2n=18 ASGPB v1.0 2008.04 Nature
Chlamydomonas reinhardtii Green algae 130 M —— Version 4.2 2007.01 Science
Chlorella variabilis NC64A Microalgae  46M 2n=24  JGI 1.0 (Sep 2010) 2010.09 Plant Cell
Cicer arietinum Chickpea 738M 2n=16 Version 1.0 2013.01 Nature biotechnology
Citrullus lanatus Watermelon 425 M 2n=22 Version 1.0 2012.11 Nature Genetics
Citrus sinensis Orange 367 M 2n=18 CITRUS v1.0 (2012) 2012.11 Nature Genetics
Cucumis sativus Cucumber 350M 2n=14 Phytozome v6.0 2009.11 Nature Genetics
Fragaria vesca Strawberry 240M 2n=14  GDR v1.0 2010.12 Nature Genetics
Glycine max Soybean 1100M 2n=40 v1.1 (Jun 2013) 2010.01 Nature
Gossypium raimondii Cotton 761.4M 2n=26 Version 2.1 2012.12 Nature
Linum usitatissimum Flax 373M 2n=30 Phytozome v9.1 v1.0 2012.07 Plant Journal
Lotus japonicus Lotus 472 M 2n=12 Release 2.5 2008.04 DNA Res.
Malus × domestica Borkh. Apple 742M 2n=34 GDR v1.0 2010.09 Nature Genetics
Medicago truncatula Barrel medic 500M 2n=16 Mt3.5 v3 (Jun 2011) 2011.11 Nature
Musa acuminata Banana 523M 2n=22 CIRAD v1.0 2012.07 Nature
Oryza sativa L. ssp.japonica Rice 466M 2n=24 IRGSP v1.0 2002.04 Science
Phaeodactylum tricornutum Diatom algae 27.4M —— JGI 2.0 (May 2007) 2008.11 Nature
Physcomitrella pattens Moss 480M —— Version 1.6 (Jan 2008) 2008.01 Science
Populus trichocarpa Western poplar 480M 2n=38 JGI 2.0 (Feb 2010) 2006.09 Science
Prunus mume Plum flower 280M 2n=16 prunusmumegenome v1.0 2012.12 Nature Communication
Ricinus communis Castor bean 350M 2n=20 Release 0.1 (May 2008) 2010.08 Nature Biotechnology
Selaginella moellendorffii  Selaginella 212M —— Version 1.0 (Dec 2007) 2011.05 Science
Sesamum indicum Sesame 357M 2n=26 Version 1.0  2014.01 Genome Biology
Setaria italica Millet 490M 2n=18 Phytozome v9.1 2012.05 Nature biotechnology
Solanum lycopersicum Tomato 900M 2n=24 Version 2.3 2012.05 Nature
Solanum tuberosum Potato 844M 2n=4X=48 Version 3.4 2011.07 Nature
Sorghum bicolor Sorghum 730M 2n=20 Sbi 1.4 (Dec 2007) 2009.01 Nature
Thellugiella parvula Rockface star-violet 140M 2n=14 Thellungiella v2.0 2011.08 Nature Genetics
Theobroma cacao Cacao 430-M 2n=20  Release 0.9 (Sep 2010) 2010.12 Nature Genetics
Vitis vinifera Grape vine 490M 2n=38 Genoscope (Aug 2007) 2007.09 Nature
Volvox carteri Green alga 138M —— JGI 1.0 (Jun 2007) 2010.07 Science
Zea mays ssp. mays L. Maize 2300M 2n=20 Release 5a (Nov 2010) 2009.11 Science
 
News
  1. 2014-06-20 The online tool of detect plant tandem repeat gene is going to develop.
  2. 2014-06-15 Sesamum indicum, Brassica oleracea were added into PTGBase.
  3. 2013-06-10 Linum usitatissimum, Musa acuminata, Citrullus lanatus, Citrus sinensis, Gossypium raimondii, Prunus mume, Cicer arietinum were added into PTGBase.
  4. 2014-05-31 Fragaria vesca, Theobroma cacao, Aureococcus anophagefferens, Arabidopsis lyrata, Selaginella moellendorffii , Solanum tuberosum, Brassica rapa, Thellugiella parvula, Cajanus cajan, Medicago truncatula, Setaria italica, Solanum lycopersicum were added into PTGBase.
  5. 2014-05-20 Phaeodactylum tricornutum, Sorghum bicolor, Cucumis sativus, Zea mays ssp. mays L., Glycine max, Brachypodium distachyon, Volvox carteri, Ricinus communis, Chlorella variabilis NC64A, Malus × domestica Borkh were added into PTGBase.
  6. 2014-05-15 Arabidopsis thaliana, Oryza sativa L. ssp.japonica, Populus trichocarpa, Chlamydomonas reinhardtii, Vitis vinifera, Physcomitrella pattensCarica papaya, Lotus japonicus were added into PTGBase.
 
How to Cite
    Jingyin Yu1,†, Tao Ke2,†, Sadia Tehrim1, Fengming Sun1, Boshou Liao1,* and Wei Hua1,*. PTGBase: an integrated database to study tandem duplicated genes in plants. Database (Oxford) 2015:bav017, doi: 10.1093/database/bav017. [PubMed]

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
This database is currently maintained by Jingyin Yu.

The Key Laboratory of Oil Crops Biology and Genetic Breeding, the Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China