SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D1623 - D1632

Published: Nov. 11, 2024

The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements sequencing technologies. However, existing databases are limited by incomplete species representation, lack of comprehensive comparative tools the absence systematic pan-genomic analyses. To address these gaps, we developed Information Resource (SoIR, https://soir.bio2db.com), genomics database for family. SoIR integrates from 81 transcriptomic 41 species, encompassing total 3 908 408 gene annotations derived Gene Ontology, nonredundant protein, Pfam, Swiss-Prot TrEMBL databases. resource also 437 115 CRISPR guide sequences, 212 395 transcription factors 19 086 genes associated with methylation modification. In addition species-specific analyses, provides extensive bioinformatics investigating family evolution, phylogenetic relationships karyotype reconstruction across 25 fully sequenced genomes. With advanced Blast, Synteny Sequence Alignment, platform users interactive intuitive visualizations conducting cross-species genomics. As first entire facilitates in-depth analysis, supporting global research initiatives plant functional crop improvement.

Language: Английский

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Genome-wide association study of salicylic acid provides genetic insights for tea plant selective breeding

Horticulture Research, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

Salicylic acid (SA) is a phenolic phytohormone widely believed to regulate plant growth and stress response. Despite its significance, the genetic basis of SA-mediated resistance biotic stressors in tea plants little understood. Our study investigated diversity, population structure, linkage disequilibrium (LD) patterns 299 accessions using 79 560 high-quality single nucleotide polymorphisms (SNPs) obtained from genotyping-by-sequencing (GBS) data. genome-wide association identified CSS0033791.1, an essential gene encoding 9-cis-epoxycarotenoid dioxygenase (CsNCED1), which catalyzes vital step abscisic (ABA) biosynthesis. Exogenous ABA treatment transgenic overexpression CsNCED1 lowered SA content respective by inhibiting expression ICS gene. Further analysis revealed that could reduce levels receptor (NPR1) NPR1 target genes (PR1 WRKY18), increasing plant's susceptibility stressors. Furthermore, feeding behavior Spodoptera litura insect bite area on leaves was substantially more extensive than wild type (WT), implying had negative regulatory role immune This thus provides foundation for future breeding, sustainable resource usage, molecular marker-assisted (MAS) breeding.

Language: Английский

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A Comprehensive Evolutionary Analysis of the Dihydroflavonol 4-Reductase (DFR) Gene Family in Plants: Insights from 237 Species

Genes, Journal Year: 2025, Volume and Issue: 16(4), P. 396 - 396

Published: March 29, 2025

Background: Dihydroflavonol 4-reductase (DFR) is a key enzyme in the flavonoid biosynthetic pathway that regulates anthocyanin and proanthocyanidin accumulation plants. Although DFR genes have been studied various species, their origin of gene family, its distribution across plant kingdom, reasons behind emergence different subtypes Methods: This study performed whole-genome analysis 237 including algae, mosses, ferns, gymnosperms, angiosperms, integrating phylogeny, conserved motifs, duplication mechanisms, positive selection, expression pattern analyses. Results: These results indicate family originated from common ancestor extant ferns seed plants, asparagine (Asn)-type aspartic (Asp)-type DFRs associated with gymnosperms. Notably, we report for first time presence Asn-type, Asp-type, arginine (Arg)-type some which breaks previous notion Arg-type are exclusive to ferns. Tandem considered primary driving force expansion formation subtypes. Furthermore, Asn-type were highly expressed during early stages development, suggesting important role development. Conclusions: Overall, this revealed dynamic evolutionary trajectory providing theoretical foundation future research on genes.

Language: Английский

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Genome-Wide Identification of the ARF Gene Family in Safflower (Carthamus tinctorius L.) and Their Response Patterns to Exogenous Hormone Treatments

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3773 - 3773

Published: April 16, 2025

Auxin response factors (ARFs) are a class of transcription widely present in plants. As an important economic crop, research on the effects safflower ARFs endogenous auxin and effective components is relatively limited. In this study, total 23 ARF genes were identified from genome. Sequence alignment domain analysis indicated presence conserved B3 Auxin_resp domains these ARFs. Phylogenetic that CtARF could be classified into five subfamilies, conclusion also supported by gene structure, consensus motifs, compositions. Transcriptome data showed expressed all flower colors, but expression levels family members vary among different colors. CtARF19 had higher deep red flowers, CtARF3 white CtARF2/12 yellow CtARF21/22 light flowers. Protein–protein interaction network (CtARF2/3/4/5/15/18/19/22) located within network. Cis-acting element suggested may regulated hormone treatment (AuxRR-core) abiotic stress, results qRT-PCR confirmed this. Additionally, content active with colors significantly changed upon hormones affect IAA content. summary, our study provides valuable insights biological functions under exogenous conditions their components.

Language: Английский

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Identification, molecular evolution, codon bias, and expansion analysis of NLP transcription factor family in foxtail millet (Setaria italica L.) and closely related crops

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: May 21, 2024

The NODULE-INCEPTION-like protein (NLP) family is a plant-specific transcription factor (TF) involved in nitrate transport and assimilation plants, which are essential for improving plant nitrogen use efficiency. Currently, the molecular nature evolutionary trajectory of NLP genes C4 model crop foxtail millet unknown. Therefore, we performed comprehensive analysis evolution by scanning genomes representative species kingdom. We identified seven genome, all individually separately distributed on different chromosomes. They were not structurally identical to each other mainly expressed root tissues. unearthed two key ( Si5G004100.1 Si6G248300.1 ) with variety excellent characteristics. Regarding its evolution, found that Gramineae underwent dispersed duplication, but maize generated via WGD events. Other factors such as base mutations natural selection have combined promote genes. Intriguingly, plants showed gradual expansion during more duplications than losses, contrary most gene families. In conclusion, this study advances genetic resources understanding cereals.

Language: Английский

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Genome-Wide Identification and Characterization of the Aux/IAA Gene Family in Strawberry Species

Plants, Journal Year: 2024, Volume and Issue: 13(20), P. 2940 - 2940

Published: Oct. 21, 2024

Auxin is the first plant hormone found to play a dominant role in fruit growth, from set ripening. Strawberry plants represent suitable model for studying auxin's biosynthesis, sensing, and signaling machinery.

Language: Английский

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Genome-wide characterization of auxin response factor (ARF) genes in bermudagrass and ectopically functional analysis of CdARF6-B2 gene in Arabidopsis

Physiology and Molecular Biology of Plants, Journal Year: 2024, Volume and Issue: 30(12), P. 1969 - 1981

Published: Dec. 1, 2024

Language: Английский

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