In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing DOI Creative Commons
Cheng Song, Yan Wang, Muhammad Aamir Manzoor

et al.

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 23, 2022

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying origin evolution plant genomes subgenomes, population domestication, functional genomics. Orchids have tens thousands members in nature. Many them promising application potential extension conservation ecological chain, horticultural use ornamental blossoms, utilization botanical medicines. However, a large-scale gene knockout mutant library sophisticated genetic transformation system are still lacking improvement orchid germplasm resources. New editing tools, such as favored CRISPR-Cas9 or some base editors, not yet widely applied orchids. In addition to large variety cultivars, high-precision, high-throughput genome is also required mining trait-related genes. Nowadays, focus genomics research directed classification species, deletion, duplication chromosomal polyploidy, flower morphogenesis-related regulation. Here, progressing achieved molecular biology over past few decades discussed, including size polyploidization. The frequent incorporation LTR retrotransposons play important role expansion structural variation genome. event nuclear generated plenty recently tandem duplicated genes, which drove divergency loss plastid genome, mostly affected genes related photosynthesis autotrophy, demonstrated that orchids experienced more separate transitions heterotrophy than any other terrestrial plant. Moreover, resequencing provide useful SNP markers constructing maps, will facilitate breeding novel varieties. significance technologies identification provides us with representative trait-improving well mechanisms worthy further investigation. addition, promise investigation function. This knowledge may scientific reference theoretical basis studies.

Language: Английский

Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis DOI Creative Commons
Yunpeng Cao,

Tingting Fan,

Wang Li-hu

et al.

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: March 17, 2023

MYB transcription factors are widely distributed in the plant kingdom and play key roles regulatory networks governing metabolism biochemical physiological processes.Here, we first determined R2R3-MYB genes five Euphorbiaceae genomes. The three Trp (W) residues from domain (R2) were absolutely conserved, whereas W residue second (R3) was preferentially mutated. R2R3-MYBs clustered into 48 functional subfamilies, of which 34 had both species AtMYBs, four contained only R2R3-MYBs. whole-genome duplication (WGD) and/or segmental (SD) played expansion family. Unlike paralogous family members, orthologous members a higher selective pressure subject to constrained evolutionary rate. VfMYB36 specifically expressed fruit, its trend consistent with change oil content, indicating that it might be involved biosynthesis. Overexpression experiments showed could significantly provide linolenic acid (C18:3) eventually led significant increase content.Our study provides insight understanding evolution expression species, also target for production biomass diesel convenient way breeding germplasm resources high content future.

Language: Английский

Citations

13
Progress in systematics and biogeography of Orchidaceae DOI Creative Commons
Y WANG, Hanchen Wang, CHAO YE

et al.

Plant Diversity, Journal Year: 2024, Volume and Issue: 46(4), P. 425 - 434

Published: May 16, 2024

Orchidaceae are one of the largest families angiosperms in terms species richness. In last decade, numerous studies have delved into reconstructing phylogenetic framework Orchidaceae, leveraging data from plastid, mitochondrial and nuclear sources. These provided new insights systematics, diversification biogeography establishing a robust foundation for future research. Nevertheless, pronounced controversies persist regarding precise placement certain lineages within these frameworks. To address discrepancies deepen our understanding structure we provide comprehensive overview analysis focusing on contentious groups since 2015, delving discussions underlying reasons observed topological conflicts. We also novel at subtribal level. Furthermore, examine tempo mode orchid diversity perspective historical biogeography, highlighting factors contributing to extensive speciation. Ultimately, delineate avenues research aimed enhancing phylogeny diversity.

Language: Английский

Citations

4
A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity DOI Creative Commons
Temitope Opeyemi Oriowo, Ioannis Chrysostomakis, Sebastián Martín

et al.

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Abstract Background In this study, we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads chromosome conformation capture data (Hi-C). Results achieved a haploid size 940 megabase pairs (Mbp) for haplome 1 929 Mbp 2 with high scaffold N50 values 36.4 Mb 36.6 BUSCO scores 96.9% 97.2%, respectively, indicating highly complete assembly. detected notable heterozygosity (1.43%) repeat content (approximately 54%), primarily consisting DNA transposons, which contribute to rearrangements variations. found substantial variations within including insertions, deletions, inversions, translocations. These affect genes enriched in functions such as dephosphorylation, developmental pigmentation, phagocytosis, immunity, stress response. annotation protein-coding genes, 30,980 messenger RNAs 23,497 were identified completeness score, further underpins contiguity our assemblies. performed gene family evolution comparing proteome 10 other teleost species, immune system families that prioritize histone-based disease prevention over NB-LRR-related-based responses. Additionally, demographic indicates historical fluctuations effective population P. phoxinus, likely correlating past climatic changes. Conclusions This annotated, phased reference provides crucial resource resolving taxonomic complexity genus Phoxinus highlights importance haplotype-phased assemblies understanding haplotype diversity species characterized heterozygosity.

Language: Английский

Citations

0
Ultrasound-assisted metabolite detection in different extraction processes of Bletilla striata and bitter metabolite detection DOI Creative Commons
Juan Zhou, Yu‐Qi Feng, Wenhao Zhou

et al.

Ultrasonics Sonochemistry, Journal Year: 2025, Volume and Issue: 114, P. 107266 - 107266

Published: Feb. 10, 2025

Bletilla striata, a medicinal orchidaceous plant, is recognized for its significant pharmacological value. However, the lack of comparative metabolomic data across different extraction methods analyzing bioactive components has significantly undervalued application potential B. striata in traditional Chinese medicine market. Using six ultrasound-assisted and UPLC-MS/MS, this study identified 1,945 metabolites extracts. The dominant categories were lipids (51.35%), flavonoids (18.00%), phenolic acids (12.51%). KEGG analysis revealed alterations isoflavonoids biosynthesis pathways. Thirteen bitter metabolites, including cinnamic acid, tubers, underscoring their applications, such as anti-inflammatory, antioxidant antibacterial activities. Optimizing can better preserve extracts, thereby enhancing applications food pharmaceutical industries.

Language: Английский

Citations

0
Opportunities and challenges in the application of single-cell transcriptomics in plant tissue research DOI
Man Luo, Yunpeng Cao,

Jiayi Hong

et al.

Physiology and Molecular Biology of Plants, Journal Year: 2025, Volume and Issue: 31(2), P. 199 - 209

Published: Feb. 1, 2025

Language: Английский

Citations

0
Transcriptome Analysis of Wild Bletilla striata Tubers Across Multiple Years Revealed the Molecular Mechanisms Regulating Polysaccharide Metabolism and Tuber Enlargement DOI Creative Commons
Hai Huang, Long Yang,

Chunfang Luo

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(5), P. 689 - 689

Published: Feb. 24, 2025

A Bletilla striata (Thunb.) Reichb.f., known as Bai Ji in Chinese, is a plant from the Orchidaceae family that has been used for its medicinal properties thousands of years China. B. holds significant economic value due to esteemed applications. Our study aimed analyze transcriptome wild tubers across multiple understand molecular mechanisms regulating polysaccharide metabolism and tuber enlargement. We collected samples different growth ages analyzed their chemical composition, including total phenols, polysaccharides, alkaloids, proteins. The results showed content these compounds varied with age plants. focused on analyzing genes associated accelerating seedling cycle, which immense preservation optimal utilization superior orchid resources. To further investigate underlying mechanisms, we performed comprehensive analysis explore gene expression, functional annotation, regulatory networks related development composition tubers. quality perennial herbs intricately linked age. Unfortunately, excessive resource excavation resulted premature harvesting herbs, causing decline overall effectiveness. offers valuable insights into conservation

Language: Английский

Citations

0
Centenary Progress on Orchidaceae Research: A Bibliometric Analysis DOI Open Access
Yonglu Wei, Jie Li,

Jianpeng Jin

et al.

Genes, Journal Year: 2025, Volume and Issue: 16(3), P. 336 - 336

Published: March 13, 2025

Background: Research on orchids has experienced substantial growth since the early 20th century, reflecting their ecological and evolutionary significance. Methods: This paper provides a comprehensive bibliometric analysis of orchid-related literature published between 1902 2024, based data retrieved from Web Science Core Collection™ (WoS). Results: The primary goal is to assess global research landscape by identifying key authors, institutions, journals, as well major themes in field. A thorough publication trends, citation frequencies, keyword co-occurrence networks was conducted uncover significant hotspots. findings indicate that orchid evolved foundational topics such taxonomy classification more intricate subjects, including conservation strategies, orchid-pollinator dynamics, role ecosystem functions. Additionally, biotechnology-related emerging dominant trend. study also highlights China highest output, while collaboration United States Europe continues grow. co-word keywords suggests future likely continue focus conservation, impacts climate change, pollination biology, symbiotic relationships with mycorrhizal fungi. Conclusions: review offers valuable insights for researchers conservationists, helping identify priorities strategies preservation sustainable use orchids.

Language: Английский

Citations

0
The role of nuclear factor-Y (NF-Y) transcription factor in plant growth and development DOI

Jiayi Hong,

Xiaofeng Feng, Yongping Cai

et al.

Functional Plant Biology, Journal Year: 2025, Volume and Issue: 52(4)

Published: March 26, 2025

The nuclear factor-Y (NF-Y) transcription factor, also known as heme-activator protein (HAP) or CCAAT-binding factor (CBF), is a critical widely present in eukaryotes. number of NF-Y subunits has significantly increased higher plants compared to animals and fungi. complex composed three subunits: (1) NF-YA; (2) NF-YB; (3) NF-YC. NF-YB NF-YC contain histone fold domains (HFDs), which can interact with NF-YA other factors, directly bind the promoter CCAAT box regulate downstream genes. plays significant role various plant processes, including growth development. This review elucidates structural functional aspects subunits, identified complexes, their molecular regulatory mechanisms. Understanding these facets provides valuable insights into advancing crop genetic improvement promoting sustainable agricultural practices.

Language: Английский

Citations

0
Metabolomic and transcriptomic analyses reveal the mechanism of polysaccharide and secondary metabolite biosynthesis in Bletilla striata tubers in response to shading DOI

Shenping Xu,

Yan Zhang, Fang Liang

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: unknown, P. 135545 - 135545

Published: Sept. 1, 2024

Language: Английский

Citations

3
Resequencing and Functional Analysis Revealed That BsDFR4 Could Cause the Formation of Different Flower Colors in Bletilla striata (Orchidaceae) DOI Open Access

Siting Zheng,

Zeyuan Mi,

Yuanqing Chang

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3555 - 3555

Published: April 10, 2025

The formation of flower color is closely related to anthocyanin synthesis. In this study, flowers Bletilla striata (Orchidaceae) exhibiting distinct morphs were collected and analyzed. HPLC results showed significantly higher total flavonoid contents in purple compared pink counterparts, with increases 2.20-fold (p < 0.01) 15.22-fold 0.01), respectively. Cyanidin was the predominant B. striata. Resequencing analyses highlighted SNP as primary variation associated divergence. A comprehensive screen identified 61 genes encoding enzymes critical biosynthesis pathways Among these, 16 flower-specific exhibited high expression levels harbored variations. Notably, a premature stop codon gene dihydroflavonol 4-reductase (DFR), leading truncated protein synthesis potential disruption production. Further, heterologous overexpression BsDFR4 Phalaenopsis aphrodite changed petal from white yellow-green, demonstrating that it indeed played regulatory role color. Furthermore, yeast one-hybrid assays confirmed transcription factors BsMYB36 BsMYB51 could directly bind promoter, suggesting their synergistic regulation biosynthesis. These provided conceptual basis for insights into different colors Orchidaceae.

Language: Английский

Citations

0