Expressed Sequence Tags from the oomycete Plasmopara halstedii, an obligate parasite of the sunflower

<p>Abstract</p> <p>Background</p> <p>Sunflower downy mildew is a major disease caused by the obligatory biotrophic oomycete <it>Plasmopara halstedii</it>. Little is known about the molecular mechanisms underlying its pathogenicity. In this study we used a genomics approach to gain a first insight into the transcriptome of <it>P. halstedii</it>.</p> <p>Results</p> <p>To identify genes from the obligatory biotrophic oomycete <it>Plasmopara halstedii </it>that are expressed during infection in sunflower (<it>Helianthus annuus </it>L.) we employed the suppression subtraction hybridization (SSH) method from sunflower seedlings infected by <it>P. halstedii</it>. Using this method and random sequencing of clones, a total of 602 expressed sequence tags (ESTs) corresponding to 230 unique sequence sets were identified. To determine the origin of the unisequences, PCR primers were designed to amplify these gene fragments from genomic DNA isolated either from <it>P. halstedii </it>sporangia or from <it>Helianthus annuus</it>. Only 145 nonredundant ESTs which correspond to a total of 373 ESTs (67.7%) proved to be derived from <it>P. halstedii </it>genes and that are expressed during infection in sunflower. A set of 87 nonredundant sequences were identified as showing matches to sequences deposited in public databases. Nevertheless, about 7% of the ESTs seem to be unique to <it>P. halstedii </it>without any homolog in any public database.</p> <p>Conclusion</p> <p>A summary of the assignment of nonredundant ESTs to functional categories as well as their relative abundance is listed and discussed. Annotation of the ESTs revealed a number of genes that could function in virulence. We provide a first glimpse into the gene content of <it>P. halstedii</it>. These resources should accelerate research on this important pathogen.</p

Insights into Four NAC Transcription Factors Involved in Grain Development and in Response to Moderate Heat in the Triticeae Tribe

International audienceNAC (NAM (no apical meristem)-ATAF (Arabidopsis transcription activation factor)-CUC (cup-shaped cotyledons)) are among the largest transcription factor families in plants, involved in a plethora of physiological mechanisms. This study focused on four NAC genes previously identified in bread wheat as specifically grain-expressed which could be considered as candidate genes for yield improvement under climate changes. Using in silico analyses, the Triticum aestivum "Grain-NAC" (TaGNAC) orthologs in 14 cereal species were identified. A conserved protein motif was identified only in Triticeae. The expression of TaGNAC and einkorn TmGNAC was studied in response to moderate heat stress during grain development and showed a similar expression pattern that is accelerated during cell division stages under heat stress. A conserved structure was found in the promoter of the Triticeae GNAC orthologs, which is absent in the other Poaceae species. A specific model of promoter structure in Triticeae was proposed, based on the presence of key cis-elements involved in the regulation of seed development, hormonal regulation and response to biotic and abiotic stresses. In conclusion, GNAC genes could play a central role in the regulation of grain development in the Triticeae tribe, particularly in the accumulation of storage proteins, as well as in response to heat stress and could be used as candidate genes for breeding

Expansion and Functional Diversification of SKP1-Like Genes in Wheat (Triticum aestivum L.)

The ubiquitin proteasome 26S system (UPS), involving monomeric and multimeric E3 ligases is one of the most important signaling pathways in many organisms, including plants. The SCF (SKP1/Cullin/F-box) multimeric complex is particularly involved in response to development and stress signaling. The SKP1 protein (S-phase kinase-associated protein 1) is the core subunit of this complex. In this work, we firstly identified 92 and 87 non-redundant Triticum aestivum SKP1-like (TaSKP) genes that were retrieved from the latest release of the wheat genome database (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0) and the genome annotation of the TGAC v1 respectively. We then investigated the structure, phylogeny, duplication events and expression patterns of the SKP1-like gene family in various tissues and environmental conditions using a wheat expression platform containing public data. TaSKP1-like genes were expressed differentially in response to stress conditions, displaying large genomic variations or short insertions/deletions which suggests functional specialization within TaSKP1-like genes. Finally, interactions between selected wheat FBX (F-box) proteins and putative ancestral TaSKP1-like proteins were tested using the yeast two-hybrid (Y2H) system to examine the molecular interactions. These observations suggested that six Ta-SKP1 genes are likely to be ancestral genes, having similar functions as ASK1 and ASK2 in Arabidopsis, OSK1 and OSK20 in rice and PpSKP1 and PpSKP2 in Physcomitrella patens

In silico analysis of the Seven IN Absentia (SINA) genes in bread wheat sheds light on their structure in plants

International audienceSeven IN Absentia (SINA) is a small family of genes coding for ubiquitin-ligases that play major roles in regulating various plant growth and developmental processes, as well as in plant response to diverse biotic and abiotic stresses. Here, we studied the SINA genes family in bread wheat Triticum aestivum which is a culture of major importance for food security worldwide. One hundred and forty-one SINA family genes have been identified in bread wheat and showed that their number is very high compared to other plant species such as A. thaliana or rice. The expansion of this family seems to have been more important in monocots than in eudicots. In bread wheat, the chromosome 3 distal region is the site of a massive amplification of the SINA family, since we found that 83 of the 141 SINA genes are located on this chromosome in the Chinese Spring variety. This amplification probably occurred as a result of local duplications, followed by sequences divergence. The study was then extended to 4856 SINA proteins from 97 plant species. Phylogenetic and structural analyses identified a group of putative ancestral SINA proteins in plants containing a 58 aminoacid specific signature. Based on sequence homology and the research of that "Ancestral SINA motif" of 58 amino acids, a methodological process has been proposed and lead to the identification of functional SINA genes in a large family such as the Triticae that might be used for other species. Finally, tis paper gives a comprehensive overview of wheat gene family organization and functionalization taken the SINA genes as an example

Genome-wide analysis, expansion and expression of the NAC family under drought and heat stresses in bread wheat (T. aestivum L.).

The NAC family is one of the largest plant-specific transcription factor families, and some of its members are known to play major roles in plant development and response to biotic and abiotic stresses. Here, we inventoried 488 NAC members in bread wheat (Triticum aestivum). Using the recent release of the wheat genome (IWGS RefSeq v1.0), we studied duplication events focusing on genomic regions from 4B-4D-5A chromosomes as an example of the family expansion and neofunctionalization of TaNAC members. Differentially expressed TaNAC genes in organs and in response to abiotic stresses were identified using publicly available RNAseq data. Expression profiling of 23 selected candidate TaNAC genes was studied in leaf and grain from two bread wheat genotypes at two developmental stages in field drought conditions and revealed insights into their specific and/or overlapping expression patterns. This study showed that, of the 23 TaNAC genes, seven have a leaf-specific expression and five have a grain-specific expression. In addition, the grain-specific genes profiles in response to drought depend on the genotype. These genes may be considered as potential candidates for further functional validation and could present an interest for crop improvement programs in response to climate change. Globally, the present study provides new insights into evolution, divergence and functional analysis of NAC gene family in bread wheat

Expressed Sequence Tags from the oomycete , an obligate parasite of the sunflower-2

<p><b>Copyright information:</b></p><p>Taken from "Expressed Sequence Tags from the oomycete , an obligate parasite of the sunflower"</p><p>http://www.biomedcentral.com/1471-2180/7/110</p><p>BMC Microbiology 2007;7():110-110.</p><p>Published online 6 Dec 2007</p><p>PMCID:PMC2242796.</p><p></p>like protein [GenBank:]. NT indicates the N-terminus trauncation, L1 and L2 indicate two conserved loop. The asterisk indicates the conserved Tryptophane amino acid within the L2 loop. The potential Peptide signal is also indicated

Expressed Sequence Tags from the oomycete , an obligate parasite of the sunflower-0

<p><b>Copyright information:</b></p><p>Taken from "Expressed Sequence Tags from the oomycete , an obligate parasite of the sunflower"</p><p>http://www.biomedcentral.com/1471-2180/7/110</p><p>BMC Microbiology 2007;7():110-110.</p><p>Published online 6 Dec 2007</p><p>PMCID:PMC2242796.</p><p></p>he ESTs tested here are: , HSP 70 [GenBank:]; , Pyruvate kinase [GenBank:]; , Superoxyde dismutase [GenBank:]; , Proteasome 26 S beta subunit [GenBank:]; protein; , Asparagine synthase; , Elicitor [GenBank:]; , Cyclophilin B [GenBank:]. : molecular marker. : negative control. The PCR products were separated on 1.5% agarose gel

Coexpression network and phenotypic analysis identify metabolic pathways associated with the effect of warming on grain yield components in wheat.

Wheat grains are an important source of human food but current production amounts cannot meet world needs. Environmental conditions such as high temperature (above 30°C) could affect wheat production negatively. Plants from two wheat genotypes have been subjected to two growth temperature regimes. One set has been grown at an optimum daily mean temperature of 19°C while the second set of plants has been subjected to warming at 27°C from two to 13 days after anthesis (daa). While warming did not affect mean grain number per spike, it significantly reduced other yield-related indicators such as grain width, length, volume and maximal cell numbers in the endosperm. Whole genome expression analysis identified 6,258 and 5,220 genes, respectively, whose expression was affected by temperature in the two genotypes. Co-expression analysis using WGCNA (Weighted Gene Coexpression Network Analysis) uncovered modules (groups of co-expressed genes) associated with agronomic traits. In particular, modules enriched in genes related to nutrient reservoir and endopeptidase inhibitor activities were found to be positively associated with cell numbers in the endosperm. A hypothetical model pertaining to the effects of warming on gene expression and growth in wheat grain is proposed. Under moderately high temperature conditions, network analyses suggest a negative effect of the expression of genes related to seed storage proteins and starch biosynthesis on the grain size in wheat

A RFLP map of sunflower and its applications for breeding for diseases resistances

International audienc