A compilation of soybean ESTs: generation and analysis

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 329-338 ◽  
Author(s):  
Randy Shoemaker ◽  
Paul Keim ◽  
Lila Vodkin ◽  
Ernest Retzel ◽  
Sandra W Clifton ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cdna Libraries ◽  
Sequence Length ◽  
Valuable Insight ◽  
Alternative Approach ◽  
Average Sequence Length ◽  
Expressed Sequence ◽  
Insight Into

Whole-genome sequencing is fundamental to understanding the genetic composition of an organism. Given the size and complexity of the soybean genome, an alternative approach is targeted random-gene sequencing, which provides an immediate and productive method of gene discovery. In this study, more than 120 000 soybean expressed sequence tags (ESTs) generated from more than 50 cDNA libraries were evaluated. These ESTs coalesced into 16 928 contigs and 17 336 singletons. On average, each contig was composed of 6 ESTs and spanned 788 bases. The average sequence length submitted to dbEST was 414 bases. Using only those libraries generating more than 800 ESTs each and only those contigs with 10 or more ESTs each, correlated patterns of gene expression among libraries and genes were discerned. Two-dimensional qualitative representations of contig and library similarities were generated based on expression profiles. Genes with similar expression patterns and, potentially, similar functions were identified. These studies provide a rich source of publicly available gene sequences as well as valuable insight into the structure, function, and evolution of a model crop legume genome.Key words: Glycine max, genome sequencing, functional genomics.

scholarly journals In silico differential display of defense-related expressed sequence tags from sugarcane tissues infected with diazotrophic endophytes

2001 ◽  
Vol 24 (1-4) ◽  
pp. 103-111 ◽  
Author(s):  
Marcio R. Lambais
Keyword(s):  
Hierarchical Clustering ◽  
Expressed Sequence Tags ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cdna Libraries ◽  
A Genome ◽  
Wide Scale ◽  
Clustering Approach ◽  
Diazotrophic Endophytes ◽  
Expressed Sequence

The expression patterns of 277 sugarcane expressed sequence tags (EST)-contigs encoding putative defense-related (DR) proteins were evaluated using the Sugarcane EST database. The DR proteins evaluated included chitinases, beta-1,3-glucanases, phenylalanine ammonia-lyases, chalcone synthases, chalcone isomerases, isoflavone reductases, hydroxyproline-rich glycoproteins, proline-rich glycoproteins, peroxidases, catalases, superoxide dismutases, WRKY-like transcription factors and proteins involved in cell death control. Putative sugarcane WRKY proteins were compared and their phylogenetic relationships determined. A hierarchical clustering approach was used to identify DR ESTs with similar expression profiles in representative cDNA libraries. To identify DR ESTs differentially expressed in sugarcane tissues infected with Gluconacetobacter diazotrophicus or Herbaspirillum rubrisubalbicans, 179 putative DR EST-contigs expressed in non-infected tissues (leaves and roots) and/or infected tissues were selected and arrayed by similarity of their expression profiles. Changes in the expression levels of 124 putative DR EST-contigs, expressed in non-infected tissues, were evaluated in infected tissues. Approximately 42% of these EST-contigs showed no expression in infected tissues, whereas 15% and 3% showed more than 2-fold suppression in tissues infected with G. diazotrophicus or H. rubrisubalbicans, respectively. Approximately 14 and 8% of the DR EST-contigs evaluated showed more than 2-fold induction in tissues infected with G. diazotrophicus or H. rubrisubalbicans, respectively. The differential expression of clusters of DR genes may be important in the establishment of a compatible interaction between sugarcane and diazotrophic endophytes. It is suggested that the hierarchical clustering approach can be used on a genome-wide scale to identify genes likely involved in controlling plant-microorganism interactions.

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

Genome ◽  
2006 ◽  
Vol 49 (5) ◽  
pp. 531-544 ◽  
Author(s):  
S Chao ◽  
G R Lazo ◽  
F You ◽  
C C Crossman ◽  
D D Hummel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Triticum Aestivum ◽  
Expressed Sequence Tag ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tetraploid Wheat ◽  
Gene Expression Profiles ◽  
Triticum Aestivum L ◽  
Cdna Libraries ◽  
Expressed Sequence

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.

Fluorescent protein expression in temperature tolerant and susceptible reef-building corals

2021 ◽  
pp. 1-10
Author(s):  
Exequiel Gabriel S. Dizon ◽  
Jeric P. Da-Anoy ◽  
Melissa S. Roth ◽  
Cecilia Conaco
Keyword(s):  
Spectral Properties ◽  
Coral Species ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Antioxidant Properties ◽  
Variable Expression ◽  
Acropora Digitifera ◽  
Insight Into

Abstract Fluorescent proteins (FPs) are reported to play an important role as photoprotectants and antioxidants in corals subjected to stressful conditions. Identifying the various FP genes expressed and FP gene expression patterns under stress in diverse coral species can provide insight into FP function. In this study, we identified 16 putative FP homologues from the transcriptomes of corals with varying susceptibility to elevated temperature, including Acropora digitifera, Favites colemani, Montipora digitata and Seriatopora caliendrum. Each coral expressed a different complement of FP transcripts, which were predicted to have distinct spectral properties. The most diverse and abundant repertoire of FP transcripts, including at least 6 green FPs, were expressed in the temperature-tolerant coral, F. colemani. In comparison, the other corals expressed fewer FP types. Specific FP transcripts exhibited variable expression profiles in coral fragments subjected to 32 ± 1 °C (treatment) or 28 ± 1 °C (control) for up to 72 h, suggesting that distinct FPs may have different roles. Further studies on the expression of the proteins encoded by these FP transcripts, their fluorescence activity, tissue localization, and possible antioxidant properties, are needed to reveal their contribution to thermal stress tolerance in certain species of corals.

scholarly journals Distribution of DNA repair-related ESTs in sugarcane

2001 ◽  
Vol 24 (1-4) ◽  
pp. 141-146 ◽  
Author(s):  
W.C. Lima ◽  
R. Medina-Silva ◽  
R.S. Galhardo ◽  
C.F.M. Menck
Keyword(s):  
Dna Repair ◽  
Biochemical Analysis ◽  
Excision Repair ◽  
Expression Patterns ◽  
Cdna Libraries ◽  
Nucleotide Excision ◽  
Exogenous Agents ◽  
Base Excision ◽  
Repair Genes ◽  
Expressed Sequence

DNA repair pathways are necessary to maintain the proper genomic stability and ensure the survival of the organism, protecting it against the damaging effects of endogenous and exogenous agents. In this work, we made an analysis of the expression patterns of DNA repair-related genes in sugarcane, by determining the EST (expressed sequence tags) distribution in the different cDNA libraries of the SUCEST transcriptome project. Three different pathways - photoreactivation, base excision repair and nucleotide excision repair - were investigated by employing known DNA repair proteins as probes to identify homologous ESTs in sugarcane, by means of computer similarity search. The results showed that DNA repair genes may have differential expressions in tissues, depending on the pathway studied. These in silico data provide important clues on the potential variation of gene expression, to be confirmed by direct biochemical analysis.

scholarly journals Genome-wide analysis of HSP70 gene superfamily in Pyropia yezoensis (Bangiales, Rhodophyta): identification, characterization and expression profiles in response to dehydration stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xinzi Yu ◽  
Zhaolan Mo ◽  
Xianghai Tang ◽  
Tian Gao ◽  
Yunxiang Mao
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Dehydration Stress ◽  
Pyropia Yezoensis ◽  
Genome Wide ◽  
Regulated Expression ◽  
Relative Conservation ◽  
Shock Proteins ◽  
Insight Into

Abstract Background Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Individual family members have been analyzed in previous studies, but there has not yet been a comprehensive analysis of the HSP70 gene family in Pyropia yezoensis. Results We investigated 15 putative HSP70 genes in Py. yezoensis. These genes were classified into two sub-families, denoted as DnaK and Hsp110. In each sub-family, there was relative conservation of the gene structure and motif. Synteny-based analysis indicated that seven and three PyyHSP70 genes were orthologous to HSP70 genes in Pyropia haitanensis and Porphyra umbilicalis, respectively. Most PyyHSP70s showed up-regulated expression under different degrees of dehydration stress. PyyHSP70-1 and PyyHSP70-3 were expressed in higher degrees compared with other PyyHSP70s in dehydration treatments, and then expression degrees somewhat decreased in rehydration treatment. Subcellular localization showed PyyHSP70-1-GFP and PyyHSP70-3-GFP were in the cytoplasm and nucleus/cytoplasm, respectively. Similar expression patterns of paired orthologs in Py. yezoensis and Py. haitanensis suggest important roles for HSP70s in intertidal environmental adaptation during evolution. Conclusions These findings provide insight into the evolution and modification of the PyyHSP70 gene family and will help to determine the functions of the HSP70 genes in Py. yezoensis growth and development.

scholarly journals Evolutionary Conservation and Expression Patterns of Neutral/Alkaline Invertases in Solanum

Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 763 ◽  
Author(s):  
Luzhao Pan ◽  
Qinwei Guo ◽  
Songlin Chai ◽  
Yuan Cheng ◽  
Meiying Ruan ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Solanum Melongena ◽  
In Silico Analysis ◽  
Chromosome Mapping ◽  
Sequence Length ◽  
Comparative Genomic ◽  
Solanum Pennellii

The invertase gene family in plants is composed of two subfamilies of enzymes, namely, acid- and neutral/alkaline invertases (cytosolic invertase, CIN). Both can irreversibly cleave sucrose into fructose and glucose, which are thought to play key roles in carbon metabolism and plant growth. CINs are widely found in plants, but little is reported about this family. In this paper, a comparative genomic approach was used to analyze the CIN gene family in Solanum, including Solanum tuberosum, Solanum lycopersicum, Solanum pennellii, Solanum pimpinellifolium, and Solanum melongena. A total of 40 CINs were identified in five Solanum plants, and sequence features, phylogenetic relationships, motif compositions, gene structure, collinear relationship, and expression profile were further analyzed. Sequence analysis revealed a remarkable conservation of CINs in sequence length, gene number, and molecular weight. The previously verified four amino acid residues (D188, E414, Arg430, and Ser547) were also observed in 39 out of 40 CINs in our study, showing to be deeply conserved. The CIN gene family could be distinguished into groups α and β, and α is further subdivided into subgroups α1 and α2 in our phylogenetic tree. More remarkably, each species has an average of four CINs in the α and β groups. Marked interspecies conservation and collinearity of CINs were also further revealed by chromosome mapping. Exon–intron configuration and conserved motifs were consistent in each of these α and β groups on the basis of in silico analysis. Expression analysis indicated that CINs were constitutively expressed and share similar expression profiles in all tested samples from S. tuberosum and S. lycopersicum. In addition, in CIN genes of the tomato and potato in response to abiotic and biotic stresses, phytohormones also performed. Overall, CINs in Solanum were encoded by a small and highly conserved gene family, possibly reflecting structural and functional conservation in Solanum. These results lay the foundation for further expounding the functional characterization of CIN genes and are also significant for understanding the evolutionary profiling of the CIN gene family in Solanum.

scholarly journals The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jingwen Chen ◽  
Qian Yan ◽  
Jiawei Li ◽  
Lei Feng ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Biological Processes ◽  
Temporal Expression ◽  
Litchi Chinensis ◽  
Conserved Domain ◽  
Insight Into ◽  
Gras Gene

Abstract Background The GRAS gene family plays crucial roles in multiple biological processes of plant growth, including seed development, which is related to seedless traits of litchi (Litchi chinensis Sonn.). However, it hasn’t been fully identified and analyzed in litchi, an economic fruit tree cultivated in subtropical regions. Results In this study, 48 LcGRAS proteins were identified and termed according to their chromosomal location. LcGRAS proteins can be categorized into 14 subfamilies through phylogenetic analysis. Gene structure and conserved domain analysis revealed that different subfamilies harbored various motif patterns, suggesting their functional diversity. Synteny analysis revealed that the expansion of the GRAS family in litchi may be driven by their tandem and segmental duplication. After comprehensively analysing degradome data, we found that four LcGRAS genes belong to HAM subfamily were regulated via miR171-mediated degradation. The various expression patterns of LcGRAS genes in different tissues uncovered they were involved in different biological processes. Moreover, the different temporal expression profiles of LcGRAS genes between abortive and bold seed indicated some of them were involved in maintaining the normal development of the seed. Conclusion Our study provides comprehensive analyses on GRAS family members in litchi, insight into a better understanding of the roles of GRAS in litchi development, and lays the foundation for further investigations on litchi seed development.

scholarly journals In silico characterization and expression analyses of sugarcane putative sucrose non-fermenting-1 (SNF1) related kinases

2001 ◽  
Vol 24 (1-4) ◽  
pp. 35-41 ◽  
Author(s):  
Dirce Maria Carraro ◽  
Marcio R. Lambais ◽  
Helaine Carrer
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Protein Kinases ◽  
Catalytic Domain ◽  
Expressed Sequence Tag ◽  
Higher Plants ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Cdna Libraries ◽  
Expressed Sequence

Sucrose non-fermenting-1-related protein kinases (SnRKs) may play a major role in regulating gene expression in plant cells. This family of regulatory proteins is represented by sucrose non-fermenting-1 (SNF1) protein kinase in Saccharomyces cerevisiae, AMP-activated protein kinases (AMPKs) in mammals and SnRKs in higher plants. The SnRK family has been reorganized into three subfamilies according to the evolutionary relationships of their amino acid sequences. Members of the SnRK subfamily have been identified in several plants. There is evidence that they are involved in the nutritional and/or environmental stress response, although their roles are not yet well understood. We have identified at least 22 sugarcane expressed sequence tag (EST) contigs encoding putative SnRKs. The amino acid sequence alignment of both putative sugarcane SnRKs and known SnRKs revealed a highly conserved N-terminal catalytic domain. Our results indicated that sugarcane has at least one member of each SnRK subfamily. Expression pattern analysis of sugarcane EST-contigs encoding putative SnRKs in 26 selected cDNA libraries from the sugarcane expressed sequence tag SUCEST database has indicated that members of this family are expressed throughout the plant. Members of the same subfamily showed no specific expression patterns, suggesting that their functions are not related to their phylogenic relationships based on N-terminal amino acid sequence phylogenetic relationships.

scholarly journals Genome-Wide Identification and Expression Profiling of 2OGD Superfamily Genes from Three Brassica Plants

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1399
Author(s):  
Ding Jiang ◽  
Guangguang Li ◽  
Guoju Chen ◽  
Jianjun Lei ◽  
Bihao Cao ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Gene Families ◽  
Plant Genome ◽  
Valuable Insight ◽  
Systematic Analysis ◽  
Brassica Plants ◽  
Root Tissues

The 2-oxoglutarate and Fe(II)-dependent dioxygenase (2OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation and hydroxylation reactions. Due to their important biochemical significance in metabolism, a systematic analysis of the plant 2OGD genes family is necessary. Here, we identified 160, 179, and 337 putative 2OGDs from Brassica rapa, Brassica oleracea, and Brassica napus. According to their gene structure, domain, phylogenetic features, function, and previous studies, we also divided 676 2OGDs into three subfamilies: DOXA, DOXB, and DOXC. Additionally, homologous and phylogenetic comparisons of three subfamily genes provided valuable insight into the evolutionary characteristics of the 2OGD genes from Brassica plants. Expression profiles derived from the transcriptome and Genevestigator database exhibited distinct expression patterns of the At2OGD, Br2OGD, and Bo2OGD genes in different developmental stages, tissues, or anatomical parts. Some 2OGD genes showed high expression levels in various tissues, such as callus, seed, silique, and root tissues, while other 2OGD genes were expressed at very low levels in other tissues. Analysis of six Bo2OGD genes in different tissues by qRT-PCR indicated that these genes are involved in the metabolism of gibberellin, which in turn regulates plant growth and development. Our working system analysed 2OGD gene families of three Brassica plants and laid the foundation for further study of their functional characterization.

Addressing sustainable challenges in China

2014 ◽  
Vol 3 (3) ◽  
pp. 261-274 ◽  
Author(s):  
Xiaolin Zhai ◽  
Richard Reed ◽  
Anthony Mills
Keyword(s):  
Construction Industry ◽  
Sustainable Construction ◽  
Residential Construction ◽  
Valuable Insight ◽  
Diverse Range ◽  
Content Type ◽  
Cheap Labour ◽  
Alternative Approach ◽  
Insight Into

Purpose – The purpose of this paper is to present an innovative approach to addressing increasing sustainable challenges facing China's built environment which are linked to a diverse range of factors including rapid economic and population growth. The research context includes mass urbanisation in and the Chinese construction industry's attitude towards adopting sustainable construction processes. The focus is placed on examining current on-site construction practices in China which have historically remained largely unchanged; this includes a high reliance on cheap labour accompanied by a substantial material waste. An alternative approach is to increase the uptake of off-site production in China's residential construction industry, however no previous studies have investigated the potential advantages and barriers of this alternative approach. Design/methodology/approach – In collaboration with an industry organisation a survey was completed by 110 construction professionals in China. The questionnaire referred to 21 individual factors relating to their perception about the current and potential future uptake of off-site production in construction processes in China. Findings – The results confirmed the existing level of off-site production in China's urban residential construction industry was relatively low. At present the cast-in-situ method was considered by stakeholders as the most effective approach. The findings also confirmed the benefits of off-site production are not fully understood by the housing construction industry in China. It is argued this knowledge gap reduces the Chinese construction industry's motivation levels when seeking to embrace the off-site production approach and adopt improved sustainable construction practices. Originality/value – This is an original study designed to address a gap in knowledge as there has been no previous research conducted into the use of off-site industrialised process in China. The results provide a valuable insight into the uptake of off-site production in the residential construction industry and will assist stakeholders and policymakers to increase the level of sustainability.

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