Computational and experimental analysis identifies Arabidopsis genes specifically expressed during early seed development

BMC Genomics
Cristian BecerraCarlos M Vicient

Abstract

Plant seeds are complex organs in which maternal tissues, embryo and endosperm, follow distinct but coordinated developmental programs. Some morphogenetic and metabolic processes are exclusively associated with seed development. The goal of this study was to explore the feasibility of incorporating the available online bioinformatics databases to discover Arabidopsis genes specifically expressed in certain organs, in our case immature seeds. A total of 11,032 EST sequences obtained from isolated immature seeds were used as the initial dataset (178 of them newly described here). A pilot study was performed using EST virtual subtraction followed by microarray data analysis, using the Genevestigator tool. These techniques led to the identification of 49 immature seed-specific genes. The findings were validated by RT-PCR analysis and in situ hybridization. We conclude that the combined in silico data analysis is an effective data mining strategy for the identification of tissue-specific gene expression.

References

Oct 1, 1992·The Plant Cell·J GiraudatH M Goodman
Apr 1, 1992·The Plant Cell·M Josè-EstanyolP Puigdomènech
Aug 1, 1993·Nature Genetics·M S BoguskiC M Tolstoshev
Feb 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·G VasmatzisI Pastan
Mar 17, 1999·Analytical Biochemistry·C M Vicient, M Delseny
Jun 25, 1999·Plant Molecular Biology·M L Nuccio, T L Thomas
Aug 11, 2000·Journal of Experimental Botany·C M VicientM Delseny
Aug 19, 2000·Journal of Experimental Botany·M Souter, K Lindsey
Aug 19, 2000·Current Topics in Developmental Biology·S BaiZ R Sung
Nov 15, 2000·Genome Research·L Huminiecki, R Bicknell
May 5, 2001·Annual Review of Plant Physiology and Plant Molecular Biology·Odd-Arne Olsen
Nov 1, 2001·Annual Review of Cell and Developmental Biology·A M ChaudhuryW J Peacock
Nov 15, 2001·FEBS Letters·A V BaranovaA P Kozlov
Jan 10, 2003·Nucleic Acids Research·Iris TzafrirDavid Meinke
Feb 15, 2003·Plant Physiology·David W MeinkeIris Tzafrir
Apr 17, 2004·The Plant Journal : for Cell and Molecular Biology·Julia C RedmanChristopher D Town
Jun 3, 2004·Plant Physiology·Tanya Z BerardiniSeung Y Rhee
Jul 13, 2004·Plant Biology·L BorisjukH Weber
Jul 22, 2004·Plant Physiology·Iris TzafrirDavid Meinke
Sep 18, 2004·Plant Physiology·Philip ZimmermannWilhelm Gruissem
Nov 13, 2004·Genome Biology·David Honys, David Twell
Dec 1, 2004·Annual Review of Genetics·Viola Willemsen, Ben Scheres
Apr 5, 2005·Nature Genetics·Markus SchmidJan U Lohmann
May 13, 2005·Plant Physiology·Ligeng MaXing Wang Deng
Jul 20, 2005·Plant Molecular Biology·Melissa D Lehti-ShiuDonna E Fernandez
Aug 6, 2005·Trends in Plant Science·Philip ZimmermannWilhelm Gruissem
Aug 13, 2005·The International Journal of Developmental Biology·Jesús Vicente-Carbajosa, Pilar Carbonero
Apr 23, 2008·Current Protocols in Bioinformatics·Leonore Reiser, Seung Yon Rhee

❮ Previous
Next ❯

Citations

Sep 10, 2008·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jana MoravcíkováJana Libantová
May 11, 2010·International Journal of Dentistry·Mine YildirimNurullah Keklikoglu
Oct 24, 2007·The New Phytologist·John Cairney, Gerald S Pullman
Aug 24, 2011·Cellular and Molecular Life Sciences : CMLS·Rebecca S LambSachin Teotia
Sep 24, 2019·Frontiers in Plant Science·Teresa Roldán-ArjonaDolores Córdoba-Cañero
Aug 26, 2009·Plant Signaling & Behavior·Sang-Gyu Kim, Chung-Mo Park
Nov 20, 2016·BMC Plant Biology·Irene MerinoSara von Arnold
Mar 17, 2010·Developmental Cell·Kaoru SugimotoElliot M Meyerowitz

❮ Previous
Next ❯

Datasets Mentioned

BETA
AM111128-AM111305

Methods Mentioned

BETA
PCR

Software Mentioned

BLAST
BLASTN
meta analyzer
SOTA
meta
Seedgenes
TMEV
Digital Northern tool
TIGR Multi Experiment Viewer ( TMEV )
- analyzer

Related Concepts