Gene enrichment and co-expression analysis shed light on transcriptional responses to Ralstonia solanacearum in tomato.

BACKGROUND: Tomato (Solanum lycopersicum) is both an important agricultural product and an excellent model system for studying plant-pathogen interactions. It is susceptible to bacterial wilt caused by Ralstonia solanacearum (Rs), and infection can result in severe yield and quality losses. To investigate which genes are involved in the resistance response to this pathogen, we sequenced the transcriptomes of both resistant and susceptible tomato inbred lines before and after Rs inoculation. RESULTS: In total, 75.02 Gb of high-quality reads were generated from 12 RNA-seq libraries. A total of 1,312 differentially expressed genes (DEGs) were identified, including 693 up-regulated and 621 down-regulated genes. Additionally, 836 unique DEGs were obtained when comparing two tomato lines, including 27 co-expression hub genes. A total of 1,290 DEGs were functionally annotated using eight databases, most of which were found to be involved in biological pathways such as DNA and chromatin activity, plant-pathogen interaction, plant hormone signal transduction, secondary metabolite biosynthesis, and defense response. Among the core-enriched genes in 12 key pathways related to resistance, 36 genotype-specific DEGs were identified. RT-qPCR integrated analysis revealed that multiple DEGs may play a significant role in tomato response to Rs. In particular, Solyc01g073985.1 (NLR disease resistance protein) and Solyc04g058170.1 (calcium-binding protein) in plant-pathogen interaction are likely to be involved in the resistance. CONCLUSION: We analyzed the transcriptomes of both resistant and susceptible tomato lines during control and inoculated conditions and identified several key genotype-specific hub genes involved in a variety of different biological processes. These findings lay a foundation for better understanding the molecular basis by which resistant tomato lines respond to Rs.

[Genome-wide identification, sequence characteristic and expression analysis of heat shock factors (HSFs) in cucumber].

Heat shock factors (HSFs) are ubiquitous in eukaryotes with diversification in structural feature and biological function in plants. Based on the availability of whole cucumber genome sequences, we characterized the cucumber HSFs gene family which contains at least 21 members. Sequence alignments show that all HSFs possess a specific DNA binding domain (DBD). These HSFs genes are unevenly distributed in the seven cucumber chromosomes except for Csa026480 (located on Scaffold_repeat037858). Phylogenetic analysis shows that HSFs in cucumber could be divided into three families, in which family I included three categories (A, B and C). Phylogenetic tree also reveals nine pairs of orthologous genes and three pairs of paralogous genes, suggesting that HSFs gene family have existed before the separation of cucumber and Arabidopsis thaliana. EST analysis shows that cucumber HSFs may be involved in the development of fruit, female flower and hermaphrodite flower. qRT-PCR analysis demonstrated that these genes exhibit different expression levels in heat stress treatment. These results will provide a foundation for the functions of the HSF gene family.

Comparative identification of WRKY transcription factors and transcriptional response to Ralstonia solanacearum in tomato.

In order to study the responses of tomato (Solanum lycopersicum) WRKY TFs to bacterial wilt caused by Ralstonia solanacearum, the most up-to-date genomes and transcriptional profiles were used to identify WRKY TFs in control and infected inbred lines. In total, 85 tomato WRKY TFs were identified and categorized into groups I, IIa + b, IIc, IId + e, and III. These WRKYs, especially those from group IIe, were mainly distributed at chromosome ends and in clusters. More than 45 % and 70 % of tomato WRKYs exhibited intraspecific and interspecific synteny, respectively. Nearly 60 % of tomato WRKYs (mainly in groups I and IIc) formed 73 pairs of orthologs with WRKYs in Arabidopsis and pepper, with Ka/Ks less than 1. Sixteen tomato WRKYs (mainly in groups IIa + b and IIc) responded strongly to biotic stress, and 12 differentially expressed WRKYs (mainly in groups III and IIb) were identified. RT-qPCR revealed that tomato WRKYs could respond to bacterial wilt through positive (predominant) or negative regulation. In particular, the interaction between Solyc03g095770.3 (group III) and Solyc09g014990.4 (group I) may play an important role. In brief, WRKY TFs were comprehensively identified in tomato and several bacterial wilt responsive genes were screened.

Thermoelectric Cu12 Sb4 S13 -Based Synthetic Minerals with a Sublimation-Derived Porous Network.

Pores in a solid can effectively reduce thermal conduction, but they are not favored in thermoelectric materials due to simultaneous deterioration of electrical conductivity. Conceivably, creating a porous structure may endow thermoelectric performance enhancement provided that overwhelming reduction of electrical conductivity can be suppressed. This work demonstrates such an example, in which a porous structure is formed leading to a significant enhancement in the thermoelectric figure of merit (zT). By a unique BiI3 sublimation technique, pore networks can be introduced into tetrahedrite Cu12 Sb4 S13 -based materials, accompanied by changes in their hierarchical structures. The addition of a small quantity of BiI3 (0.7 vol%) results in a ≈72% reduction in the lattice thermal conductivity, whereas the electrical conductivity is improved due to unexpected enhanced carrier mobility. As a result, an enhanced zT of 1.15 at 723 K in porous tetrahedrite and a high conversion efficiency of 6% at ΔT = 419 K in a fabricated segmented single-leg based on this porous material are achieved. This work offers an effective way to concurrently modulate the electrical and thermal properties during the synthesis of high-performance porous thermoelectric materials.

Phylogenetic Relationship of Plant MLO Genes and Transcriptional Response of MLO Genes to Ralstonia solanacearum in Tomato.

As a broad-spectrum disease resistance factor, MLO is involved in a variety of biotic and abiotic stress responses in plants. To figure out the structural features, phylogenetic relationships, and expression patterns of MLO genes, we investigated the genome and transcriptome sequencing data of 28 plant species using bioinformatics tools. A total of 197 MLO genes were identified. They possessed 5-7 transmembrane domains, but only partially contained a calmodulin-binding domain. A total of 359 polymorphic sites and 142 haplotypes were found in 143 sequences, indicating the rich nucleotide diversity of MLO genes. The MLO genes were unevenly distributed on chromosomes or scaffolds and were mainly located at the ends, forming clusters (24.1% genes), tandem duplicates (5.7%), and segment duplicates (36.2%). The MLO genes could be classified into three groups by phylogenetic analysis. The angiosperm genes were mainly in subgroup IA, Selaginella moellendorffii genes were in subgroup IA and IIIB, Physcomitrella patens genes were in subgroup IB and IIIA, and almost all algae genes were in group II. About half of the MLO genes had homologs within and across species. The Ka/Ks values were all less than 1, varying 0.01-0.78, suggesting that purifying selection had occurred in MLO gene evolution. In tomato, RNA-seq data indicated that SlMLO genes were highly expressed in roots, followed by flowers, buds, and leaves, and also regulated by different biotic stresses. qRT-PCR analysis revealed that SlMLO genes could respond to tomato bacterial wilt, with SlMLO1, SlMLO2, SlMLO4, and SlMLO6 probably involved in the susceptibility response, whereas SlMLO14 and SlMLO16 being the opposite. These results lay a foundation for the isolation and application of related genes in plant disease resistance breeding.