Calcineurin B-like protein (CBL)-CBL-interacting protein kinase (CIPK) network is one of the vital regulatory mechanisms which decode calcium signals triggered by environmental stresses. Although the complicated regulation mechanisms and some novel functions of CBL-CIPK signaling network in plants need to be further elucidated, numerous advances have been made in its roles involved in the abiotic stresses. This review chiefly introduces the progresses about protein interaction, classification and expression pattern of different CBLs and CIPKs in Arabidopsis thaliana, summarizes the physiological roles of CBL-CIPK pathway while pointing out some new research ideas in the future, and finally presents some unique perspectives for the further study. The review might provide new insights into the functional characterization of CBL-CIPK pathway in Arabidopsis, and contribute to a deeper understanding of CBL-CIPK network in other plants or stresses.

The NAC family is one of the largest families of plant-specific transcription factors (TFs) and NAC proteins play important regulatory roles in a variety of developmental and stress response processes in plants. Members of the NAC family TFs have been shown to be important regulators of leaf senescence in a number of plant species. Here we report the identification of the NAC family in tobacco (Nicotiana tabacum) and characterization of the potential role of some of the tobacco NAC TFs in regulating leaf senescence. A total of 154 NAC genes (NtNACs) were identified and clustered together with the Arabidopsis NAC family into fifteen groups (a-o). Transcriptome data analysis followed by qRT-PCR validation showed that the majority of the senescence-up-regulated NtNACs fall into subgroups NAC-b and f. A number of known senescence regulators from Arabidopsis also belong to these two subgroups. Among these senescence-up-regulated NtNACs, NtNAC080, a close homolog of AtNAP, is a positive regulator of leaf senescence. Overexpression of NtNAC080 caused early senescence in Arabidopsis leaves and NtNAC080 mutation induced by Cas9/gRNA in tobacco led to delayed leaf senescence.

Genetic map is a linear arrangement of the relative positions of sites in the chromosome or genome based on the recombination frequency between genetic markers. It is the important basis for genetic analysis. Several kinds of software have been designed for genetic mapping, but all these tools require users to write or edit code, making it time-costing and difficult for researchers without programming skills to handle with. Here, MG2C, a new online tool was designed, based on PERL and SVG languages.Users can get a standard genetic map, only by providing the location of genes (or quantitative trait loci) and the length of the chromosome, without writing additional code. The operation interface of MG2C contains three sections: data input, data output and parameters. There are 33 attribute parameters in MG2C, which are further divided into 8 modules. Values of the parameters can be changed according to the users’ requirements. The information submitted by users will be transformed into the genetic map in SVG file, which can be further modified by other image processing tools.MG2C is a user-friendly and time-saving online tool for drawing genetic maps, especially for those without programming skills. The tool has been running smoothly since 2015, and updated to version 2.1. It significantly lowers the technical barriers for the users, and provides great convenience for the researchers.

Members of the plant-specific B3 transcription factor superfamily play important roles in various growth and developmental processes in plants. Even though there are many valuable studies on B3 genes in other species, little is known about the B3 superfamily in tobacco. We identified 114 B3 proteins from tobacco using comparative genome analysis. These proteins were classified into four subfamilies based on their phylogenetic relationships, and include the ARF, RAV, LAV, and REM subfamilies. The chromosomal locations, gene structures, conserved protein motifs, and sub-cellular localizations of the tobacco B3 proteins were analyzed. The patterns of exon-intron numbers and arrangement and the protein structures of the tobacco B3 proteins were in general agreement with their phylogenetic relationships. The expression patterns of 114 B3 genes revealed that many B3 genes show tissue-specific expression. The expression levels of B3 genes in axillary buds after topping showed that the REM genes are mainly up-regulated in response to topping, while the ARF genes are down-regulated after topping.

Cadmium (Cd) is known as one of the most hazardous elements in the environment and a persistent soil constraint toxic to all flora and fauna. In this study, we conducted physiological, biochemical, and transcriptomic analyses of Nicotiana rustica (N. rustica) and Nicotiana tabacum (N. tabacum) treated with CdCl2 to know the underlying molecular mechanisms of Cd accumulation. As a result, N. rustica had more dry weight than N. tabacum. Additionally, N. rustica accumulated higher Cd concentration (69.65 times), Cd2+ influx (1.32‐fold), glutathione S‐transferases (GST) enzyme activity (2.54 times), GSH/GSSG (oxidized form of GSH) ratio, increase of superoxide dismutase and CAT and a lower H2O2 and superoxide (O2•−) accumulation in their roots than N. tabacum. Cd mainly distributed in the cytoplasm of both species and N. rustica had a significant proportion in the cell wall. Furthermore, the transcriptomic analysis revealed 173 and 710 differentially expressed genes (DEGs) between control and Cd‐stressed plants in the leaves and roots of N. rustica, while 576 and 1543 DEGs were found in the leaves and roots of N. tabacum, respectively. In N. rustica, phenylpropanoid biosynthesis and phenylalanine metabolism were the most enriched pathways, while GSH metabolism, ATP‐binding cassette transporters and phenylpropanoid biosynthesis were the most enriched in N. tabacum. Finally, we found that DEGs related to metal influx, sequestration, remobilization, and chelation were responsible for Cd accumulation. These results indicated that N. rustica accumulated higher Cd content than N. tabacum, suggesting that each species utilized different response mechanism under the same Cd stress conditions. The DEGs identified in this study might lead to the identification of genes or pathways related to Cd regulation. This study identifies important regulators related to Cd accumulation.

The basic leucine zipper (bZIP) transcription factors play important regulatory roles, influencing plant growth and responses to environmental stresses. In the present study, 132 bZIP genes identified in the tobacco genome were classified into 11 groups with Arabidopsis and tomato bZIP members, based on the results of a phylogenetic analysis. An examination of gene structures and conserved motifs revealed relatively conserved exon/intron structures and motif organization within each group. The results of an investigation of whole-genome duplication events indicated that segmental duplications were crucial for the expansion of the bZIP gene family in tobacco. Expression profiles confirmed that the NtbZIP genes are differentially expressed in various tissues, and several genes are responsive to diverse stresses. Notably, NtbZIP62, which was identified as an AtbZIP37/ABF3 homolog, was highly expressed in response to salinity. Subcellular localization analyses proved that NtbZIP62 is a nuclear protein. Furthermore, the overexpression of NtbZIP62 in tobacco significantly enhanced the salt stress tolerance of the transgenic plants. The results of this study may be relevant for future functional analyses of the bZIP genes in tobacco.

BackgroudHorizontal gene transfer and gene duplication are two major mechanisms contributing to the evolutionary adaptation of organisms. Previously, polygalacturonase genes (PGs) were independently horizontally transferred and underwent multiple duplications in insects (e.g., mirid bugs and beetles). Here, we chose three phytozoophagous mirid bugs (Adelphocoris suturalis, A. fasciaticollis, A. lineolatus) and one zoophytophagous mirid bug (Nesidiocoris tenuis) to detect whether the duplication, molecular evolution, and expression levels of PGs were related to host range expansion in mirid bugs.ResultsBy RNA-seq, we reported 30, 20, 19 and 8 PGs in A. suturalis, A. fasciaticollis, A. lineolatus and N. tenuis, respectively. Interestingly, the number of PGs was significantly positive correlation to the number of host plants (P = 0.0339) in mirid bugs. Most PGs (> 17) were highly expressed in the three phytozoophagous mirid bugs, while only one PG was relatively highly expressed in the zoophytophagous mirid bug. Natural selection analysis clearly showed that a significant relaxation of selection pressure acted on the PGs in zoophytophagous mirid bugs (K = 0.546, P = 0.0158) rather than in phytozoophagous mirid bugs (K = 1, P = 0.92), suggesting a function constraint of PGs in phytozoophagous mirid bugs.ConclusionTaken together with gene duplication, molecular evolution, and expression levels, our results suggest that PGs are more strictly required by phytozoophagous than by zoophytophagous mirid bugs and that the duplication of PGs is associated with the expansion of host plant ranges in mirid bugs.Electronic supplementary materialThe online version of this article (10.1186/s12862-019-1351-1) contains supplementary material, which is available to authorized users.

The complete genome of a novel virus from Nesidiocoris tenuis was determined by RNA-seq and rapid amplification of cDNA ends. This virus has a single-stranded RNA genome of 10633 nucleotides (nt) in length, not including the poly(A) tail, and contains two putative open reading frames (ORFs). ORF1 encodes a polypeptide of 1320 amino acids (aa) with a predicted molecular mass of 147.92 kDa and theoretical isoelectric point (pI) of 6.96. ORF2 encodes a polypeptide of 1728 aa with a predicted molecular mass of 197.09 kDa and pI of 6.73. Phylogenetic analysis with the deduced aa sequences of the conserved RNA dependent RNA polymerase domain as well as whole genome nt sequences indicated that the virus clusters with viruses classified within the genus Iflavirus, with a high bootstrap value in the maximum-likelihood and neighbor-joining trees. However, this virus has a distinct genome structure with two ORFs, iflaviruses normally having one, suggesting the virus might be a prototype of a new genus. We named the virus isolate Nesidiocoris tenuis virus 1 (NtV-1). The prevalence of NtV-1 infection in wild samples of N. tenuis was at a low level (7.32%, 6 positive in 82 samples), suggesting a possible harmful effect to its host.