PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida DOI Creative Commons
Eugene Koh,

William Goh,

Irene Julca

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 22, 2023

Abstract The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ∼60,000 manually annotated RNA-seq samples, and more than four million genes. tool allows users explore the patterns of genes different organs, identify organ-specific genes, discover top co-expressed for any interest. PEO also functional annotations each gene, allowing identification genetic modules pathways. designed facilitate comparative kingdom-wide analysis provide valuable resource biology research. We two case studies demonstrate utility in identifying candidate pollen coat biosynthesis investigating biosynthetic pathway components capsaicin Capsicum annuum . database freely available at https://expression.plant.tools/

Language: Английский

Integration of metabolomics and transcriptomics reveals the regulation mechanism of the phenylpropanoid biosynthesis pathway in insect resistance traits in Solanum habrochaites DOI Creative Commons
Meiliang Wang, Yudan Wang, Xinzhi Li

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(2)

Published: Jan. 9, 2024

Abstract Solanum habrochaites (SH), a wild species closely related to ‘Ailsa Craig’ (AC), is an important germplasm resource for modern tomato breeding. Trichomes, developed from epidermal cells, have role in defense against insect attack, and their secretions are of non-negligible value. Here, we found that the glandular heads type VI trichomes were clearly distinguishable between AC SH under cryo-scanning electron microscopy, difference indicating could secrete more anti-insect metabolites than AC. Pest preference experiments showed aphids mites preferred feed near compared with SH. Integration analysis transcriptomics metabolomics data revealed phenylpropanoid biosynthesis pathway was secondary metabolic plants, secreted larger amounts phenylpropanoids flavonoids by upregulating expression relevant genes this pathway, may contribute greater resistance phytophagous insects. Notably, virus-induced silencing Sl4CLL6 not only decreased downstream (SlHCT, SlCAD, SlCHI), but also reduced tomato. These findings provided new genetic resources synthesis compounds breeding S. theoretical basis improvement traits cultivated

Language: Английский

Citations

19
Accelerating crop improvement via integration of transcriptome-based network biology and genome editing DOI
Izreen Izzati Razalli, Muhammad‐Redha Abdullah‐Zawawi, Amin Asyraf Tamizi

et al.

Planta, Journal Year: 2025, Volume and Issue: 261(4)

Published: March 17, 2025

Language: Английский

Citations

1
Research progress of engineering microbial cell factories for pigment production DOI

Shumin Xu,

Song Gao, Yingfeng An

et al.

Biotechnology Advances, Journal Year: 2023, Volume and Issue: 65, P. 108150 - 108150

Published: April 10, 2023

Language: Английский

Citations

16
Transcriptome-guided selection of reference genes from field-grown adult trees and seedlings exposed to defense phytohormones in Erythrina velutina DOI

Daisy Sotero Chacon,

Cibele Tesser da Costa, Fábio Antônio Antonelo

et al.

Plant Gene, Journal Year: 2025, Volume and Issue: 42, P. 100496 - 100496

Published: March 1, 2025

Language: Английский

Citations

0
Genome-wide identification and analysis of phosphate utilization related genes (PURs) reveal their roles involved in low phosphate responses in Brassica napus L. DOI Creative Commons

Yibing Shen,

Jiaqi Chen, Haijiang Liu

et al.

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: March 13, 2025

Phosphorus (P) is an essential macronutrient for Brassica napus L. growth and development, mainly acquired from the soil as phosphate (Pi). However, there no research on system analysis of Pi utilization related genes (PURs) in B. yet. In this study, 285 PURs were identified genome, including 4 transcription factor (TF) gene families (83 genes) 17 structural (202 genes). Subcellular localization showed that proteins encoded by located nucleus (~ 46.0%) cell membrane 36.5%). Chromosome suggested distributed An (131) Cn (149) subgenomes without bias. Analysis 35 representative species confirmed widely present plants ranging Chlorophyta to angiosperms with a rapid expansion trend. Collinearity revealed allopolyploidization small-scale duplication events resulted large PURs. For each pair PURs, sequence identity promoter was significantly lower than CDS, proving significant difference region might be divergence expression function. Transcription binding site prediction, cis-element analysis, microRNA prediction expressions are regulated multiple factors 32 TF (362), 108 types CRE (29,770) 25 miRNAs (66). Spatiotemporal demonstrated expressed during whole developmental stages, most synteny-gene pairs (76.42%) shared conserved patterns. RNA-seq analyses induced low stress, hub generally transporter (PHT) family members. qRT-PCR proved levels four positively correlated root architecture three varieties under supply at seedling stage. The strong LP inducible profile. Our findings regarding evolution, transcriptional regulation, provide valuable information further functional research.

Language: Английский

Citations

0
Simulation study of factors affecting the accuracy of transcriptome models under complex environments DOI

Dan Eiju,

Yoichi Hashida, Taro Maeda

et al.

Plant Molecular Biology, Journal Year: 2025, Volume and Issue: 115(2)

Published: March 28, 2025

Language: Английский

Citations

0
Comparative Transcriptome Reveals Conserved Gene Expression in Reproductive Organs in Solanaceae DOI Open Access
Lingkui Zhang,

Yipeng Chong,

Xiaolong Yang

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3568 - 3568

Published: April 10, 2025

The Solanaceae family, which includes key crops such as tomato, pepper, eggplant, wolfberry, and groundcherry, is distinguished by its diversity of fruit types. However, the conservation gene expression regulatory networks across different species remains poorly understood. This study utilizes comparative transcriptomics to analyze 293 transcriptome samples from 22 species, focusing on profiles reproductive organ (flower fruit)-specific genes. Our results reveal evolutionary in patterns these genes, particularly within pathways essential for plant reproduction. A detailed analysis between tomato pepper reveals common governing development. Furthermore, through co-expression network analysis, we identified functional partners YABBY flower/fruit development found that genes coordinate spatiotemporal dynamic expression, shaping role. These findings provide valuable insights can guide future research species.

Language: Английский

Citations

0
Gene Co-Expression Network Tools and Databases for Crop Improvement DOI Creative Commons
Rabiatul‐Adawiah Zainal‐Abidin, Sarahani Harun, Vinothienii Vengatharajuloo

et al.

Plants, Journal Year: 2022, Volume and Issue: 11(13), P. 1625 - 1625

Published: June 21, 2022

Transcriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems. The generated transcriptomics data can be utilised to produce gene co-expression network that is one essential downstream omics analyses. To date, several databases store correlation values, profiles, names and descriptions have been developed. Although these resources remain scattered across Internet, such complement each other support efficient growth in area. This review presents features most recent crops summarises present status tools are widely used constructing network. highlights presented here will pave way robust interpretation biologically relevant information. With this effort, researcher would able explore utilise improvement.

Language: Английский

Citations

16
Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How DOI Open Access
Ana M. Maldonado‐Alconada, María Ángeles Castillejo, María-Dolores Rey

et al.

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(17), P. 9980 - 9980

Published: Sept. 1, 2022

The holm oak (Quercus ilex L.) is the dominant tree species of Mediterranean forest and Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since prehistoric period, an important part Iberian population from a social, cultural, religious point view, providing ample variety goods services, forming basis economy in rural areas. Currently, there renewed interest its use for dietary diversification sustainable food production. cultural richness, both economically (tangible) environmentally (intangible), must be preserved future generations. However, worrisome degradation associated ecosystems occurring, observed increase decline mortality, which requires urgent action. Breeding programs based on selection elite genotypes by molecular markers only plausible biotechnological approach. To this end, authors’ group started, 2004, research line aimed at characterizing biology Q. ilex. been challenging task due to biological characteristics (long life cycle, allogamous, high phenotypic variability) recalcitrant nature. characterized following central dogma using omics cascade. Molecular responses biotic abiotic stresses, as well seed maturation germination, are two main objectives our research. contributions knowledge level DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, metabolomics discussed here. Moreover, data compared with those reported Quercus spp. All generated, genome available, will integrated morphological physiological systems direction. Thus, we propose possible related resilient productive used reforestation programs. In addition, nutritional value acorn derivate products, bioactive compounds (peptides phenolics) allergens, suggested. Subsequently, selected validated genome-wide association functional genomic analyses.

Language: Английский

Citations

16
Integration of biological and information technologies to enhance plant autoluminescence DOI
Jieyu Ge,

Xuye Lang,

Jiayi Ji

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(11), P. 4703 - 4715

Published: Aug. 21, 2024

Abstract Autoluminescent plants have been genetically modified to express the fungal bioluminescence pathway (FBP). However, a bottleneck in precursor production has limited brightness of these luminescent plants. Here, we demonstrate effectiveness utilizing computational model guide multiplex five-gene-silencing strategy by an artificial microRNA array enhance caffeic acid (CA) and hispidin levels By combining loss-of-function-directed metabolic flux with tyrosine-derived CA pathway, achieved substantially enhanced levels. We successfully generated eFBP2 that emit considerably brighter for naked-eye reading integrating all validated DNA modules. Our analysis revealed luminous energy conversion efficiency is currently very low, suggesting luminescence intensity can be improved future iterations. These findings highlight potential plant through integration biological information technologies.

Language: Английский

Citations

3