Research Progress of Genomics Applications in Secondary Metabolites of Medicinal Plants: A Case Study in Safflower DOI Open Access
Zhihua Wu,

Yan Na Hu,

Rui Hao

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3867 - 3867

Published: April 19, 2025

Medicinal plants, recognized as significant natural resources, have gained prominence in response to the increasing global demand for herbal medicines, necessitating large-scale production of these plants and their derivatives. are exposed a variety internal external factors that interact influence biosynthesis accumulation secondary metabolites. With rapid development omics technologies such genomics, transcriptomics, proteomics, metabolomics, multi-omics become important tools revealing complexity functionality organisms. They conducive further uncovering biological activities metabolites medicinal clarifying molecular mechanisms underlying Also, artificial intelligence (AI) technology accelerates comprehensive utilization high-dimensional datasets offers transformative potential analysis. However, there is currently no systematic review summarizing genomic metabolite plants. Safflower (Carthamus tinctorius L.) has rich diverse bioactive flavonoids, among which Hydroxysafflor yellow A (HSYA) specific safflower emerging medication treating wide range diseases. Hence, progress been made study an excellent example regulation recent years. Here, we on understanding main at level, summarize various types contents, with particular focus flavonoids. This aims provide insight into regulatory from perspective genomics.

Language: Английский

Opportunities and Challenges of In Vitro Tissue Culture Systems in the Era of Crop Genome Editing DOI Open Access
Zelalem Eshetu Bekalu, Michael Panting, Inger Bæksted Holme

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(15), P. 11920 - 11920

Published: July 25, 2023

Currently, the development of genome editing (GE) tools has provided a wide platform for targeted modification plant genomes. However, lack versatile DNA delivery systems large variety crop species been main bottleneck improving crops with beneficial traits. generation plants heritable mutations induced by GE mostly goes through tissue culture. Unfortunately, current culture restrict successful results to only limited number and genotypes. In order release full potential tools, procedures need be genotype independent. This review provides an in-depth summary insights into various in vitro used economically important barley, wheat, rice, sorghum, soybean, maize, potatoes, cassava, millet uncovers new opportunities challenges already-established platforms crops.

Language: Английский

Citations

14
Genomic variation of 363 diverse tea accessions unveils the genetic diversity, domestication, and structural variations associated with tea adaptation DOI
Wei Tong, Yanli Wang, Fangdong Li

et al.

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(10), P. 2175 - 2190

Published: July 11, 2024

ABSTRACT Domestication has shaped the population structure and agronomic traits of tea plants, yet complexity genetic variation that determines these remains unclear. We here investigated resequencing data 363 diverse accessions collected extensively from almost all distributions found plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The diversity in China decreased southwest to east as latitude increased. Results also indicated Camellia sinensis var. assamica (CSA) illustrated divergent selection signatures (CSS). domesticated genes CSA mainly involved leaf development, flavonoid alkaloid biosynthesis, while CSS participated amino acid metabolism, aroma compounds cold stress. Comparative genomics further identified ~730 Mb novel sequences, generating 6,058 full‐length protein‐encoding genes, significantly expanding gene pool plants. discovered 217,376 large‐scale structural variations 56,583 presence absence (PAVs) across accessions, some associated quality stress resistance. Functional experiments demonstrated two PAV ( CSS0049975 CSS0006599 ) likely drive trait diversification tolerance between overall findings not only revealed domestication but underscored vital role plant traits.

Language: Английский

Citations

6
Genomics and bioinformatics applications in crop stress: Unraveling molecular mechanisms for sustainable agriculture DOI
Heba Talat Ebeed, Stanislaus Antony Ceasar

South African Journal of Botany, Journal Year: 2024, Volume and Issue: 170, P. 38 - 47

Published: May 15, 2024

Language: Английский

Citations

5
Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes DOI Creative Commons
Sushma Naithani, Cecilia Deng, Sunil Kumar Sahu

et al.

Biomolecules, Journal Year: 2023, Volume and Issue: 13(9), P. 1403 - 1403

Published: Sept. 17, 2023

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution build clade-specific pan-genomes several crops. crops constructed various cultivars, accessions, landraces, wild ancestral represent compendium genes structural variations allow researchers search for the novel alleles that were inadvertently lost in domesticated during historical process crop domestication or extensive plant breeding. Fortunately, many valuable associated with desirable traits like disease resistance, abiotic stress tolerance, architecture, nutrition qualities exist species, relatives. ancestors landraces can be introduced back high-yielding varieties modern by implementing classical breeding, selection, transgenic/gene editing approaches. Thus, pan-genomic represents great leap research offers new avenues targeted breeding mitigate impact global climate change. Here, we summarize tools used pan-genome assembly annotations, web-portals hosting pan-genomes, etc. Furthermore, highlight few discoveries using approach future potential this emerging field study.

Language: Английский

Citations

12
PanKmer: k-mer-based and reference-free pangenome analysis DOI Creative Commons
Anthony Aylward,

Semar Petrus,

Allen Mamerto

et al.

Bioinformatics, Journal Year: 2023, Volume and Issue: 39(10)

Published: Oct. 1, 2023

Abstract Summary Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope identifying structural variants (SVs), incur bias by relying on genome. Here, we present PanKmer, toolkit designed for reference-free pangenome datasets consisting dozens thousands individual genomes. PanKmer decomposes set input into table observed k-mers and presence–absence values in each These stored an efficient k-mer index data format encodes SNPs, INDELs, SVs. It also includes functions downstream index, such calculating similarity statistics between individuals at whole-genome local scales. For example, can be “anchored” any quantify variability conservation specific locus. This facilitates workflows with various biological applications, e.g. cases hybridization plant species. provides researchers valuable convenient means explore full genetic variation population, without bias. Availability implementation is implemented Python package components written Rust, released under BSD license. The source code available from Package Index (PyPI) https://pypi.org/project/pankmer/ well Gitlab https://gitlab.com/salk-tm/pankmer. Full documentation https://salk-tm.gitlab.io/pankmer/.

Language: Английский

Citations

12
Engineering the future cereal crops with big biological data: toward an intelligence-driven breeding by design DOI
Lei Liu,

Jimin Zhan,

Jianbing Yan

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: 51(8), P. 781 - 789

Published: March 24, 2024

Language: Английский

Citations

4
Plant pangenomics, current practice and future direction DOI Creative Commons
Haifei Hu, Jian Wang, Shuai Nie

et al.

Agriculture Communications, Journal Year: 2024, Volume and Issue: 2(2), P. 100039 - 100039

Published: March 30, 2024

A pangenome encompasses the complete genetic diversity of a species, by assembling range representative individuals from various populations. This review describes advances in plant pangenomics, tracing its evolution since initial genome sequencing 2000, and provides comprehensive best-practice advice to build linear or graphical pangenome, delineating strengths limitations different construction methods. The also examines challenges data visualisation, graph-based pangenomes their utility investigating potential function variation. Furthermore, we examine application breeding, including identification for crop improvement, integration multi-omics into databases advance breeding.

Language: Английский

Citations

4
The evolution, variation and expression patterns of the annexin gene family in the maize pan-genome DOI Creative Commons
Xin Liu, Minghu Zhang, Xin Zhao

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 17, 2025

Language: Английский

Citations

0
RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection DOI Creative Commons
Cassandra Elphinstone,

Rob Elphinstone,

Marco Todesco

et al.

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: March 4, 2025

ABSTRACT Tandem repeats play an important role in centromere structure, subtelomeric regions, DNA methylation, recombination and the regulation of gene activity. Analysis their distribution genomes offers a potential means for predicting putative locations, which continues to be challenge genome annotation. Here we present RepeatOBserver ( https://github.com/celphin/RepeatOBserverV1 ), new tool visualising repeat patterns identifying using Fourier transform walks. can identify visualise broad range perfect imperfect (3–5000 bp long) assemblies without any priori knowledge sequences or need optimising parameters. heatmaps distinguish between tandem retrotransposon repeats. We analysed 159 chromosomes with experimentally‐verified positions from 12 plant animal species. find that 93% centromeres occur regions low sequence diversity 97% high abundance lengths. Depending on type predicted by heatmaps, locations either genomic Shannon index sum. also locate other interest including neocentromeres copy variation. Split inverted at inversion boundaries suggest chromosomal inversions mis‐assemblies located. is flexible comprehensive characterisation used variety assemblies.

Language: Английский

Citations

0
Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms DOI
Marius Arend,

Emilian Paulitz,

Yunli Eric Hsieh

et al.

Metabolic Engineering, Journal Year: 2025, Volume and Issue: 90, P. 67 - 77

Published: March 11, 2025

Language: Английский

Citations

0