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Fusarium crown rot (FCR) of wheat and barley, predominantly caused by the fungal pathogen Fusarium pseudograminearum, is a disease of economic significance. The quantitative nature of FCR resistance within cultivated wheat germplasm has significantly limited breeding efforts to enhanced FCR resistance in wheat. In this study, we characterized the molecular responses of Brachypodium distachyon (Brachypodium hereafter) to F. pseudograminearum infection using RNA-seq to determine whether Brachypodium can be exploited as a model system towards better understanding of F. pseudograminearum-wheat interaction. The transcriptional response to infection in Brachypodium was strikingly similar to that previously reported in wheat, both in shared expression patterns of wheat homologs of Brachypodium genes and functional overlap revealed through comparative gene ontology analysis in both species. Metabolites produced by various biosynthetic pathways induced in both wheat and Brachypodium were quantified, revealing a high degree of overlap between these two species in metabolic response to infection but also showed Brachypodium does not produce certain defence-related metabolites found in wheat. Functional analyses of candidate genes identified in this study will improve our understanding of resistance mechanisms and may lead to the development of new strategies to protect cereal crops from pathogen infection.

Introduction Polyploidy, forming new species by enveloping two or more genomes within a single nucleus, is a prominent speciation process. Previous studies show that polyploidization was likely involved in the [...], Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were not detected between these two types of polyploid genotypes, although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes. Key words: asymmetric evolution, subgenome asymmetry, diploid donor, polyploids, progenitor. L'asymetrie des sous-genomes (AS) est generalement attribuee a l'acquisition, au cours de l ' evolution, de reponses differentes a divers stimuli entre les sous-genomes presents chez un polyploide. Dans ce travail, les auteurs ont compare les differences entre sous-genomes pour ce qui est du ratio de genes et de la diversite relative entre genotypes naturels et artificiels chez plusieurs especes allopolyploides. Etonnamment, des differences ont regulierement n'ont pas ete detectees entre ces deux types de genotypes polyploides bien qu'ils different dans la duree de leur exposition a la selection. Le ratio estime de genes partages entre un sous-genome et le genome de l'espece ancestrale etait invariablement plus eleve chez les allopolyploides artificiels que chez les genotypes naturels, un resultat attendu puisqu'il est bien connu que plusieurs genes ne sont pas presents chez tous les individus d'une espece. Comme le parent diploide exact n'est pas connu pour un sous-genome donne, les ratios estimes de genes partages avec les genotypes naturels pourraient egalement inclure des differences entre genotypes distincts de l'espece diploide ancestrale. De plus, les auteurs ont detecte la presence dAS chez des genotypes avant le terme de la polyploidisation de meme que chez ceux qui n' etaient pas issus de la polyploidisation. Ces resultats indiquent que l 'AS pourrait, en grande partie, refleter des differences entre les especes diploides ancestrales ou que les changements survenus au cours de l ' evolution des polyploides sont definis par les genomes ancestraux. [Traduit par la Redaction] Mots-cles : evolution asymetrique, asymetrie des sous-genomes, diploide ancestral, polyploide, progeniteur.

Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread [...]

Introduction It is widely believed that chromosome translocation is an important driving force in shaping genomes during evolution (Brown and O'Neill 2010; Burt et al. 1999; Colson et al. 2004; [...], Chromosome translocation is an important driving force in shaping genomes during evolution. Detailed knowledge of chromosome translocations in a given species and its close relatives should increase the efficiency and precision of chromosome engineering in crop improvement. To identify genes flanking the breakpoints of translocations and inversions as a step toward identifying breakpoints in bread wheat, we systematically analysed genes in the Brachypodium genome against wheat survey sequences and bin-mapped ESTs (expressed sequence tags) derived from the hexaploid wheat genotype 'Chinese Spring'. In addition to those well-known translocations between group 4, 5, and 7 chromosomes, this analysis identified genes flanking the three pericentric inversions on chromosomes 2B, 4B, and 5A. However, numerous chromosomal rearrangements reported in early studies could not be confirmed. The genes flanking the breakpoints reported in this study are valuable for isolating these breakpoints. Key words: genome evolution, bread wheat, inversion, translocation breakpoint, Brachypodium. La translocation chromosomique est l'un des moteurs de l'evolution des genomes. Une connaissance approfondie des translocations chromosomiques au sein d'une espece et ses proches parents pourrait augmenter l'efficience et la precision de l'ingenierie chromosomique en amelioration varietale. Afin d'identifier les genes bordant les jonctions de translocations et d'inversions, en vue d'identifier ces jonctions chez le ble tendre, les auteurs ont systematiquement compare les genes du genome de Brachypodium avec les sequences de survol et les EST (expressed sequence tags) assignes a la carte genetique chez le ble pour le genotype hexpaploide 'Chinese Spring'. En plus des translocations bien connues entre les chromosomes des groupes 4, 5 et 7, cette analyse a permis d'identifier des genes bordant trois inversions pericentriques sur les chromosomes 2B, 4B et 5A. Cependant, de nombreux rearrangements chromosomiques rapportes dans des etudes anterieures n'ont pas ete confirmes. Les genes bordant les jonctions rapportees dans ce travail seront utiles pour isoler ces jonctions. [Traduit par la Redaction] Mots-cles : evolution du genome, ble tendre, inversion, jonction de translocation, Brachypodium.

Introduction Association mapping is being driven by changes in technology that permit the discovery of large numbers of genetic variants and the screening for these genetic variations across large populations. [...], Association mapping currently relies on the identification of genetic markers. Several technologies have been adopted for genetic marker analysis, with single nucleotide polymorphisms (SNPs) being the most popular where a reasonable quantity of genome sequence data are available. We describe several tools we have developed for the discovery, annotation, and visualization of molecular markers for association mapping. These include autoSNPdb for SNP discovery from assembled sequence data; TAGdb for the identification of gene specific paired read Illumina GAII data; CMap3D for the comparison of mapped genetic and physical markers; and BAC and Gene Annotator for the online annotation of genes and genomic sequences. Key words: SNP discovery, association mapping, comparative genomics, second generation genome sequencing. L'analyse d'association repose presentement sur l'identification de marqueurs genetiques. Plusieurs technologies ont ete employees pour l'analyse de marqueurs genetiques, les polymorphismes mononucleeotidiques (SNP) etant les plus populaires la oil une information genomique suffisante etait disponible. Les auteurs decrivent plusieurs outils qu'ils ont deeveloppees pour l'identification, l'annotation et la visualisation des marqueurs moleeculaires pour des fins d'analyse d'association. Ceux-ci incluent autoSNPdb pour l'identification de SNP au sein de donneees de sequence, TAGdb pour l'identification d'etiquettes specifiques d'un gene au sein de collections d'etiquettes de sequence Illumina GAII, CMap3D pour la comparaison de marqueurs genetiques et physiques, et un annotateur de clones BAC et de genes pour effectuer l'annotation automatiseedegenes et de sequences geenomiques. Mots-cles: identification de SNP, analyse d'association, genomique comparee, sequencjage genomique de seconde geeneration.

Research designed to identify the regulatory elements that function early in nodule induction has involved characterizing a transposon-tagged Lotus japonicus mutant, nin, arrested at the stage of bacterial recognition. It has been established that nin is needed for the formation of infection threads and the initiation of primordia. The phenotype of the nin mutants shows that Nin is involved in the inception of root nodules. The characteristics of NIN the protein indicate that it acts as a transcriptional regulator of genes needed for nodule development.

Abstract Background The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes. Results We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome. Conclusions The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.

Summary: Wild barley (Hordeum spontaneum) is the progenitor of cultivated barley (Hordeum vulgare) and provides a rich source of genetic variations for barley improvement. Currently, the genome sequences of wild barley and its differences with cultivated barley remain unclear. In this study, we report a high‐quality draft assembly of wild barley accession (AWCS276; henceforth named as WB1), which consists of 4.28 Gb genome and 36 395 high‐confidence protein‐coding genes. BUSCO analysis revealed that the assembly included full lengths of 95.3% of the 956 single‐copy plant genes, illustrating that the gene‐containing regions have been well assembled. By comparing with the genome of the cultivated genotype Morex, it is inferred that the WB1 genome contains more genes involved in resistance and tolerance to biotic and abiotic stresses. The presence of the numerous WB1‐specific genes indicates that, in addition to enhance allele diversity for genes already existing in the cultigen, exploiting the wild barley taxon in breeding should also allow the incorporation of novel genes. Furthermore, high levels of genetic variation in the pericentromeric regions were detected in chromosomes 3H and 5H between the wild and cultivated genotypes, which may be the results of domestication. This H. spontaneum draft genome assembly will help to accelerate wild barley research and be an invaluable resource for barley improvement and comparative genomics research. [ABSTRACT FROM AUTHOR]

Bread wheat ( Triticum aestivum L.) is an allopolyploid species containing three ancestral genomes. Therefore, three homoeologous copies exist for the majority of genes in the wheat genome. Whether different homoeologs are differentially expressed (homoeolog expression bias) in response to biotic and abiotic stresses is poorly understood. In this study, we applied a RNA-seq approach to analyse homoeolog-specific global gene expression patterns in wheat during infection by the fungal pathogen Fusarium pseudograminearum, which causes crown rot disease in cereals. To ensure specific detection of homoeologs, we first optimized read alignment methods and validated the results experimentally on genes with known patterns of subgenome-specific expression. Our global analysis identified widespread patterns of differential expression among homoeologs, indicating homoeolog expression bias underpins a large proportion of the wheat transcriptome. In particular, genes differentially expressed in response to Fusarium infection were found to be disproportionately contributed from B and D subgenomes. In addition, we found differences in the degree of responsiveness to pathogen infection among homoeologous genes with B and D homoeologs exhibiting stronger responses to pathogen infection than A genome copies. We call this latter phenomenon as 'homoeolog induction bias'. Understanding how homoeolog expression and induction biases operate may assist the improvement of biotic stress tolerance in wheat and other polyploid crop species. [ABSTRACT FROM AUTHOR]