Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective DOI Creative Commons

Maria Ganopoulou,

Aliki Xanthopoulou, Michail Michailidis

et al.

Agronomy, Journal Year: 2023, Volume and Issue: 14(1), P. 8 - 8

Published: Dec. 19, 2023

Causal discovery is a highly promising tool with broad perspective in the field of biology. In this study, causal structure robustness assessment algorithm proposed and employed on structures obtained, based transcriptomic, proteomic, combined datasets, emerging from quantitative proteogenomic atlas 15 sweet cherry (Prunus avium L.) cv. ‘Tragana Edessis’ tissues. The assesses impact intervening datasets structures, using various criteria. results showed that specific tissues exhibited an intense were considered. addition, case demonstrated biologically related referred to same organ induced similar considered, as was expected. However, result subtler both transcriptomic proteomic cases. Furthermore, single omic analysis found be impacted larger extent, compared case, probably due distinctive biological features proteome or transcriptome. This study showcases significance assessing databases, conjunction discovery, reveals advantages when employing multiomics (proteogenomic) single-omic (transcriptomic, proteomic) analysis.

Language: Английский

The role of pangenomics in orphan crop improvement DOI Creative Commons
Haifei Hu, Junliang Zhao, William J. W. Thomas

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 2, 2025

Global food security depends heavily on a few staple crops, while orphan despite being less studied, offer the potential benefits of environmental adaptation and enhanced nutritional traits, especially in changing climate. Major crops have benefited from genomics-based breeding, initially using single genomes later pangenomes. Recent advances DNA sequencing enabled pangenome construction for several offering more comprehensive understanding genetic diversity. Orphan crop research has now entered pangenomics era applying these pangenomes with advanced selection methods genome editing technologies can transform neglected species into broader agricultural significance. A reference is not enough to harness full variation species. Here, authors review principles, applications improvement, discuss possible ways support pangenomics-driven molecular breeding.

Language: Английский

Citations

3
Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine DOI
Shang‐Tong Li,

Yunzhuo Ke,

Yunke Zhu

et al.

Nature Plants, Journal Year: 2024, Volume and Issue: 10(8), P. 1201 - 1214

Published: July 12, 2024

Language: Английский

Citations

13
Plant genome information facilitates plant functional genomics DOI Creative Commons

Judith Jazmín Bernal-Gallardo,

Stefan de Folter

Planta, Journal Year: 2024, Volume and Issue: 259(5)

Published: April 9, 2024

Abstract Main conclusion In this review, we give an overview of plant sequencing efforts and how impacts functional genomics research. Plant genome sequence information greatly facilitates the studies biology, genomics, evolution genomes genes, domestication processes, phylogenetic relationships, among many others. More than two decades have boosted number available sequenced genomes. The first genome, Arabidopsis, was published in year 2000 currently, 4604 from 1482 species been published. Various large initiatives are running, which planning to produce tens thousands near future. on status use different research areas.

Language: Английский

Citations

9
Navigating the landscape of plant proteomics DOI Open Access
Tian Sang, Zhen Zhang,

Guting Liu

et al.

Journal of Integrative Plant Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 15, 2025

In plants, proteins are fundamental to virtually all biological processes, such as photosynthesis, signal transduction, metabolic regulation, and stress responses. Studying protein distribution, function, modifications, interactions at the cellular tissue levels is critical for unraveling complexities of these pathways. Protein abundance localization highly dynamic vary widely across proteome, presenting a challenge global quantification analysis. Mass spectrometry-based proteomics approaches have proven be powerful tools addressing this complex issue. review, we summarize recent advancements in research their applications plant biology, with an emphasis on current state challenges studying post-translational single-cell proteomics, protein-protein interactions. Additionally, discuss future prospects highlighting potential opportunities that technologies offer advancing biology research.

Language: Английский

Citations

1
Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation DOI Creative Commons
Baopeng Ding, Haifei Hu, Yunpeng Cao

et al.

Horticultural Plant Journal, Journal Year: 2024, Volume and Issue: 10(6), P. 1274 - 1290

Published: Aug. 14, 2024

The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled annotated genomes of maternal (PsbM) paternal (PsbF) lines hybrid 'Yuluxiang' constructed pangenome 1.15 Gb by combining these two with five previously published representing cultivated wild germplasm. Using pangenome, identified 21 224 gene PAVs (Presence-absence variation) 1 158 812 SNPs (Single Nucleotide Polymorphism) in non-reference genome that were absent PsbM reference genome. Compared SNP markers, PAV-based analysis provides additional insights into population structure. In addition, some genes associated fruit quality traits have differential occurrence frequencies expression between Asian European populations. Moreover, our revealed a mutated an insertion promoter region PsbMGH3.1 potentially enhance sepal shedding 'Xuehuali' which vital quality. may play role IAA pathway, contributing to distinct low-auxin phenotype observed plants heterologously overexpressing this gene. This research helps capture populations genomic resources accelerating breeding.

Language: Английский

Citations

8
PbRbohH/J mediates ROS generation to regulate the growth of pollen tube in pear DOI
Hao Zhang, Xueying Liu, Chao Tang

et al.

Plant Physiology and Biochemistry, Journal Year: 2024, Volume and Issue: 207, P. 108342 - 108342

Published: Jan. 6, 2024

Language: Английский

Citations

7
Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants DOI

Yu‐Chen Song,

Debatosh Das, Youjun Zhang

et al.

Trends in biotechnology, Journal Year: 2023, Volume and Issue: 41(12), P. 1532 - 1548

Published: June 24, 2023

Language: Английский

Citations

14
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study DOI Creative Commons
Jian Hu,

Baisha Huang,

Hao Yin

et al.

Database, Journal Year: 2023, Volume and Issue: 2023

Published: Jan. 1, 2023

Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges cope with burgeoning sets of multiomics data are rapidly increasing. Here, we constructed Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome population variation data, aimed provide a portal for accessing analyzing pear data. A variety online tools were built including gene search, BLAST, JBrowse, expression heatmap, synteny analysis primer design. The information DNA methylation sites single-nucleotide polymorphisms can be retrieved through custom providing opportunity explore genetic linked phenotype variation. Moreover, different families involving transcription factors, regulators disease resistance (nucleotide-binding site leucine-rich repeat) identified compiled quick search. In particular, biosynthetic clusters (BGCs) in genomes, specialized webpages set up show detailed BGCs, laying foundation studying metabolic diversity among varieties. Overall, PearMODB provides platform genomics, genetics breeding studies. URL http://pearomics.njau.edu.cn.

Language: Английский

Citations

10
Chronology of transcriptome and proteome expression during early Arabidopsis flower development DOI Creative Commons
Raquel Álvarez-Urdiola, José Tomás Matus, Víctor M González

et al.

Journal of Experimental Botany, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Abstract The complex gene regulatory landscape underlying early flower development in Arabidopsis has been extensively studied through transcriptome profiling, and networks controlling floral organ have derived from the analyses of genome wide binding key transcription factors. In contrast, dynamic nature proteome during process is much less understood. this study, we characterized at different stages correlated it with unbiased transcript expression data. Shotgun proteomics profiling were conducted using an APETALA1-based induction system. A specific analysis pipeline to time-course data was developed. total, 8,924 proteins 23,069 transcripts identified. Co-expression revealed that RNA-protein pairs clustered various pattern modules. An overall positive correlation between RNA protein level changes observed, but subgroups RNA/protein anticorrelated also identified found be enriched hormone responsive pathways. addition, RNA-seq dataset reported here further expanded identification genes whose development, its combination previously published AP1 ChIP-seq datasets allowed additional direct high-confidence targets.

Language: Английский

Citations

0
Transcriptome and Metabolome Analyses of ‘Bartlett’ and ‘Xiang Shuomi’ Pears (Pyrus communis L.) Unveil the Candidate Pathways and Genes Regulating Leaf and Fruit Size DOI Creative Commons

Fudong Jiang,

Yiju Wang, Jianzhao Li

et al.

Horticulturae, Journal Year: 2025, Volume and Issue: 11(2), P. 215 - 215

Published: Feb. 18, 2025

The size of leaves and fruits is a crucial agronomic economic trait for fruit trees. ‘Bartlett’ pear famous cultivar with succulent delicious cultivated globally. ‘Xiang shuomi’ bud sport the pear, discovered in our breeding work, exhibits enlarged fruits. However, specific regulatory mechanism this superior still elusive. In study, comprehensive transcriptome metabolome analyses were performed to explore differences gene expression metabolite accumulation between these two cultivars. analysis showed total 1279 differentially expressed genes (DEGs), flavonoid biosynthetic process being most significant enriched biological process. Metabolome data indicated detection 412 abundant metabolites (DAMs), biosynthesis significantly. integrative transcriptomic metabolomics further confirmed pivotal role distinguishing Importantly, that encoded enzymes related biosynthesis, including CHS, CHI, HCT, LAR CYP75B1, increased their expressions pear. Correspondingly, galangin, chlorogenic acid, luteolin catechin found accumulate Overall, research identified key pathways influencing leaf pears, providing fundamental information high-yield

Language: Английский

Citations

0