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

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application DOI Open Access
Francis Martin, Marcel G. A. van der Heijden

New Phytologist, Journal Year: 2024, Volume and Issue: 242(4), P. 1486 - 1506

Published: Jan. 31, 2024

Summary Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, ecosystem sustainability. More than 250 000 species associated with mycorrhizal fungi. Recent advances in genomics related approaches have revolutionized our understanding of biology ecology associations. The genomes 250+ been released hundreds genes that play pivotal roles regulating symbiosis development metabolism characterized. rDNA metabarcoding metatranscriptomics provide novel insights into ecological cues driving communities functions expressed by these associations, linking to traits such as acquisition organic matter decomposition. Here, we review genomic studies revealed involved uptake development, discuss adaptations fundamental evolution lifestyles. We also evaluated services provided networks how hold promise sustainable agriculture forestry enhancing stress tolerance. Overall, unraveling intricate dynamics is paramount promoting sustainability addressing current pressing environmental concerns. This ends major frontiers further research.

Language: Английский

Citations

60
Rosaceae phylogenomic studies provide insights into the evolution of new genes DOI Creative Commons
Lan Jiang,

Xiaoxu Li,

Kun Lyu

et al.

Horticultural Plant Journal, Journal Year: 2024, Volume and Issue: unknown

Published: May 1, 2024

Rosa banksiae, known as Lady Banks' rose, is a perennial ornamental crop and versatile herb in traditional Chinese medicine. Given the lack of genomic resources, we assembled HiFi Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality R. banksiae genome with scaffold N50 = 63.90 Mb. The exhibited no lineage-specific whole-genome duplication compared other Rosaceae. phylogenomic analysis 13 Rosaceae Arabidopsis through comparative genomics study showed that numerous gene families were both before after diversification Some these genes are candidates for new have evolved from parental fusion events. Fusion divided into three types: Type-I Type-II contain two generated by duplication, distributed same different regions genome, respectively; Type-III can only be detected one gene. Here, found to more relaxed selection pressure lower Ks values than Type-II, indicating newly may play important roles driving phenotypic evolution. Functional formed regulate phenotype traits plant growth development, suggesting functional significance genes. This identifies could responsible evolution provides information on evolutionary history recently diverged species genus. Our data represents major progress understanding pattern an invaluable resource studies plants.

Language: Английский

Citations

16
Recent Advances in Assembly of Complex Plant Genomes DOI Creative Commons
Weilong Kong, Yibin Wang, Shengcheng Zhang

et al.

Genomics Proteomics & Bioinformatics, Journal Year: 2023, Volume and Issue: 21(3), P. 427 - 439

Published: April 25, 2023

Abstract Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those nonvascular plants to flowering plants. However, complex genome assembly is still challenging remains difficult fully resolve conventional methods due high heterozygosity, highly repetitive sequences, or ploidy characteristics genomes. Herein, we summarize challenges assembly, including feasible experimental strategies, upgrades technology, existing methods, different phasing algorithms. Moreover, list actual cases projects for readers refer draw upon solve future problems related Finally, expect that accurate, gapless, telomere-to-telomere, phased could soon become routine.

Language: Английский

Citations

40
Advances and prospects of orchid research and industrialization DOI Creative Commons
Diyang Zhang, Xuewei Zhao, Yuanyuan Li

et al.

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together human influences also make it a keystone group biodiversity conservation. The advent sequencing technologies transgenic techniques represents quantum leap orchid research, enabling molecular approaches to be employed resolve historically interesting puzzles basic applied biology. To date, 16 different genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, Orchidoideae) been released. genome projects given rise massive data greatly empowers studies pertaining key innovations evolutionary mechanisms for breadth species. extensive exploration transcriptomics, comparative genomics, recent advances gene engineering linked important traits orchids multiplicity regulating networks, providing great potential genetic enhancement improvement. In this review, we summarize progress achievement fundamental research industrialized application particular focus tools, future prospects breeding post-genomic comprehensive assemblage state art knowledge industrialization.

Language: Английский

Citations

39
Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt DOI Creative Commons
Yunpeng Cao,

Wanzhen Mo,

Yanli Li

et al.

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Feb. 27, 2024

Abstract Background Most disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS) domains, which belong to the NBS-LRR family. The sequenced genomes of Fusarium wilt-susceptible Vernicia fordii its resistant counterpart, montana , offer significant resources for functional characterization discovery novel tung tree. Results Here, we identified 239 across two tree genomes: 90 V. 149 . Five VmNBS-LRR paralogous were predicted 43 orthologous detected between gene pair Vf11G0978-Vm019719 exhibited distinct expression patterns : Vf11G0978 showed downregulated while Vm019719 demonstrated upregulated indicating this may be responsible wilt from activated by VmWRKY64 was shown confer a virus-induced silencing (VIGS) experiment. However, susceptible allelic an ineffective defense response, attributed deletion promoter’s W-box element. Conclusions This study provides first systematic analysis identifies candidate can utilized marker-assisted breeding control

Language: Английский

Citations

13
Identification of Bletilla striata and related decoction pieces: a data fusion method combining electronic nose, electronic tongue, electronic eye, and high-performance liquid chromatography data DOI Creative Commons
Han Li, Panpan Wang,

Zhaozhou Lin

et al.

Frontiers in Chemistry, Journal Year: 2024, Volume and Issue: 11

Published: Jan. 10, 2024

Introduction: We here describe a new method for distinguishing authentic Bletilla striata from similar decoctions (namely, Gastrodia elata , Polygonatum odoratum and ochracea schltr ). Methods: Preliminary identification analysis of four types decoction pieces were conducted following the Chinese Pharmacopoeia local standards. Intelligent sensory data then collected using an electronic nose, tongue, eye, chromatography obtained via high-performance liquid (HPLC). Partial least squares discriminant (PLS-DA), support vector machines (SVM), back propagation neural network (BP-NN) models built each set single-source authenticity (binary classification B. vs. other samples) species determination (multi-class sample identification). Features extracted all datasets unsupervised approach [principal component (PCA)] supervised (PLS-DA). Mid-level fusion was used to combine features effects feature extraction methods on model performance compared. Results Discussion: Gas chromatography–ion mobility spectrometry (GC-IMS) showed significant differences in abundances volatile organic compounds between types. In determination, PLS-DA SVM based fused latent variables (LVs) performed best, with 100% accuracy both calibration validation sets. identification, principal components (PCs) or LVs had best performance, just one misclassification set. models, better than PCs. Model identify PCs that strongly contributed accurate classification, PC factor loading matrix assess correlation original variables. This study serves as reference future efforts accurately evaluate quality medicine pieces, promoting medicinal formulation safety.

Language: Английский

Citations

12
De novo gene integration into regulation networks via interaction with conserved genes in peach DOI Creative Commons
Yunpeng Cao,

Jiayi Hong,

Yun Zhao

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(12)

Published: Sept. 5, 2024

Language: Английский

Citations

12
A long road ahead to reliable and complete medicinal plant genomes DOI Creative Commons

L. Cheng,

Zilong Wang, Qian‐Hao Zhu

et al.

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

Published: March 4, 2025

Language: Английский

Citations

1
From single- to multi-omics: future research trends in medicinal plants DOI Creative Commons
Lifang Yang, Ye Yang, Luqi Huang

et al.

Briefings in Bioinformatics, Journal Year: 2022, Volume and Issue: 24(1)

Published: Nov. 22, 2022

Abstract Medicinal plants are the main source of natural metabolites with specialised pharmacological activities and have been widely examined by plant researchers. Numerous omics studies medicinal performed to identify molecular markers species functional genes controlling key biological traits, as well understand biosynthetic pathways bioactive regulatory mechanisms environmental responses. Omics technologies applied plants, including taxonomics, transcriptomics, metabolomics, proteomics, genomics, pangenomics, epigenomics mutagenomics. However, because complex regulation network, single usually fail explain specific phenomena. In recent years, reports integrated multi-omics increased. Until now, there few assessments developments upcoming trends in plants. We highlight research summarise typical bioinformatics resources available for analysing datasets, discuss related future directions challenges. This information facilitates further refinement current approaches leads new ideas.

Language: Английский

Citations

32
Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits DOI Creative Commons
Xiaoni Zhang,

Quanshu Wu,

Lan Lan

et al.

Molecular Horticulture, Journal Year: 2024, Volume and Issue: 4(1)

Published: April 16, 2024

Roses are consistently ranked at the forefront in cut flower production. Increasing demands of market and changing climate conditions have resulted need to further improve diversity quality traits. However, frequent hybridization leads highly heterozygous nature, including allelic variants. Therefore, absence comprehensive genomic information them making it challenging molecular breeding. Here, two haplotype-resolved chromosome genomes for Rosa chinensis 'Chilong Hanzhu' (2n = 14) which is high diploid old Chinese rose generated. An amount genetic variation (1,605,616 SNPs, 209,575 indels) identified. 13,971 genes show differential expression patterns between haplotypes. Importantly, these differences hold valuable insights into regulatory mechanisms RcMYB114b can influence cyanidin-3-glucoside accumulation its promoter activity, as a factor control petal color. Moreover, gene family expansion may contribute abundance terpenes floral scents. Additionally, RcANT1, RcDA1, RcAG1 RcSVP1 involved regulation number size under heat stress treatment. This study provides foundation breeding important characteristics roses.

Language: Английский

Citations

8