Structure et expression des gènes mitochondriaux de Diplonema papillatum

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

Comparative Analysis of WRKY Genes Potentially Involved in Salt Stress Responses in Triticum turgidum L. ssp. durum

WRKY transcription factors are involved in multiple aspects of plant growth, development and responses to biotic stresses. Although they have been found to play roles in regulating plant responses to environmental stresses, these roles still need to be explored, especially those pertaining to crops. Durum wheat is the second most widely produced cereal in the world. Complex, large and unsequenced genomes, in addition to a lack of genomic resources, hinder the molecular characterization of tolerance mechanisms. This paper describes the isolation and characterization of five TdWRKY genes from durum wheat(TriticumturgidumL.ssp.durum).APCR-based screening of aT.turgidum BAC genomic library using primers within the conserved region of WRKY genes resulted in the isolation of five BAC clones. Following sequencing fully the five BACs, fine annotation through Triannot pipeline revealed 74.6% of the entire sequences as transposable elements and a 3.2% gene content with genes organized as islands with in oceans of TEs. Each BAC clone harbored a TdWRKY gene .The study showed a very extensive conservation of genomic structure between TdWRKYs and their orthologs from Brachypodium, barley, and T. aestivum. The structural features of TdWRKY proteins suggested that they are novel members of the WRKY family in durum wheat. TdWRKY1/2/4 , TdWRKY3, and TdWRKY5 belong to the group Ia, IIa, andIIc, respectively. Enrichmentofcis- regulatory elements related to stress responses in the promoters of some TdWRKY genes indicated their potential roles inmediating plant responses to a wide variety of environmental stresses. TdWRKY genes displayed different expression patterns in response to salt stress that distinguishes two durum wheat genotypes with contrasting salt stress tolerance phenotypes. TdWRKY genes tended to react earlier with a down-regulation in sensitive genotype leaves and with an up-regulation intolerant genotype leaves. The TdWRKY transcripts levels in roots increased intolerant genotype compared to sensitive genotype. The present results indicate that these genes might play some functional role in the salt tolerance in durum wheat

Isolation and molecular characterization of ERF1, an ethylene response factor gene from durum wheat (Triticum turgidum L. subsp. durum), potentially involved in salt-stress responses

As food crop, wheat is of prime importance for human society. Nevertheless, our understanding of the genetic and molecular mechanisms controlling wheat productivity conditions has been, so far, hampered by the lack of sufficient genomic resources. The present work describes the isolation and characterization of TdERF1, an ERF gene from durum wheat (Triticum turgidum L. subsp. durum). The structural features of TdERF1 supported the hypothesis that it is a novel member of the ERF family in durum wheat and, considering its close similarity to TaERF1 of Triticum aestivum, it probably plays a similar role in mediating responses to environmental stresses. TdERF1 displayed an expression pattern that discriminated between two durum wheat genotypes contrasted with regard to salt-stress tolerance. The high number of cis-regulatory elements related to stress responses present in the TdERF1 promoter and the ability of TdERF1 to regulate the transcription of ethylene and drought-responsive promoters clearly indicated its potential role in mediating plant responses to a wide variety of environmental constrains. TdERF1 was also regulated by abscisic acid, ethylene, auxin, and salicylic acid, suggesting that it may be at the crossroads of multiple hormone signalling pathways. Four TdERF1 allelic variants have been identified in durum wheat genome, all shown to be transcriptionally active. Interestingly, the expression of one allelic form is specific to the tolerant genotype, further supporting the hypothesis that this gene is probably associated with the susceptibility/tolerance mechanism to salt stress. In this regard, the TdERF1 gene may provide a discriminating marker between tolerant and sensitive wheat varieties

Systematically fragmented genes in a multipartite mitochondrial genome

Arguably, the most bizarre mitochondrial DNA (mtDNA) is that of the euglenozoan eukaryote Diplonema papillatum. The genome consists of numerous small circular chromosomes none of which appears to encode a complete gene. For instance, the cox1 coding sequence is spread out over nine different chromosomes in non-overlapping pieces (modules), which are transcribed separately and joined to a contiguous mRNA by trans-splicing. Here, we examine how many genes are encoded by Diplonema mtDNA and whether all are fragmented and their transcripts trans-spliced. Module identification is challenging due to the sequence divergence of Diplonema mitochondrial genes. By employing most sensitive protein profile search algorithms and comparing genomic with cDNA sequence, we recognize a total of 11 typical mitochondrial genes. The 10 protein-coding genes are systematically chopped up into three to 12 modules of 60–350 bp length. The corresponding mRNAs are all trans-spliced. Identification of ribosomal RNAs is most difficult. So far, we only detect the 3′-module of the large subunit ribosomal RNA (rRNA); it does not trans-splice with other pieces. The small subunit rRNA gene remains elusive. Our results open new intriguing questions about the biochemistry and evolution of mitochondrial trans-splicing in Diplonema

Kinesin 9 family members perform separate functions in the trypanosome flagellum

KIF9B localizes to the axoneme and basal body and is needed for flagella assembly, whereas KIF9A localizes only to the axoneme and controls flagella motility without affecting their structure

Wheat receptor-kinase-like protein Stb6 controls gene-for-gene resistance to fungal pathogen Zymoseptoria tritici

Deployment of fast-evolving disease-resistance genes is one of the most successful strategies used by plants to fend off pathogens. In gene-for-gene relationships, most cloned disease-resistance genes encode intracellular nucleotide-binding leucine-rich-repeat proteins (NLRs) recognizing pathogensecreted isolate-specific avirulence (Avr) effectors delivered to the host cytoplasm. This process often triggers a localized hypersensitive response, which halts further disease development. Here we report the map-based cloning of the wheat Stb6 gene and demonstrate that it encodes a conserved wallassociated receptor kinase (WAK)-like protein, which detects the presence of a matching apoplastic effector and confers pathogen resistance without a hypersensitive response. This report demonstrates gene-for-gene disease resistance controlled by this class of proteins in plants. Moreover, Stb6 is, to our knowledge, the first cloned gene specifying resistance to Zymoseptoria tritici, an important foliar fungal pathogen affecting wheat and causing economically damaging septoria tritici blotch (STB) disease

Unique Mitochondrial Genome Structure in Diplonemids, the Sister Group of Kinetoplastids

Kinetoplastid flagellates are characterized by uniquely massed mitochondrial DNAs (mtDNAs), the kinetoplasts. Kinetoplastids of the trypanosomatid group possess two types of mtDNA molecules: maxicircles bearing protein and mitoribosomal genes and minicircles specifying guide RNAs, which mediate uridine insertion/deletion RNA editing. These circles are interlocked with one another to form dense networks. Whether these peculiar mtDNA features are restricted to kinetoplastids or prevail throughout Euglenozoa (euglenids, diplonemids, and kinetoplastids) is unknown. Here, we describe the mitochondrial genome and the mitochondrial ultrastructure of Diplonema papillatum, a member of the diplonemid flagellates, the sister group of kinetoplastids. Fluorescence and electron microscopy show a single mitochondrion per cell with an ultrastructure atypical for Euglenozoa. In addition, DNA is evenly distributed throughout the organelle rather than compacted. Molecular and electron microscopy studies distinguish numerous 6- and 7-kbp-sized mitochondrial chromosomes of monomeric circular topology and relaxed conformation in vivo. Remarkably, the cox1 gene (and probably other mitochondrial genes) is fragmented, with separate gene pieces encoded on different chromosomes. Generation of the contiguous cox1 mRNA requires trans-splicing, the precise mechanism of which remains to be determined. Taken together, the mitochondrial gene/genome structure of Diplonema is not only different from that of kinetoplastids but unique among eukaryotes as a whole

Medicago sativa cv. Mercedes genome sequence

Note on the methodology used to obtain the genome sequence of Medicago sativa, and results obtained, as a complementary information to the portal containing the data: https://medicago.toulouse.inra.fr/MsatMercedes-NRGENE-20181029/An alfalfa (or lucerne) genome reference sequence is an essential tool for breeding of this major legume species. A clone of Flemish origin has been sequenced and the genome assembly has been carried out with NRGene protocols. A total of almost 190 000 scaffolds have been generated and this genome assembly reaches 2.6 Gb (80% of the 3.2 Gb expected). Genome annotation has provided 233 049 protein-coding genes and 36 752 non-protein coding genes. A genome portal based on JBrowse has been developed for searching the annotated genome (https://medicago.toulouse.inra.fr/MsatMercedes-NRGENE-20181029/)

The unusual S locus of Leavenworthia is composed of two sets of paralogous loci

International audienceThe Leavenworthia self-incompatibility locus (S locus) consists of paralogs (Lal2, SCRL) of the canonical Brassicaceae S locus genes (SRK, SCR), and is situated in a genomic position that differs from the ancestral one in the Brassicaceae. Unexpectedly, in a small number of Leavenworthia alabamica plants examined, sequences closely resembling exon 1 of SRK have been found, but the function of these has remained unclear. BAC cloning and expression analyses were employed to characterize these SRK-like sequences. An SRK-positive Bacterial Artificial Chromosome clone was found to contain complete SRK and SCR sequences located close by one another in the derived genomic position of the Leavenworthia S locus, and in place of the more typical Lal2 and SCRL sequences. These sequences are expressed in stigmas and anthers, respectively, and crossing data show that the SRK/SCR haplotype is functional in self-incompatibility. Population surveys indicate that < 5% of Leavenworthia S loci possess such alleles. An ancestral translocation or recombination event involving SRK/SCR and Lal2/SCRL likely occurred, together with neofunctionalization of Lal2/SCRL, and both haplotype groups now function as Leavenworthia S locus alleles. These findings suggest that S locus alleles can have distinctly different evolutionary origins