Abstract
The transcriptome-wide endosperm-preferred expression of maize genes was addressed by analyzing a large database of expressed sequence tags (ESTs). We generated 30,531 high quality sequence-reads from the 5′-ends of cDNA libraries from maize endosperm harvested at 10, 15, and 20 days after pollination. A further 196,900 maize sequence-reads retrieved from public databases were added to this endosperm collection to generate MAIZEST, a database with tools for data storage and analysis. MAIZEST contains 227,431 ESTs, one third of which represents developing endosperm and the remaining two-thirds represent transcripts from 49 cDNA libraries constructed from different organs and tissues. Assembling the MAIZEST ESTs generated 29,206 putative transcripts, of which a set of 4032 assembled sequences was composed exclusively of sequences derived from endosperm cDNA libraries. After sequence analysis using overlapping parameters, a sub-set of 2403 assembled sequences was functionally annotated and revealed a wide variety of putative new genes involved in endosperm development and metabolism.
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S.F. Altschul T.L. Madden A.A. Schäffer J. Zhang Z. Zhang W. Miller D.J. Lipman (1997) ArticleTitleGapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 3389–3402 Occurrence Handle10.1093/nar/25.17.3389 Occurrence Handle9254694
P. Arruda E.L. Kemper F. Papes A. Leite (2000) ArticleTitleRegulation of lysine catabolism in higher plants Trends Plant Sci. 5 324–330 Occurrence Handle10.1016/S1360-1385(00)01688-5 Occurrence Handle10908876
S. Audic J.M. Claverie (1997) ArticleTitleThe significance of digital gene expression profiles Genome Res 7 986–995 Occurrence Handle9331369
H.W. Bass C. Webster G.R. Obrian J.K.M. Roberts R.S. Boston (1992) ArticleTitleA maize ribosome-inactivating protein is controlled by the transcriptional activator Opaque2 Plant Cell 4 225–234 Occurrence Handle10.1105/tpc.4.2.225 Occurrence Handle1633495
D.A. Benson I. Karsch-Mizrachi D.J. Lipman J. Ostell B.A. Rapp D.L. Wheeler (2000) ArticleTitleGenBank Nucleic Acids Res. 28 15–18 Occurrence Handle10.1093/nar/28.1.15 Occurrence Handle10592170
F. Berger (1999) ArticleTitleEndosperm development Curr. Opin. Plant. Biol. 2 28–32 Occurrence Handle10.1016/S1369-5266(99)80006-5 Occurrence Handle10047564
B. Boeckmann A. Bairoch R. Apweiler M.-C. Blatter A. Estreicher E. Gasteiger M.J. Martin K. Michoud C. O’Donovan I. Phan S. Pilbout M. Schneider (2003) ArticleTitleThe SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res. 31 365–370 Occurrence Handle10.1093/nar/gkg095 Occurrence Handle12520024
G. Cord Neto J.A. Yunes A.L. Vettore M.J. Da Silva P. Arruda A. Leite (1995) ArticleTitleThe involvement of Opaque2 on β-prolamin gene regulation in maize and Coix suggests a more general role for this transcriptional activator Plant Mol. Biol 27 1015–1029 Occurrence Handle10.1007/BF00037028 Occurrence Handle7766871
Q. Dong L. Roy M. Freeling V. Walbot V. Brendel (2003) ArticleTitleZmDB, an integrated database for maize genome research Nucleic Acids Res 31 244–247 Occurrence Handle10.1093/nar/gkg082 Occurrence Handle12519992
B. Ewing L.A. Hillier M.C. Wendl P. Green (1998) ArticleTitleBase-calling of automated sequencer traces using Phred. I. Accuracy assessment Genome Res. 8 175–185 Occurrence Handle9521921
J. Fernandes V. Brendel X. Gai S. Lal V.L. Chandler R.P. Elumalai D.W. Galbraith E.A. Pierson V. Walbot (2002) ArticleTitleComparison of RNA expression profiles based on maize-expressed sequence tag frequency analysis and micro-array hybridization Plant Physiol 128 896–910 Occurrence Handle10.1104/pp.010681 Occurrence Handle11891246
X. Gai S. Lal L. Xing V. Brendel V. Walbot (2000) ArticleTitleGene discovery using the maize genome database ZmDB Nucleic Acids Res 28 94–96 Occurrence Handle10.1093/nar/28.1.94 Occurrence Handle10592191
P. Gallusci S. Varott M. Matsuoko M. Maddaloni R.D. Thompson (1996) ArticleTitleRegulation of cytosolic pyruvate, orthophosphate dikinase expression in developing maize endosperm Plant Mol. Biol. 31 45–55 Occurrence Handle10.1007/BF00020605 Occurrence Handle8704158
M.J. Giroux C. Boyer G. Feix L.C. Hannah (1994) ArticleTitleCoordinated transcriptional regulation of storage product genes in the maize endosperm Plant Physiol. 106 713–722 Occurrence Handle12232363
M. Guo M.A. Rupe O.N. Danilevskaya X. Yang Z. Hu (2003) ArticleTitleGenome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm Plant J. 36 30–44 Occurrence Handle10.1046/j.1365-313X.2003.01852.x Occurrence Handle12974809
J.E. Habben A.W. Kirleis B.A. Larkins (1993) ArticleTitleThe origin of lysine-containing proteins in the opaque-2 maize endosperm Plant Mol. Biol. 23 825–838 Occurrence Handle10.1007/BF00021537 Occurrence Handle8251635
X. Huang A. Madan (1999) ArticleTitleCAP3: a DNA sequence assembly program Genome Res. 9 868–877 Occurrence Handle10.1101/gr.9.9.868 Occurrence Handle10508846
B.G. Hunter M.K. Beatty G.W. Singletary B.R. Hamaker B.P. Dilkes B.A. Larkins R. Jung (2002) ArticleTitleMaize opaque endosperm mutations create extensive changes in patterns of gene expression Plant Cell. 14 2591–2612 Occurrence Handle10.1105/tpc.003905 Occurrence Handle12368507
InstitutionalAuthorNameInternational Human Genome Sequencing Consortium (2004) ArticleTitleFinishing the euchromatic sequence of the human genome Nature 431 931–945
D. Job (2002) ArticleTitleGénoplante: the French national network in plant genomics GenomXPress 4 13–17
E.L. Kemper G. Cord Neto F. Papes K.C.M. Moraes A. Leite P. Arruda (1999) ArticleTitleThe role of Opaque2 in the control of lysine-degrading activities in developing maize endosperm Plant Cell 11 1981–1993 Occurrence Handle10.1105/tpc.11.10.1981 Occurrence Handle10521527
J. Lai N. Dey C.S. Kim A.K. Bharti S. Rudd K.F. Mayer B.A. Larkins P. Becraft J. Messing (2004) ArticleTitleCharacterization of the maize endosperm transcriptome and its comparison to the rice genome Genome Res. 14 1932–1937 Occurrence Handle10.1101/gr.2780504 Occurrence Handle15466291
S. Lohmer M. Maddaloni M. Motto N. Di Fonzo H. Hartings F. Salamini R.D. Thompson (1991) ArticleTitleThe maize regulatory locus Opaque-2 encodes a DNA-binding protein which activates the transcription of the b-32 gene EMBO J. 10 617–624 Occurrence Handle2001677
M.A. Lopes B.A. Larkins (1993) ArticleTitleEndosperm origin, development, and function Plant Cell 5 1383–1399 Occurrence Handle8281040
A. Maizel D. Weigel (2004) ArticleTitleTemporally and spatially controlled induction of gene expression in Arabidopsis thaliana Plant J. 38 164–171 Occurrence Handle10.1111/j.1365-313X.2004.02027.x Occurrence Handle15053769
K. Manning (1991) ArticleTitleIsolation of nucleic acids from plants by differential solvent precipitation Anal. Biochem. 195 45–50 Occurrence Handle10.1016/0003-2697(91)90292-2 Occurrence Handle1716071
M. Muller G. Dues C. Balconi F. Salamini R.D. Thompson (1997) ArticleTitleNitrogen and hormonal responsiveness of the 22 kDa alpha-zein and b-32 genes in maize endosperm is displayed in the absence of the transcriptional regulator Opaque-2 Plant J. 12 281–291 Occurrence Handle10.1046/j.1365-313X.1997.12020281.x Occurrence Handle9301081
M.G. Neuffer W.F. Sheridan (1980) ArticleTitleDefective kernel mutants of maize I Genetic and lethality studies Genetics 95 929–944
F.T.S. Nogueira V.E. Rosa ParticleDe SuffixJr M. Menossi E.C. Ulian P. Arruda (2003) ArticleTitleRNA expression profiles and data mining of sugarcane response to low temperature Plant Physiol. 132 1811–1824 Occurrence Handle10.1104/pp.102.017483 Occurrence Handle12913139
O-A. Olsen (2004) ArticleTitleNuclear endosperm development in cereals and Arabidopsis thaliana Plant Cell 16 S214–S227 Occurrence Handle10.1105/tpc.017111 Occurrence Handle15010513
D. Samson F. Legeai E. Karsenty S. Reboux J-B. Veyrieras J. Just E. Barillot (2003) ArticleTitleGénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics Nucleic Acids Res 31 179–182 Occurrence Handle10.1093/nar/gkg060 Occurrence Handle12519976
M.J. Scanlon PS. Stinard M.G. James A.M. Myers D.S. Robertson (1994) ArticleTitleGenetic analysis of 63 mutations affecting maize kernel development isolated from Mutator stocks Genetics 136 281–294 Occurrence Handle8138165
M.J. Scanlon A.M. Myers (1998) ArticleTitlePhenotypic analysis and molecular cloning of discolored-1 (dsc1), a maize gene required for early kernel development Plant Mol. Biol. 37 483–493 Occurrence Handle10.1023/A:1005998830723 Occurrence Handle9617815
M. Schmid T.S. Davison S.R. Henz U.J. Pape M. Demar M. Vingron B. Scholkopf D. Weigel J.U. Lohmann (2005) ArticleTitleA gene expression map of Arabidopsis thaliana development Nat. Gen. 37 IssueID5 501–6 Occurrence Handle10.1038/ng1543
R.J. Schmidt M. Ketudat M.J. Aukerman G. Hoschek (1992) ArticleTitleOpaque2 is a transcriptional activator that recognizes a specific target site in 22 kDa zein gene Plant Cell 4 689–700 Occurrence Handle10.1105/tpc.4.6.689 Occurrence Handle1392590
V. Stolc Z. Gauhar C. Mason G. Halasz M.F. Batenburg Particlevan S.A. Rifkin S. Hua T. Herreman W. Tongprasit P.E. Barbano H.J. Bussemaker K.P. White (2004) ArticleTitleA gene expression map for the euchromatic genome of Drosophila melanogaster Science 306 655–660 Occurrence Handle10.1126/science.1101312 Occurrence Handle15499012
G.P. Telles M.D.V. Braga Z. Dias T-L. Lin J.A.A. Quitzau F.R. da Silva J. Meidanis (2001) ArticleTitleBioinformatics of the sugarcane EST project Genet Mol. Biol. 24 9–15
G.P. Telles F.R. da Silva (2001) ArticleTitleTrimming and clustering sugarcane ESTs Genet. Mol. Biol. 24 17–23
J.H. Tuteja S.J. Clough W.C. Chan L.O. Vodkin (2004) ArticleTitleTissue-specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max Plant Cell 16 819–835 Occurrence Handle10.1105/tpc.021352 Occurrence Handle15064367
V.E. Velculescu S.L. Madden L. Zhang A.E. Lash J. Yu C. Rago A. Lal C.J. Wang G.A. Beaudry K.M. Ciriello B.P. Cook M.R. Dufault A.T. Ferguson Y. Gao T.C. He H. Hermeking S.K. Hiraldo P.M. Hwang M.A. Lopez H.F. Luderer B. Mathews J.M. Petroziello K. Polyak L. Zawel K.W. Kinzler (1999) ArticleTitleAnalysis of human transcriptomes Nat. Genet. 23 387–388 Occurrence Handle10.1038/70487
A.L. Vettore F.R. da Silva E.L. Kemper P. Arruda (2001) ArticleTitleThe libraries that made SUCEST Genet. Mol. Biol. 24 1–7 Occurrence Handle10.1590/S1415-47572001000100002
A.L. Vettore F.R. da Silva E.L. Kemper G.M. Souza A.M. da Silva M.I. Ferro F. Henrique-Silva E.A. Giglioti M.V. Lemos L.L. Coutinho (2003) ArticleTitleAnalysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane Genome Res. 13 2725–2735 Occurrence Handle10.1101/gr.1532103 Occurrence Handle14613979
C.W. Whitfield M.R. Band M.F. Bonaldo C.G. Kumar L. Liu J.R. Pardinas H.M. Robertson M.B. Soares G.E. Robinson (2002) ArticleTitleAnnotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee Genome Res. 12 555–566 Occurrence Handle10.1101/gr.5302 Occurrence Handle11932240
Y.M. Woo D.W.N. Hu B.A. Larkins R. Jung (2001) ArticleTitleGenomics analysis of genes expressed in maize endosperm identifies novel seed proteins and clarifies patterns of zein gene expression Plant Cell 13 2297–2317 Occurrence Handle10.1105/tpc.13.10.2297 Occurrence Handle11595803
J. Yu S. Hu J. Wang G.K. Wong S. Li B. Liu Y. Deng L. Dai Y. Zhou X. Zhang (2002) ArticleTitleA draft sequence of the rice genome (Oryza sativa L ssp. indica) Science 296 79–92 Occurrence Handle10.1126/science.1068037 Occurrence Handle11935017
L. Yu T.L. Setter (2003) ArticleTitleComparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit Plant physio 131 568–582 Occurrence Handle10.1104/pp.014365
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Verza, N.C., e Silva, T.R., Neto, G.C. et al. Endosperm-preferred Expression of Maize Genes as Revealed by Transcriptome-wide Analysis of Expressed Sequence Tags. Plant Mol Biol 59, 363–374 (2005). https://doi.org/10.1007/s11103-005-8924-7
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DOI: https://doi.org/10.1007/s11103-005-8924-7