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opencc-zeroJan 2022View details →

Data from: Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane

Sugarcane (Saccharum spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes, two MOTHER OF FT AND TFL (MFT)-like genes, and four TERMINAL FLOWER (TFL)-like genes. As expected, these genes all show very high homology to their corresponding genes in Sorghum, and also to FT-like, MFT-like, and TFL-like genes in maize, rice, and Arabidopsis. Functional analysis in Arabidopsis showed that the sugarcane ScFT3 gene can rescue the late flowering phenotype of the Arabidopsis ft-10 mutant, whereas ScFT5 cannot. High expression levels of ScFT3 in leaves of short day-induced sugarcane plants coincided with initial stages of floral induction in the shoot apical meristem as shown by histological analysis of meristem dissections. This suggests that ScFT3 is likely to play a role in floral induction in sugarcane; however, other sugarcane FT-like genes may also be involved in the flowering process.

zenodo36/100

Dataset of gene family analysis for Gekko japonicus and other sauropsids

We assembled a chromosome-level genome of Gekko japonicus and then performed a series of gene family analyses on it and other representative sauropsids generated a dataset containing predicted sequences, sequence alignments and phylogenetic trees of the corresponding genes.

opencc-by-4.0Oct 2022View details →

opencc-zeroMay 2023View details →

Comparative genomic analysis of chemosensory-related gene families in gastropods

Chemoreception is critical for the survival and reproduction of animals. Except for a reduced group of insects and spiders, the molecular identity of chemosensory proteins is poorly understood in invertebrates. Gastropoda is the extant mollusk class with the greatest species richness, including marine, freshwater, and terrestrial lineages, and likely, highly diverse chemoreception systems. Here, we performed a comprehensive comparative genome analysis taking advantage of the chromosome-level information of two Gastropoda species, one of which belongs to a lineage that underwent a whole genome duplication event. We identified thousands of previously uncharacterized chemosensory-related genes, the majority of them encoding G protein-coupled receptors (GPCR), mostly organized into clusters distributed across all chromosomes. We also detected gene families encoding degenerin epithelial sodium channels (DEG-ENaC), ionotropic receptors (IR), sensory neuron membrane proteins (SNMP), Niemann–Pick type C2 (NPC2) proteins, and lipocalins, although much smaller in size. Our phylogenetic analysis of the GPCR gene family across protostomes revealed: (i) large gene family expansions in Gastropoda; (ii) clades including members from all protostomes; and (iii) species-specific clades with a huge number of receptors. For the first time, we provide new and valuable knowledge into the evolution of the chemosensory gene families in invertebrates other than arthropods.

publicMay 2023View details →

Comparative genomic analysis of chemosensory-related gene families in gastropods

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publicJan 2022View details →

Data from: Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane

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dryad32/100

cDNA sequence of E2 gene family in Arabidopsis thaliana and data of statistical analysis

E2 ubiquitin-conjugating enzymes act as a heart role in the ubiquitination process and are responsible for catalysis ubiquitin transfer. Although the function of ubiquitin-protein ligases (E3s) in plant response to diverse abiotic stress by targeting specific substrates has been well studied, the E2s' involvement in environmental responses and their downstream targets are not well understood. Here, we demonstrated that the E2 ubiquitin-conjugating enzyme 18 (UBC18) regulates the stability of FREE1 to modulate iron deficiency stress. UBC18 affects the ubiquitination of FREE1 and promotes its degradation, overexpression of UBC18 in plants decreases their sensitivity to iron deficiency by reducing the level of FREE1, and high accumulation of FREE1 in the ubc18 mutant resulted in sensitivity to iron deficiency. In addition, we demonstrated the lysine residues K227, K295, K315, and K540 are required for FREE1 ubiquitination and stability regulation, and mutation of these lysines of FREE1 residues resulted in sensitivity to iron starvation in plants. Taken together, our findings reveal a mechanism of UBC18 in response to iron deficiency stress by altering the abundance of FREE1, and further elucidate the role of ubiquitination sites in FREE1 stability regulation and the plant iron deficiency response.

opencc-zeroJan 2024View details →

Fig. 9 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 9. Effects of hypoxic treatment on earlier responses of gene expression. Relative transcript levels calculated by real-time RT-PCR using DcUbq3-7 as a standard were compared before (black bars) and after 3 or 12 h of incubation under normoxic (gray bars) and hypoxic (white bars) conditions. Significant differences (P <0.05) detected by Tukey's multiple comparison test are indicated by different letters above the bars.

Fig. 5 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 5. Phylogenetic tree of sucrose synthase (SUS). Amino acid sequences deduced from SUS genes of Arabidopsis, rice, and carnation, distinguished by AGI ID, locus identifier, or ORF no. shown in parentheses, were aligned by ClustalW. The tree was constructed by the neighbor-joining method using MEGA7.0 software. * indicates carnation SUS described in this study.

Fig. 8 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 8. Expression profiles of sucrose synthase (SUS) gene family of carnation in petals under sucrose and hypoxic treatments. Relative transcript levels calculated by real-time RT-PCR using DcUbq3-7 as a standard were compared among petals after 24 h of incubation with distilled water (plain bars) or sucrose solution (hatched bars), under normoxic (gray bars) and hypoxic (white bars) conditions. Data are expressed as mean ± SE of three separate samples. The results of two-way analysis of variance (ANOVA) are shown below each graph; NS, *, and ** indicate not significant and significant at P <0.05 and P <0.01, respectively.

Fig. 7 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 7. Expression profiles of invertase (INV) gene family of carnation in petals under sucrose and hypoxic treatments. Relative transcript levels calculated by realtime RT-PCR using DcUbq3-7 as a standard were compared among petals after 24 h of incubation with distilled water (plain bars) or sucrose solution (hatched bars), under normoxic (gray bars) and hypoxic (white bars) conditions. Data are expressed as mean ± SE of three separate samples. The results of two-way analysis of variance (ANOVA) are shown below each graph; NS, *, and ** indicate not significant and significant at P <0.05 and P <0.01, respectively.

Fig. 6 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 6. Expression profiles of invertase (INV) and sucrose synthase (SUS) gene families of carnation among organs. Relative transcript levels of gene families of cellwall INV (A), vacuolar INV (B), cytoplasmic INV (C), and SUS (D) calculated by real-time RT-PCR using DcUbq3-7 as a standard were compared among leaves (dotted bars) and petals (black bars). The graph for the gene with an eminent value is shown as an inset. Data are expressed as mean ± SE of three separate samples. The result of Student's t-test is shown above the bars; NS, *, and ** indicate not significant and significant at P <0.05 and P <0.01, respectively.

Fig. 2 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 2. Sugar content in carnation petals. Contents of reducing sugars (A), sucrose (B), and starch (C) were compared among petals after 24 h of incubation following pretreatment with silver-thiosulfate (STS), and supplied with distilled water (plain bars) or sucrose solution (hatched bars), under normoxic (gray bars) and hypoxic (white bars) conditions. Data are expressed as mean ± SE of three separate samples. The results of two-way analysis of variance (ANOVA) are shown below each graph; NS, *, and ** indicate not significant and significant at P <0.05 and P <0.01, respectively. *** indicates significant difference at P <0.05 detected by Dunnett's test.

Fig. 1 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 1. Effects of chemical treatment on flower senescence of carnation. Carnation florets pretreated with silver-thiosulfate (STS) or incubated with sucrose (Suc, not pretreated with STS) were compared to non-pretreated control florets incubated with distilled water (DW).

Fig. 3 in Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.)

Fig. 3. Enzymatic activities of invertase (INV) and sucrose synthase (SUS) in carnation petals. Activities of cell-wall INV (A), vacuolar INV (B), cytoplasmic INV (C), and SUS (D) were compared among petals after 24 h of incubation following pretreatment with silver-thiosulfate (STS), and supplied with distilled water (plain bars) or sucrose solution (hatched bars), under normoxic (gray bars) and hypoxic (white bars) conditions. Data are expressed as mean ± SE of three separate samples. The results of two-way analysis of variance (ANOVA) are shown below each graph; NS and * indicate not significant and significant at P <0.05, respectively.

Fig. 7 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 7. Expression profiles analysis of OsFBNs under different temperature stresses. Eleven OsFBN genes in rice were detected for their transcript levels in leave tissues of seedlings at the three-leaf stage with different time intervals after the 35 ̊C (heat stress) and 6 ̊C (cold stress) stresses in the growth chamber, separately. The OsUBQ gene was used as a normalization control; data was measured as the mean values ± SD of three replicates, respectively.

Fig. 4 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 4. Phylogenetic and exon-intron structure analysis of FBN family genes in rice and Arabidopsis. The phylogenetic analysis was performed using the amino acid sequences of 25 FBN family proteins in rice and Arabidopsis (Left). The unrooted phylogenetic tree was generated by the neighbor-joining method and displayed using MEGA7 software. Numbers above or below branches of the evolution tree indicated the bootstrap values; The exon-intron structures of 25 FBN family genes in rice and Arabidopsis were analyzed (Right), the exons were represented by yellow boxes, the UTR by blue, black lines connecting two exons were introns. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 6. The in vitro lipid binding assays of PAP-domains. A and C, schematic representations of the mutant residues in OsFBN2 and OsFBN4 proteins in the in vitro lipid binding assays. B and D, the in vitro lipid-binding activity assays were performed by a fluorescence lipid probe P-96 (1 mM), fatty acids with C12:0, C14:0, C16:0, C18:0, C20:0, C22:0, with each (0.5 mM) of wild type (Wt) and mutant fusion protein (Mut) of PAP domains in OsFBN2 and OsFBN4 proteins, respectively. Detection experiments were performed with three biological replicates. * and ** symbols indicated the significant difference levels of P <0.05 or P <0.01 between mutant and wild type, respectively.

Fig. 5 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 5. Subcellular localization of CTP domains-fused GFP proteins. These constructs of p35S-FBN1-11-CTP-GFP or p35S-Trxm5-GFP, separately, were transiently expressed in Nicotiana benthamiana mesophyll cells. The co-localizations of fluorescence patterns of CTP domains of ten OsFBN proteins except OsFBN8 fused GFP were observed with the autofluorescence of chlorophyll in chloroplasts in protoplasts. The Trxm5-GFP was used as a chloroplast marker.

Fig. 3 in Phylogeny, structural diversity and genome-wide expression analysis of fibrillin family genes in rice

Fig. 3. PKC domain analysis of FBN11 clade in plants. A, Homology analysis of PKC domain sequences in FBN11 clades; B, evolutionary tree analysis of PKC domain in five plant species (Oryza sativa (Os), Selaginella moellendorffii (Smo), Arabidopsis thaliana (At), Glycine max (Gm), and Zea mays (Zm)) and algae (Monoraphidium neglectum (Mon), Chlorella sorokiniana (Chlo), Chlamydomonas sp. UWO 241 (Chla), and Haemato coccus lacustris (Hae); C, the conserved motif analysis of PKC domain in FBN11 protein clades in higher plants.