Expression data of Defensin-like genes (DEFLs) from different parts and treatments of Medicago truncatula and Arabidopsis thaliana
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana Medicago truncatula
PROVIDER: GSE34401 | GEO | 2013/02/23
SECONDARY ACCESSION(S): PRJNA149633
REPOSITORIES: GEO
Similar Datasets
Project description:Since most of the DEFLs were recently discovered and many are not well represented on standard microarrays, little is known about their expression pattterns. To address this gap, we have designed a custom Affymetrix microarray (AtMtDEFL array) with known and predicted Arabidopsis and Medicago DEFL genes and the closely related maternally expressed gene family. The custom array was utilized for hybridizations of mRNAs from a wide range of conditions and tissues from both plant species, enabling a comparative analysis in the two model plant species. The custom chip transcript analysis provided the first expression evidence for many of the computationally identified DEFLs previously lacking gene expression evidence, and indicated both common and unique patterns of DEFL gene expression between the two model plant species.
2013-02-23 | GSE34311 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-02-23 | E-GEOD-34401 | biostudies-arrayexpress
Project description:Plant genomes contain several hundred defensin-like (DEFL) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species.
| S-EPMC3601123 | biostudies-literature
Project description:Since most of the DEFLs were recently discovered and many are not well represented on standard microarrays, little is known about their expression pattterns. To address this gap, we have designed a custom Affymetrix microarray (AtMtDEFL array) with known and predicted Arabidopsis and Medicago DEFL genes and the closely related maternally expressed gene family. The custom array was utilized for hybridizations of mRNAs from a wide range of conditions and tissues from both plant species, enabling a comparative analysis in the two model plant species. The custom chip transcript analysis provided the first expression evidence for many of the computationally identified DEFLs previously lacking gene expression evidence, and indicated both common and unique patterns of DEFL gene expression between the two model plant species. The custom designed Affymetrix chip consisting of nearly all DEFLs from Medicago truncatula was used for transcript profiling study in a variety of plant organs, developmental stages, and during symbiotic and pathogenic associations totalling 13 different treatments. Each treatment was supported by three biological replicates giving a grand total of 39 samples.
2013-02-23 | E-GEOD-34311 | biostudies-arrayexpress
Project description:Since most of the DEFLs were recently discovered and many are not well represented on standard microarrays, little is known about their expression pattterns. To address this gap, we have designed a custom Affymetrix microarray (AtMtDEFL array) with known and predicted Arabidopsis and Medicago DEFL genes and the closely related maternally expressed gene family. The custom array was utilized for hybridizations of mRNAs from a wide range of conditions and tissues from both plant species, enabling a comparative analysis in the two model plant species. The custom chip transcript analysis provided the first expression evidence for many of the computationally identified DEFLs previously lacking gene expression evidence, and indicated both common and unique patterns of DEFL gene expression between the two model plant species.
2013-02-23 | GSE34398 | GEO
Project description:Since most of the DEFLs were recently discovered and many are not well represented on standard microarrays, little is known about their expression pattterns. To address this gap, we have designed a custom Affymetrix microarray (AtMtDEFL array) with known and predicted Arabidopsis and Medicago DEFL genes and the closely related maternally expressed gene family. The custom array was utilized for hybridizations of mRNAs from a wide range of conditions and tissues from both plant species, enabling a comparative analysis in the two model plant species. The custom chip transcript analysis provided the first expression evidence for many of the computationally identified DEFLs previously lacking gene expression evidence, and indicated both common and unique patterns of DEFL gene expression between the two model plant species. The custom designed Affymetrix chip consisting of nearly all DEFLs from Arabidopsis thaliana was used for transcript profiling study in a variety of plant organs, developmental stages, and pathogenic associations totalling 16 different treatments. Each treatment was supported by three biological replicates giving a grand total of 48 samples.
2013-02-23 | E-GEOD-34398 | biostudies-arrayexpress
Project description:BackgroundRecent genome sequencing enables mega-base scale comparisons between related genomes. Comparisons between animals, plants, fungi, and bacteria demonstrate extensive synteny tempered by rearrangements. Within the legume plant family, glimpses of synteny have also been observed. Characterizing syntenic relationships in legumes is important in transferring knowledge from model legumes to crops that are important sources of protein, fixed nitrogen, and health-promoting compounds.ResultsWe have uncovered two large soybean regions exhibiting synteny with M. truncatula and with a network of segmentally duplicated regions in Arabidopsis. In all, syntenic regions comprise over 500 predicted genes spanning 3 Mb. Up to 75% of soybean genes are colinear with M. truncatula, including one region in which 33 of 35 soybean predicted genes with database support are colinear to M. truncatula. In some regions, 60% of soybean genes share colinearity with a network of A. thaliana duplications. One region is especially interesting because this 500 kbp segment of soybean is syntenic to two paralogous regions in M. truncatula on different chromosomes. Phylogenetic analysis of individual genes within these regions demonstrates that one is orthologous to the soybean region, with which it also shows substantially denser synteny and significantly lower levels of synonymous nucleotide substitutions. The other M. truncatula region is inferred to be paralogous, presumably resulting from a duplication event preceding speciation.ConclusionThe presence of well-defined M. truncatula segments showing orthologous and paralogous relationships with soybean allows us to explore the evolution of contiguous genomic regions in the context of ancient genome duplication and speciation events.
| S-EPMC1201151 | biostudies-literature
Project description:We have undertaken a detailed study to identify mechanisms regulating expression of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in different stages of nodule development. Additionally, rhizobial mutants were used to understand the importance of the rhizobial components in induction of NCRs. Early NCRs were detected during the initial infection of rhizobia in nodules and continue to be expressed into the late stages of nodule development. Late NCRs were induced concomittant with bacteroid development in the nodules. The induction of these groups of genes was correlated with the number and morphology of rhizobia in the nodule.
2013-03-05 | GSE34803 | GEO
Project description:Root nodules are the symbiotic organ of legumes that house nitrogen-fixing bacteria. Many genes are specifically induced in nodules during the interactions between the host plant and symbiotic rhizobia. Information regarding the regulation of expression for most of these genes is lacking. One of the largest gene families expressed in the nodules of the model legume Medicago truncatula is the nodule cysteine-rich (NCR) group of defensin-like (DEFL) genes. We used a custom Affymetrix microarray to catalog the expression changes of 566 NCRs at different stages of nodule development. Additionally, bacterial mutants were used to understand the importance of the rhizobial partners in induction of NCRs. Expression of early NCRs was detected during the initial infection of rhizobia in nodules and expression continued as nodules became mature. Late NCRs were induced concomitantly with bacteroid development in the nodules. The induction of early and late NCRs was correlated with the number and morphology of rhizobia in the nodule. Conserved 41 to 50 bp motifs identified in the upstream 1,000 bp promoter regions of NCRs were required for promoter activity. These cis-element motifs were found to be unique to the NCR family among all annotated genes in the M. truncatula genome, although they contain sub-regions with clear similarity to known regulatory motifs involved in nodule-specific expression and temporal gene regulation.
| S-EPMC3613412 | biostudies-literature
Project description:BackgroundElongation factor 1 A (EF1A), an essential regulator for protein synthesis, has been reported to participate in abiotic stress responses and environmental adaption in plants. However, the role of EF1A in abiotic stress response was barely studied in Medicago truncatula. Here, we identified elongation factor (EF) genes of M. truncatula and studied the salt stress response function of MtEF1A1 (MTR_6g021805).ResultsA total of 34 EF genes were identified in the M. truncatula genome. Protein domains and motifs of EFs were highly conserved in plants. MtEF1A1 has the highest expression levels in root nodules and roots, followed by the leaves and stems. Transgenic Arabidopsis thaliana overexpressing MtEF1A1 was more resistant to salt stress treatment, with higher germination rate, longer roots, and more lateral roots than wild type plant. In addition, lower levels of H2O2 and malondialdehyde (MDA) were also detected in transgenic Arabidopsis. Similarly, MtEF1A1 overexpressing M. truncatula was more resistant to salt stress and had lower levels of reactive oxygen species (ROS) in leaves. Furthermore, the expression levels of abiotic stress-responsive genes (MtRD22A and MtCOR15A) and calcium-binding genes (MtCaM and MtCBL4) were upregulated in MtEF1A1 overexpressing lines of M. truncatula.ConclusionThese results suggested that MtEF1A1 play a positive role in salt stress regulation. MtEF1A1 may realize its function by binding to calmodulin (CaM) or by participating in Ca2+-dependent signaling pathway. This study revealed that MtEF1A1 is an important regulator for salt stress response in M. truncatula, and provided potential strategy for salt-tolerant plant breeding.
| S-EPMC10009949 | biostudies-literature