ppdb: plant promoter database version 3.0

ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27 000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.

[1]  Yoshihiro Ugawa,et al.  Plant cis-acting regulatory DNA elements (PLACE) database: 1999 , 1999, Nucleic Acids Res..

[2]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..

[3]  Kazuo Shinozaki,et al.  Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones , 2007, BMC Genomics.

[4]  K. Akiyama,et al.  Functional Annotation of a Full-Length Arabidopsis cDNA Collection , 2002, Science.

[5]  Naoki Sato,et al.  Gclust: trans-kingdom classification of proteins using automatic individual threshold setting , 2009, Bioinform..

[6]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[7]  Junichi Obokata,et al.  ppdb: a plant promoter database , 2007, Nucleic Acids Res..

[8]  T. Sakurai,et al.  Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. , 2009, The Plant journal : for cell and molecular biology.

[9]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[10]  Hiroyuki Koyama,et al.  Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data , 2011, BMC Plant Biology.

[11]  Sumio Sugano,et al.  Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis , 2007, Nucleic acids research.

[12]  T. Sakurai,et al.  Identification of plant promoter constituents by analysis of local distribution of short sequences , 2007, BMC Genomics.

[13]  Stephane Rombauts,et al.  Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions , 2013, BMC Genomics.

[14]  Mitsuyasu Hasebe,et al.  Digital Gene Expression Profiling by 5′-End Sequencing of cDNAs during Reprogramming in the Moss Physcomitrella patens , 2012, PloS one.

[15]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[16]  J. Kawai,et al.  Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice , 2003, Science.

[17]  J. Bennetzen,et al.  The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants , 2008, Science.