Gramene: a bird's eye view of cereal genomes

Authors: JAISWAL, PANKAJ - CORNELL UNIVERSITY; NI, JUNJIAN - CORNELL UNIVERSITY; YAP, IMMANUEL - CORNELL UNIVERSITY; Ware, Doreen; SPOONER, WILLIAM - COLD SPRING HARBOR LAB; YOUENS-CLARK, KEN - COLD SPRING HARBOR LAB; REN, LIYA - COLD SPRING HARBOR LAB; LIANG, CHENGZHI - COLD SPRING HARBOR LAB; ZHAO, WEI - COLD SPRING HARBOR LAB; RATNAPU, KIRAN - COLD SPRING HARBOR LAB; FAGA, BEN - COLD SPRING HARBOR LAB; CANARAN, PAYAN - COLD SPRING HARBOR LAB; FOGLEMAN, MOLLY - CORNELL UNIVERSITY; HEBBARD, CLAIRE - CORNELL UNIVERSITY; AVRAHAM, SHULAMIT - COLD SPRING HARBOR LAB; SCHMIDT, STEVEN - COLD SPRING HARBOR LAB; CASSTEVENS, TERRY - CORNELL UNIVERSITY; Buckler, Edward - Ed; STEIN, LINCOLN - COLD SPRING HARBOR LAB; MCCOUCH, SUSAN - CORNELL UNIVERSITY

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2007
Publication Date: 6/4/2007
Citation: Jaiswal, P., Ni, J., Yap, I., Ware, D., Spooner, W., Youens-Clark, K., Ren, L., Liang, C., Zhao, W., Ratnapu, K., Faga, B., Canaran, P., Fogleman, M., Hebbard, C., Avraham, S., Schmidt, S., Casstevens, T., Buckler Iv, E.S., Stein, L., Mccouch, S. 2007. Gramene: a bird's eye view of cereal genomes. Nucleic Acids Research. 34:D717-D723. Available: http://nar.oxfordjournals.org/

Interpretive Summary: Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. At the time of this publication, only rice, with a relatively small sized genome, consisting of 400 mega base pairs of nucleotides, has been sequenced. Previous work in grasses demonstrated that many of these large grass genomes have conserved gene order along long stretches of DNA known as synteny. The Gramene project (www.gramene.org) makes use of the conserved gene order to provide resources for other grass genomes such as maize or wheat to use this information in the absence of a genome sequence in their respective species. The publication reports on updates to the Gramene database since 2002.

Technical Abstract: Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication.