Partial Sequence Analysis of 130 Randomly Selected Maize cDNA Clones

Keith, Carlyn S.; Hoang, Danee O.; Barrett, Bruce M.; Feigelman, Barry; Nelson, Mary C.; Thai, Henry; Baysdorfer, Chris

doi:10.1104/pp.101.1.329

Cited by 76 publications

(47 citation statements)

References 12 publications

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“…Among the 628 cDNA clones, 184 showed significant sequence similarity to known nucleotide sequences in the databases, and 142 clones shared significant nucleotide sequence identity with plant ESTs previously reported from Arabidopsis (Hofte et al, 1993;Newman et al, 1994), maize (Keith et al, 1993), and rice (Uchimiya et al, 1992;Sasaki et al, 1994). To examine the significance of this finding, we again compared the Brassica cDNAs and the matching EST at the amino acid level using the TFASTA program.…”

Section: Characterization Of Estsmentioning

confidence: 97%

“…Various other organisms, such as nematode (McCombie et al, 1992; * Corresponding author; e-mail mjcho@nongae.gsr,w.ac.kr; fax 82-591-759-9363. Waterston et al, 1992), mouse (Hoog, 1991), and severa1 plants (Uchimiya et al, 1992;Hofte et al, 1993;Keith et al, 1993;Park et al, 1993;Newman et al, 1994;Sasaki et al, 1994) have also been examined by extensive sequencing of randomly selected cDNA clones. The enormous accumulation of ESTs has thus led to the establishment of dbEST (Boguski et al, 1993(Boguski et al, , 1994.…”

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confidence: 99%

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Expressed Sequence Tags of Chinese Cabbage Flower Bud cDNA

Lim

Kim

et al. 1996

Plant Physiology

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We randomly selected and partially sequenced cDNA clones from a library of Chinese cabbage (Brassica campestris L. ssp. pekinensis) flower bud cDNAs. Out of 1216 expressed sequence tags (ESTs), 904 cDNA clones were unique or nonredundant. Five hundred eighty-eight clones (48.4%) had sequence homology to functionally defined genes at the peptide level. Only 5 clones encoded known flower-specific proteins. Among the cDNAs with no similarity to known protein sequences (628), 184 clones had significant similarity to nucleotide sequences registered in the databases. Among these 184 clones, 142 exhibited similarities at the nucleotide level only with plant ESTs. Also, sequence similarities were evident between these 142 ESTs and their matching ESTs when compared using the deduced amino acid sequences. Therefore, it is possible that the anonymous ESTs encode plant-specific ubiquitous proteins. Our extensive EST analysis of genes expressed in floral organs not only contributes to the understanding of the dynamics of genome expression patterns in floral organs but also adds data to the repertoire of all genomic genes.

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Section: Characterization Of Estsmentioning

confidence: 97%

mentioning

confidence: 99%

Expressed Sequence Tags of Chinese Cabbage Flower Bud cDNA

Lim

Kim

et al. 1996

Plant Physiology

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“…Also, an approach has been taken to construct equalized cDNA library for the isolation of cDNA clones of low abundance (Kohchi et al, 1995, Kohchi, 1997 Conversely, by selecting strong signal clones, it is easy to obtain sequence information of abundant cDNA clones. Previous studies in the plant random sequencing project revealed that the cDNA clones encoding putative ribosomal proteins were dominant among cDNA libraries and more than 20% of the clones identified in those works were classified into a group of genes functioning in translation processes (Uchimiya et al, 1992, Keith et al, 1993, Hofte et al,1993, Newman et al, 1994, Sasaki et al,1994, Hihara et al, 1997. As summarized in Table 1, cDNA clones identified in this study exhibited homology to a broad spectrum of genes.…”

Section: Discussionmentioning

confidence: 57%

“…Recently, a large number of cDNA clones were identified by random sequencing from plants including maize (Keith et al, 1993), Arabidopsis thaliana (Hofte et al, 1993;Newman et al, 1994), Brassica napes (Park et al, 1993) and rice (Uchimiya et al,1992;Sasaki et al,1994). Our objective is to obtain information for genes expressed at meiosis in higher plants.…”

Section: Introductionmentioning

confidence: 99%

Large-scale Sequencing of Meiosis-associated Genes from a cDNA Library of Lily Microsporocytes.

Morohashi

Takase

Hotta

et al. 2000

Plant Biotechnology

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Lily, Lilium longiflorum has been used to study meiosis for advantages of the synchronous development among sporogenous cells within an anther. In order to identify genes expressed at meiosis, we carried out random sequencing of a cDNA library which represented the mRNAs from microsporocytes of L. longiflorum at the zygotene stage of meiotic prophase. To avoid redundancy of eDNA clones and to obtain novel sequence information efficiently, weexploited a simple and versatile "self hybridization" strategy . Single -run DNA sequence data were obtained from 418 cDNA clones.Deduced amino acid sequences of 171 cDNA clones, which comprised 41% of the selected cDNA clones, showed significant similarity to amino acid sequences registered in the database. These included eDNA sequences for previously identified meiosis-associated genes. However, 59% of the selected clones showed no significant homology to known gene products.

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“…By adding datasets obtained using such highthroughput sequencers, genomes of many plants have been published; reviewed by Paterson et al (2010). In addition, EST datasets have been published for hundreds of plant species, subspecies, and cultivars, before and in parallel with these genome decoding; reports on plant EST datasets of every family and genus are listed in Table 1 and Supplementary table, respectively, and reviewed (Batley et al 2003;Fedorova et al 2002;Hofte et al 1993;Keith et al 1993;Michalek et al 2002;Newman et al 1994;Park et al 1993;Rounsley et al 1996;Rudd 2003;Sasaki et al 1994;Shoemaker et al 2002;Uchimiya et al 1992;Yamamoto and Sasaki 1997;Yuan et al 2011).…”

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confidence: 99%

Plant expressed sequence tags databases: practical uses and the improvement of their searches using network module analysis

Ogata

Suzuki

2011

Plant Biotechnology

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Sequencing technology has been rapidly advancing. Giga-sequencers, which produce several gigabases of fragmented sequences per run, are attractive for decoding genomes and expressed sequence tags (ESTs). A variety of plant genomes and ESTs have been sequenced since the decoding of the genome of Arabidopsis thaliana, the model plant. ESTs are useful for functional analyses of genes and proteins and as biomarkers, which are used to identify particular tissues and conditions due to the specificity of their expression. Sequenced plant genomes and ESTs have been entered into public databases, where they are freely downloadable. Sequences representative of particular functions or structures have been collected from public databases to curate smaller databases useful for studying protein function. Here, we discuss the uses of the currently available plant EST datasets. We also demonstrate the use of network module analysis to perform more stable (or irrespective of the difference of performance in each analyzing PC) homology searches and to provide more information on molecular functions of plant ESTs and proteins.Key words: Database, expressed sequence tag (EST), homology search, network module analysis.Plant Biotechnology 28, 351-360 (2011) DOI: 10.5511/plantbiotechnology.11.0818a Abbreviations: BLAST, Basic Local Alignment Search Tool; EST, expressed sequence tags; GBFF, GenBank flatfile; GFF, General Feature Format; GPFF, GenPept flatfime. This article can be found at http://www.jspcmb.jp/ Published online September 25, 2011 perform more stable homology searches and to provide more information on molecular functions of ESTs, downsizing while maintaining the precision of homology search and also constructing local modules, in which sequences are highly homologous and thus belong to a group with a common feature, are useful. The PSI-BLAST algorithm and its derivatives (Altschul et al. 1997;Lee et al. 2009;Li et al. 2011) focus on sequenceto-sequence hits between multiple sequences. To evaluate relationships between multiple elements (e.g., gene or metabolite), network module analysis is a useful approach (Saito et al. 2008). Network module analyses have been applied to plant gene co-expression, in which a plant gene is related to other genes based on similar expression profiles (Aoki et al. 2007;Ficklin and Feltus 2011;Huber et al. 2007;Marino-Ramirez et al. 2009;Ogata et al. 2010;Winden et al. 2011). This approach allows a co-expression module, which includes coexpressed gene to be assigned to a particular biological process. By identifying homologies between sequences, network module analysis can be used to create, a homology network in which a sequence (node) is connected to other sequences on the basis of high homology. To perform such analysis for a homology network, we used our algorithm (Ogata et al. 2009) according to the following processes: 1) performing BLAST for any pairs of sequences, 2) calculating association indices between pairs as described in "Userfriendly tools for using plant EST a...

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Partial Sequence Analysis of 130 Randomly Selected Maize cDNA Clones

Cited by 76 publications

References 12 publications

Expressed Sequence Tags of Chinese Cabbage Flower Bud cDNA

Expressed Sequence Tags of Chinese Cabbage Flower Bud cDNA

Large-scale Sequencing of Meiosis-associated Genes from a cDNA Library of Lily Microsporocytes.

Plant expressed sequence tags databases: practical uses and the improvement of their searches using network module analysis

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