An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

BackgroundMitogen-activated protein kinase kinase kinases (MAPKKKs) are the important components of MAPK cascades, which play the crucial role in plant growth and development as well as in response to diverse stresses. Although this family has been systematically studied in many plant species, little is known about MAPKKK genes in wheat (Triticum aestivum L.), especially those involved in the regulatory network of stress processes.ResultsIn this study, we identified 155 wheat MAPKKK genes through a genome-wide search method based on the latest available wheat genome information, of which 29 belonged to MEKK, 11 to ZIK and 115 to Raf subfamily, respectively. Then, chromosome localization, gene structure and conserved protein motifs and phylogenetic relationship as well as regulatory network of these TaMAPKKKs were systematically investigated and results supported the prediction. Furthermore, a total of 11 homologous groups between A, B and D sub-genome and 24 duplication pairs among them were detected, which contributed to the expansion of wheat MAPKKK gene family. Finally, the expression profiles of these MAPKKKs during development and under different abiotic stresses were investigated using the RNA-seq data. Additionally, 10 tissue-specific and 4 salt-responsive TaMAPKKK genes were selected to validate their expression level through qRT-PCR analysis.ConclusionsThis study for the first time reported the genome organization, evolutionary features and expression profiles of the wheat MAPKKK gene family, which laid the foundation for further functional analysis of wheat MAPKKK genes, and contributed to better understanding the roles and regulatory mechanism of MAPKKKs in wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2993-7) contains supplementary material, which is available to authorized users.

Comparative chloroplast genome analysis presents new opportunities for performing molecular phylogeny studies and revealing the significant evolutionary features in higher plants, which has been widely documented from conifers to grass family. However, a systematic analysis of chloroplast genomes in Asteraceae family has not been conducted up to now. In this study, we compared and analyzed the gene content, genomic organization, and RNA editing sites of eight representative Asteraceae chloroplast genomes. Results showed that Asteraceae chloroplast had relatively conservative gene content. No gain or loss events occurred in the proteincoding genes, while some differences were found to be present in the gene structure and transfer RNA (tRNA) abundance. Genome structure analysis found some Asteraceae-specific or species-specific structure variations, and sequence rearrangement events were present in these genomes, suggesting specific evolutionary processes have occurred in this family. Some DNA regions containing parsimony-informative characters higher than 5 % were also identified, which could be used as the new molecular markers for phylogenetic analysis and plant identification of Asteraceae species. Furthermore, RNA editing in these genomes was investigated through computational analysis, and some species-specific sites were identified. Finally, phylogenetic analysis of 81 genes from 70 species supported the monophyly of the Asteraceae. Our study for the first time compared the organization, structure, and sequence divergence of eight Asteraceae chloroplast genomes, which will provide the valuable resource for molecular phylogeny of Asteraceae species and also facilitate the genetic and evolutionary studies in this family.

Penicillium expansum, as a main postharvest pathogen of fruits, can secrete patulin (PAT), causing fruit decay and health problems. In this study, the antifungal test, SEM (scanning electron microscope) observation, transcriptional profile, PAT biosynthesis, and physiological characters of P. expansum exposed to cinnamaldehyde and citral combination (Cin/Cit) were evaluated. Cin/Cit could inhibit the mycelial growth and spore germination of P. expansum in a dose-dependent manner. Besides, Cin/Cit caused spores and mycelia wrinkled and depressed by SEM observation. Gene expression profiles of P. expansum were conducted by RNA sequencing (RNA-seq) in the presence or absence of Cin/Cit treatment. A total of 1713 differentially expressed genes (DEGs) were obtained, including 793 down-regulated and 920 up-regulated genes. Most of the DEGs participated in the biosynthesis of secondary metabolites, amino acid metabolism, and oxidation-reduction process, etc. Cin/Cit induced the dysfunction of the mitochondrial membrane, causing the potential influence on energy metabolism and reactive oxidative species production. The changes of superoxide dismutase (SOD) and catalase (CAT) activities combing with the increase of hydrogen peroxide content indicated the oxidative stress on P. expansum induced by Cin/Cit, which corresponded well with the transcriptional results. Moreover, both the RNA-seq data and the qRT-PCR showed the remarkable down-regulation of genes included in the PAT biosynthetic pathway under the Cin/Cit treatment. These findings provided more useful information about the antifungal mechanism of Cin/Cit against P. expansum at molecular and gene levels and suggested that Cin/Cit is a potential candidate to control P. expansum.

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BackgroundThe AP2/ERF transcription factor is one of the most important gene families in plants, which plays the vital role in regulating plant growth and development as well as in response to diverse stresses. Although AP2/ERFs have been thoroughly characterized in many plant species, little is known about this family in the model plant Brachypodium distachyon, especially those involved in the regulatory network of stress processes.ResultsIn this study, a comprehensive genome-wide search was performed to identify AP2/ERF gene family in Brachypodium and a total of 141 BdAP2/ERFs were obtained. Phylogenetic analysis classified them into four subfamilies, of which 112 belonged to ERF, four to RAV and 24 to AP2 as well as one to soloist subfamily respectively, which was in accordance with the number of AP2 domains and gene structure analysis. Chromosomal localization, gene structure, conserved protein motif and cis-regulatory elements as well as gene duplication events analysis were further performed to systematically investigate the evolutionary features of these BdAP2/ERF genes. Furthermore, the regulatory network between BdAP2/ERF and other genes were constructed using the orthology-based method, and 39 BdAP2/ERFs were found to be involved in the regulatory network and 517 network branches were identified. The expression profiles of BdAP2/ERF during development and under diverse stresses were investigated using the available RNA-seq and microarray data and ten tissue-specific and several stress-responsive BdAP2/ERF genes were identified. Finally, 11 AP2/ERF genes were selected to validate their expressions in different tissues and under different stress treatments using RT-PCR method and results verified that these AP2/ERFs were involved in various developmental and physiological processes.ConclusionsThis study for the first time reported the characteristics of the BdAP2/ERF family, which will provide the invaluable information for further evolutionary and functional studies of AP2/ERF in Brachypodium, and also contribute to better understanding the molecular basis for development and stresses tolerance in this model species and beyond.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2968-8) contains supplementary material, which is available to authorized users.

Salinity is a major limiting factor for agricultural production worldwide. A better understanding of the mechanisms of salinity stress response will aid efforts to improve plant salt tolerance. In this study, a combination of small RNA and mRNA degradome sequencing was used to identify salinity responsive-miRNAs and their targets in barley. A total of 152 miRNAs belonging to 126 families were identified, of which 44 were found to be salinity responsive with 30 up-regulated and 25 down-regulated respectively. The majority of the salinity-responsive miRNAs were up-regulated at the 8h time point, while down-regulated at the 3h and 27h time points. The targets of these miRNAs were further detected by degradome sequencing coupled with bioinformatics prediction. Finally, qRT-PCR was used to validate the identified miRNA and their targets. Our study systematically investigated the expression profile of miRNA and their targets in barley during salinity stress phase, which can contribute to understanding how miRNAs respond to salinity stress in barley and other cereal crops.

Mitogen-activated protein kinase (MAPK) cascades are the conserved and universal signal transduction modules in all eukaryotes, which play the vital roles in plant growth, development, and in response to multiple stresses. In this study, we used bioinformatics methods to identify 86 MAPKKK protein encoded by 73 MAPKKK genes in Brachypodium. Phylogenetic analysis of MAPKKK family from Arabidopsis, rice, and Brachypodium has classified them into three subfamilies, of which 28 belonged to MEKK, 52 to Raf, and 6 to ZIK subfamily, respectively. Conserved protein motif, exon-intron organization, and splicing intron phase in kinase domains supported the evolutionary relationships inferred from the phylogenetic analysis. And gene duplication analysis suggested the chromosomal segment duplication happened before the divergence of the rice and Brachypodium, while all of three tandem duplicated gene pairs happened after their divergence. We further demonstrated that the MAPKKKs have evolved under strong purifying selection, implying the conservation of them. The splicing transcripts expression analysis showed that the splicesome translating longest protein tended to be adopted. Furthermore, the expression analysis of BdMAPKKKs in different organs and development stages as well as heat, virus and drought stresses revealed that the MAPKKK genes were involved in various signaling pathways. And the circadian analysis suggested there were 41 MAPKKK genes in Brachypodium showing cycled expression in at least one condition, of which seven MAPKKK genes expressed in all conditions and the promoter analysis indicated these genes possessed many cis-acting regulatory elements involved in circadian and light response. Finally, the co-expression network of MAPK, MAPKK, and MAPKKK in Brachypodium was constructed using 144 microarray and RNA-seq datasets, and ten potential MAPK cascades pathway were predicted. To conclude, our study provided the important information for evolutionary and functional characterization of MAPKKK family in Brachypodium, which will facilitate the functional analysis of BdMAPKKK genes, and also will facilitate better understanding the MAPK signal pathway in Brachypodium and beyond.