Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivum L.)

Lazo, Gerard R.; Chao, Shiaoman; Dd, Hummel; Edwards, H; Cc, Crossman; Lui, N; De, Matthews; Vl, Carollo; Dl, Hane; Fm, You; Ge, Butler; Moon, Re; Tj, Close; Jh, Peng; Nl, Lapitan; Jp, Gustafson; Ll, Qi; Echalier, Benjamin; Gill, BS; Dilbirliği, Muharrem; Hs, Randhawa; Ks, Gill; Ra, Greene; Me, Sorrells; Ed, Akhunov; Dvořák, Jan; Linkiewicz, Anna; Dubcovsky, Jorge; Kg, Hossain; Kalavacharla,; Sf, Kianian; Aa, Mahmoud; Miftahudin, Miftahudin; Xf, Ma; Conley, E. J.; Anderson, J. A.; Ms, Pathan; Ht, Nguyen; Pe, McGuire; Qualset, C. O.; Od, Anderson

doi:10.1534/genetics.104.034777

Cited by 89 publications

(20 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Wortman et al (2003) and the International Rice Genome Sequencing Project (2005) recently estimated the number of genes in Arabidopsis and rice to be 28,952 and 37,544, respectively. In light of these gene number estimates and the fact that gene number inflation may be a common artifact within EST assemblies (Close et al 2004;Lazo et al 2004), one might expect that the 33,665 exemplar sequences from Gossypium identified here may be an overestimate of the number of putative genes in the assembly. By their very nature, ESTs undersample the genic content of genomes; at the end of the year 2000, for example, 105,000 Arabidopsis ESTs identified only ∼60% of the genes (The Arabidopsis Genome Initiative 2000).…”

Section: Discussionmentioning

confidence: 92%

A global assembly of cotton ESTs

Udall¹,

Swanson²,

Haller³

et al. 2006

Genome Res.

141

153

View full text Add to dashboard Cite

Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; AT and DT genomes) as well as its two diploid progenitors, Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to recognition of 33,665 exemplar sequences that represent a nonredundant set of putative Gossypium genes containing partial or full-length coding regions and usually one or two UTRs. The assembly, along with their UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public resource for cotton genomics. Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, we were in many cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign them to either the A or D genome. The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.

show abstract

Section: Discussionmentioning

confidence: 92%

A global assembly of cotton ESTs

Udall¹,

Swanson²,

Haller³

et al. 2006

Genome Res.

141

153

View full text Add to dashboard Cite

show abstract

“…The use of nullisomic-tetrasomic, ditelo- Gill et al , 1996aDelany et al 1995; laboratories. Information on the cDNA libraries is available in Zhang et al (2004) and the development of EST singletons Faris et al 2000;Qi and Gill 2001;Sandhu et al 2001; has been described by Lazo et al (2004). ESTs were mapped to Weng and Lazar 2002;Akhunov et al 2003a;Qi et al chromosome bin locations on the chromosomes via Southern 2004).…”

mentioning

confidence: 99%

“…Chromosome bin mapping and data verification ditelosomic, and deletion lines. The chromosome karyoprocedures have been described by Lazo et al (2004). Loci types detailing breakpoints and chromosome bins for mapped to group 2 chromosomes by any of the 10 mapping the cytogenetic stocks used in the wheat EST mapping labs were confirmed by the University of Minnesota lab on the basis of the autoradiogram image available in the online project can be found online at http://wheat.pw.usda.…”

mentioning

confidence: 99%

A 2600-Locus Chromosome Bin Map of Wheat Homoeologous Group 2 Reveals Interstitial Gene-Rich Islands and Colinearity With Rice

et al. 2004

Self Cite

View full text Add to dashboard Cite

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a highdensity EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.H EXAPLOID common wheat (Triticum aestivum L.) related diploid genomes designated A, B, and D with seven chromosomes each (2n ϭ 6x ϭ 42). Extensive is one of the most important staple crops globally. The hexaploid wheat genome is composed of three genetic and cytogenetic characterization of diploid, tetraploid, and hexaploid wheat relatives has made it a model system for the study of allopolyploid evolution.

show abstract

“…The procedures used to generate EST data and the bioinformatics pipeline developed for large-scale EST data processing were reported in Lazo et al (2004). EST assembly was carried out using the program Phrap (University of Washington, Seattle, http://www.genome.washington.edu/ UWGC/analysistools/Phrap.cfm).…”

Section: Large-scale Est Generation Data Processing Annotation Andmentioning

confidence: 99%

Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivumL.)

Chao

Lazo²,

You

et al. 2006

Genome

Self Cite

View full text Add to dashboard Cite

Abstract:The US Wheat Genome Project, funded by the National Science Foundation, developed the first large public Triticeae expressed sequence tag (EST) resource. Altogether, 116 272 ESTs were produced, comprising 100 674 5′ ESTs and 15 598 3′ ESTs. These ESTs were derived from 42 cDNA libraries, which were created from hexaploid bread wheat (Triticum aestivum L.) and its close relatives, including diploid wheat (T. monococcum L. and Aegilops speltoides L.), tetraploid wheat (T. turgidum L.), and rye (Secale cereale L.), using tissues collected from various stages of plant growth and development and under diverse regimes of abiotic and biotic stress treatments. ESTs were assembled into 18 876 contigs and 23 034 singletons, or 41 910 wheat unigenes. Over 90% of the contigs contained fewer than 10 EST members, implying that the ESTs represented a diverse selection of genes and that genes expressed at low and moderate to high levels were well sampled. Statistical methods were used to study the correlation of gene expression patterns, based on the ESTs clustered in the1536 contigs that contained at least 10 5′ EST members and thus representing the most abundant genes expressed in wheat. Analysis further identified genes in wheat that were significantly upregulated (p < 0.05) in tissues under various abiotic stresses when compared with control tissues. Though the function annotation cannot be assigned for many of these genes, it is likely that they play a role associated with the stress response. This study predicted the possible functionality for 4% of total wheat unigenes, which leaves the remaining 96% with their functional roles and expression patterns largely unknown. Nonetheless, the EST data generated in this project provide a diverse and rich source for gene discovery in wheat.Key words: Expressed sequence tags, ESTs, gene expression profiles, wheat, Triticeae. Résumé :Le projet américain sur le génome du blé, financé par la « National Science Foundation », a développé la première grande collection publique d'EST chez les hordées. Au total, 116 272 EST ont été produits à partir de 42 Des analyses statistiques ont été employées pour étudier la corrélation entre les motifs d'expression génique en s'appuyant sur les EST compris au sein des 1 536 contigs qui comptaient au moins 10 EST en 5′ (ceux qui représentent vraisemblablement les gènes le plus fortement exprimés chez le blé). Des analyses ont également permis d'identifier des gènes dont l'expression était significativement plus élevée (p < 0,05) au sein de tissus ayant subi divers stress par rapport aux tissus témoins. Bien qu'on ne puisse assigner aucune fonction à plusieurs de ces gènes, il est probable qu'ils jouent un rôle dans la réponse aux stress. Cette étude a permis de prédire une fonction pour 4 % des unigènes chez le blé, ce qui laisse 96 % de gènes pour lesquels la fonction demeure largement inconnue. Néanmoins, les données produites sur les EST au cours de ce travail constituent une vaste et riche ressource pour la découverte de gènes chez le blé.

show abstract

Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivum L.)

Cited by 89 publications

References 30 publications

A global assembly of cotton ESTs

A global assembly of cotton ESTs

A 2600-Locus Chromosome Bin Map of Wheat Homoeologous Group 2 Reveals Interstitial Gene-Rich Islands and Colinearity With Rice

Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivumL.)

Contact Info

Product

Resources

About