Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris

CRISPR/Cas9-mediated mutagenesis of FT/TFL1 in petunia improves plant architecture and early flowering

Petunias are renowned ornamental species widely cultivated as pot plants for their aesthetic appeal both indoors and outdoors. The preference for pot plants depends on their compact growth habit and abundant flowering. While genome editing has gained significant popularity in many crop plants in addressing growth and development and abiotic and biotic stress factors, relatively less emphasis has been placed on its application in ornamental plant species. Genome editing in ornamental plants opens up possibilities for enhancing their aesthetic qualities, offering innovative opportunities for manipulating plant architecture and visual appeal through precise genetic modifications. In this study, we aimed to optimize the procedure for an efficient genome editing system in petunia plants using the highly efficient multiplexed CRISPR/Cas9 system. Specifically, we targeted a total of six genes in Petunia which are associated with plant architecture traits, two paralogous of FLOWERING LOCUS T (PhFT) and four TERMINAL FLOWER-LIKE1 (PhTFL1) paralogous genes separately in two constructs. We successfully induced homogeneous and heterogeneous indels in the targeted genes through precise genome editing, resulting in significant phenotypic alterations in petunia. Notably, the plants harboring edited PhTFL1 and PhFT exhibited a conspicuously early flowering time in comparison to the wild-type counterparts. Furthermore, mutants with alterations in the PhTFL1 demonstrated shorter internodes than wild-type, likely by downregulating the gibberellic acid pathway genes PhGAI, creating a more compact and aesthetically appealing phenotype. This study represents the first successful endeavor to produce compact petunia plants with increased flower abundance through genome editing. Our approach holds immense promise to improve economically important potting plants like petunia and serve as a potential foundation for further improvements in similar ornamental plant species.

Comparative transcriptome analysis reveals lineage- and environment-specific adaptations in cacti from the Brazilian Atlantic Forest

MAIN CONCLUSION

Natural selection influenced adaptive divergence between Cereus fernambucensis and Cereus insularis, revealing key genes governing abiotic stress responses and supporting neoteny in C. insularis. Uncovering the molecular mechanisms driving adaptive divergence in traits related to habitat adaptation remains a central challenge. In this study, we focused on the cactus clade, which includes Cereus sericifer F.Ritter, Cereus fernambucensis Lem., and Cereus insularis Hemsley. These allopatric species inhabit distinct relatively drier regions within the Brazilian Atlantic Forest, each facing unique abiotic conditions. We leveraged whole transcriptome data and abiotic variables datasets to explore lineage-specific and environment-specific adaptations in these species. Employing comparative phylogenetic methods, we identified genes under positive selection (PSG) and examined their association with non-synonymous genetic variants and abiotic attributes through a PhyloGWAS approach. Our analysis unveiled signatures of selection in all studied lineages, with C. fernambucensis northern populations and C. insularis showing the most PSGs. These PSGs predominantly govern abiotic stress regulation, encompassing heat tolerance, UV stress response, and soil salinity adaptation. Our exclusive observation of gene expression tied to early developmental stages in C. insularis supports the hypothesis of neoteny in this species. We also identified genes associated with abiotic variables in independent lineages, suggesting their role as environmental filters on genetic diversity. Overall, our findings suggest that natural selection played a pivotal role in the geographic range of these species in response to environmental and biogeographic transitions.

Network interactions with functional roles and evolutionary relationships for BURP domain-containing proteins in chickpea and model species

The functional significance and evolutionary relationships of BURP domain-containing genes unique to plants is of interest. Network analysis reveals different associations of BURP proteins with other proteins and functional terms, throwing light on their involvement in various biological processes and pathways. The gene expression data reveals that BURP genes are affected by salinity stress, reflecting diverse expression patterns in roots and shoots.

Genome-wide identification and expression analysis of the BURP domain-containing genes in Malus domestica

The conserved BURP-containing proteins are specific to plants and play a crucial role in plant growth, development, and response to abiotic stresses. However, less is known about the systematic characterization of BURP-containing proteins in apple. This study aimed to identify and analyze all BURP-containing genes in the apple genome, as well as to examine their expression patterns through various bioinformatics methods. Eighteen members of BURP-containing genes were identified in apple, six members lacked signal peptides, and the secondary structure was mainly a Random coil of BURP-containing genes. Gene structure and Motif analysis showed that proteins have similar structures and are conserved at the C-terminal. Cis-acting element analysis revealed that the proteins contain phytohormone and stress response elements, and chromosomal localization revealed that the family is unevenly distributed across eight chromosomes, with duplication of fragments leading to the expansion of family proteins. Tissue expression showed that MdPG3 and MdPG4 were expressed in different tissues and different varieties, MdRD2 and MdRD7 were highly expressed in 'M74' fruits and MdRD7 in 'M49' leaves, while MdUSP1 was highly expressed in 'GD' roots. The quantitative real-time PCR analysis showed that the expressions of six and seven genes were significantly up-regulated under NaCl and PEG treatments, respectively, whereas MdRD7 was significantly up-regulated under NaCl and PEG treatment over time. This study offers a comprehensive identification and expression analysis of BURP-containing proteins in apple. The findings provide a theoretical foundation for further exploration of the functions of this protein family.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01393-7.

Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.

Investigation and Expression Analysis of R2R3-MYBs and Anthocyanin Biosynthesis-Related Genes during Seed Color Development of Common Bean (Phaseolus vulgaris)

Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks  <  1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume.

Identification and expression analysis of BURP domain-containing genes in jujube and their involvement in low temperature and drought response

Background

Plant-specific BURP domain-containing genes are involved in plant development and stress responses. However, the role of BURP family in jujube (Ziziphus jujuba Mill.) has not been investigated.

Results

In this study, 17 BURP genes belonging to four subfamilies were identified in jujube based on homology analysis, gene structures, and conserved motif confirmation. Gene duplication analysis indicated both tandem duplication and segmental duplication had contributed to ZjBURP expansion. The ZjBURPs were extensively expressed in flowers, young fruits, and jujube leaves. Transcriptomic data and qRT-PCR analysis further revealed that ZjBURPs also significantly influence fruit development, and most genes could be induced by low temperature, salinity, and drought stresses. Notably, several BURP genes significantly altered expression in response to low temperature (ZjPG1) and drought stresses (ZjBNM7, ZjBNM8, and ZjBNM9).

Conclusions

These results provided insights into the possible roles of ZjBURPs in jujube development and stress response. These findings would help selecting candidate ZjBURP genes for cold- and drought-tolerant jujube breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08907-9.