Genome-wide identification and functional analyses of calmodulin genes in Solanaceousspecies

Abstract

BackgroundCalmodulin (CaM) is a major calcium sensor in all eukaryotes. It binds calcium and modulates the activity of a wide range of downstream proteins in response to calcium signals. However, little is known about the CaM gene family in Solanaceous species, including the economically important species, tomato (Solanum lycopersicum), and the gene silencing model plant, Nicotiana benthamiana. Moreover, the potential function of CaM in plant disease resistance remains largely unclear.ResultsWe performed genome-wide identification of CaM gene families in Solanaceous species. Employing bioinformatics approaches, multiple full-length CaM genes were identified from tomato, N. benthamiana and potato (S. tuberosum) genomes, with tomato having 6 CaM genes, N. benthamiana having 7 CaM genes, and potato having 4 CaM genes. Sequence comparison analyses showed that three tomato genes, SlCaM3/4/5, two potato genes StCaM2/3, and two sets of N. benthamiana genes, NbCaM1/2/3/4 and NbCaM5/6, encode identical CaM proteins, yet the genes contain different intron/exon organization and are located on different chromosomes. Further sequence comparisons and gene structural and phylogenetic analyses reveal that Solanaceous species gained a new group of CaM genes during evolution. These new CaM genes are unusual in that they contain three introns in contrast to only a single intron typical of known CaM genes in plants. The tomato CaM (SlCaM) genes were found to be expressed in all organs. Prediction of cis-acting elements in 5' upstream sequences and expression analyses demonstrated that SlCaM genes have potential to be highly responsive to a variety of biotic and abiotic stimuli. Additionally, silencing of SlCaM2 and SlCaM6 altered expression of a set of signaling and defense-related genes and resulted in significantly lower resistance to Tobacco rattle virus and the oomycete pathogen, Pythium aphanidermatum.ConclusionsThe CaM gene families in the Solanaceous species tomato, N. benthamiana and potato were identified through a genome-wide analysis. All three plant species harbor a small set of genes that encode identical CaM proteins, which may manifest a strategy of plants to retain redundancy or enhanced quantitative gene function. In addition, Solanaceous species have evolved one new group of CaM genes during evolution. CaM genes play important roles in plant disease resistance to a variety of pathogens.

Characterization and Expression Profiling Analysis of Calmodulin Genes in Response to Salt and Osmotic Stresses in Pear (Pyrus bretschneideriRehd.) and in Comparison withArabidopsis

“…These results revealed that the orthologous expansion of these subfamily members is highly restricted, especially in group I, which may possess more conserved functions. Interestingly, all CaM genes in pear were disrupted by the first intron at the Gly26 codon, which has been previously reported in Arabidopsis and solanaceous CaMs [7, 26]. The majority of the first intron is located in the region of the EF-hand 1, while the second exon encodes multiple EF-hands (Figure 2).…”

“…Due to the multiple functions of CaMs and the increase in the availability of sequenced plant genomes, many CaM genes have been identified at the whole genome level in several plant species including Arabidopsis [5, 7], rice [25], and several species in the Solanaceae family [26]. Pear ( Pyrus bretschneideri ), a species within Rosaceae, is cultivated worldwide as a fruit tree, whose growth, development, and productivity are frequently affected by abiotic stress, such as salinity and drought [27].…”

Characterization and Functional Analysis of Calmodulin and Calmodulin-Like Genes in Fragaria vesca

“…Transient over-expression of Capsicum annuum calmodulin 1 ( CaCaM1 ) activated the ROS burst and NO generation, and it induced HR-like cell death in pepper leaves (Choi et al, 2009). Silencing of Solanum lycopersicum SICaM2 and SICaM6 resulted in reduced resistance to Tobacco rattle virus and the oomycete pathogen, Pythium aphanidermatum , via VIGS (Zhao et al, 2013). Accordingly, we transiently expressed five FvCaM and FvCML genes in N. benthamiana leaves and exposed them to both the presence (Ca 2+ treatment) and absence (EGTA treatment) of Ca 2+ .…”

Genome-Wide Identification of Dicer-Like, Argonaute, and RNA-Dependent RNA Polymerase Gene Families in Brassica Species and Functional Analyses of Their Arabidopsis Homologs in Resistance to Sclerotinia sclerotiorum

“…Real-time quantitative PCR (RT-qPCR) was carried out using SYBR Premix Ex Taq (TakaRa, China) on StepOne Real-Time PCR System (ABI, USA).The RT-qPCR analyses were conducted three times, with three replicates for each gene and the relative fold changes were calculated using the 2 −ΔΔCt method as described (Zhao et al, 2013). A B. napus elongation factor gene was used as the reference gene and primers used for RT-qPCR are listed in Table S2.…”