Cargando…

A pangenome analysis pipeline provides insights into functional gene identification in rice

BACKGROUND: A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Gr...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wang, Jian, Yang, Wu, Zhang, Shaohong, Hu, Haifei, Yuan, Yuxuan, Dong, Jingfang, Chen, Luo, Ma, Yamei, Yang, Tifeng, Zhou, Lian, Chen, Jiansong, Liu, Bin, Li, Chengdao, Edwards, David, Zhao, Junliang
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2023
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9878884/ https://www.ncbi.nlm.nih.gov/pubmed/36703158 http://dx.doi.org/10.1186/s13059-023-02861-9

Ejemplares similares

Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice
por: Ma, Yamei, et al.
Publicado: (2022)

Mining candidate genes for rice cadmium accumulation in the shoot through a genome-wide association study and transcriptomic analysis
por: Wang, Jian, et al.
Publicado: (2022)

Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures
por: Yang, Wu, et al.
Publicado: (2022)

Genome-wide association mapping and gene expression analysis reveal candidate genes for grain chalkiness in rice
por: Huo, Xing, et al.
Publicado: (2023)

The 14-3-3 protein OsGF14f interacts with OsbZIP23 and enhances its activity to confer osmotic stress tolerance in rice
por: Ma, Yamei, et al.
Publicado: (2023)

Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.)
por: Yang, Tifeng, et al.
Publicado: (2023)

Genome-Wide Identification, Expression and Functional Analysis Reveal the Involvement of FCS-Like Zinc Finger Gene Family in Submergence Response in Rice
por: Ma, Yamei, et al.
Publicado: (2021)

Overexpression of OsGF14f Enhances Quantitative Leaf Blast and Bacterial Blight Resistance in Rice
por: Ma, Yamei, et al.
Publicado: (2022)

Overexpression of OsGF14C enhances salinity tolerance but reduces blast resistance in rice
por: Dong, Jingfang, et al.
Publicado: (2023)

Genome-Wide Association Mapping and Gene Expression Analysis Reveal the Negative Role of OsMYB21 in Regulating Bacterial Blight Resistance in Rice
por: Yang, Wu, et al.
Publicado: (2021)

The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)
por: Yang, Tifeng, et al.
Publicado: (2020)

The OsOXO2, OsOXO3 and OsOXO4 Positively Regulate Panicle Blast Resistance in Rice
por: Dong, Jingfang, et al.
Publicado: (2021)

Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection
por: Zhao, Junliang, et al.
Publicado: (2018)

A novel functional gene associated with cold tolerance at the seedling stage in rice
por: Zhao, Junliang, et al.
Publicado: (2017)

Integrating Small RNA Sequencing with QTL Mapping for Identification of miRNAs and Their Target Genes Associated with Heat Tolerance at the Flowering Stage in Rice
por: Liu, Qing, et al.
Publicado: (2017)

OsWRKY67 positively regulates blast and bacteria blight resistance by direct activation of PR genes in rice
por: Liu, Qing, et al.
Publicado: (2018)

Producing polished prokaryotic pangenomes with the Panaroo pipeline
por: Tonkin-Hill, Gerry, et al.
Publicado: (2020)

The poplar pangenome provides insights into the evolutionary history of the genus
por: Zhang, Bingyu, et al.
Publicado: (2019)

Pangenome of white lupin provides insights into the diversity of the species
por: Hufnagel, Bárbara, et al.
Publicado: (2021)

The MKKK62-MKK3-MAPK7/14 module negatively regulates seed dormancy in rice
por: Mao, Xingxue, et al.
Publicado: (2019)

Identification and validation of a novel major QTL for harvest index in rice (Oryza sativa L.)
por: Zhang, Shaohong, et al.
Publicado: (2017)

Transcriptome and Metabolome Analyses Reveal New Insights into the Regulatory Mechanism of Head Milled Rice Rate
por: Yang, Wu, et al.
Publicado: (2022)

Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)
por: Amas, Junrey C., et al.
Publicado: (2023)

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
por: Li, Zhengcao, et al.
Publicado: (2023)

MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks
por: Peng, Ye, et al.
Publicado: (2018)

Protocol for post-processing of bacterial pangenome data using Pagoo pipeline
por: Ferrés, Ignacio, et al.
Publicado: (2021)

Artificially Selected Grain Shape Gene Combinations in Guangdong Simiao Varieties of Rice (Oryza sativa L.)
por: Yang, Tifeng, et al.
Publicado: (2023)

Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium
por: Kim, Minji, et al.
Publicado: (2023)

Trait associations in the pangenome of pigeon pea (Cajanus cajan)
por: Zhao, Junliang, et al.
Publicado: (2020)

Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication
por: Jia, Yong, et al.
Publicado: (2023)

Pangenomic analysis of Wolbachia provides insight into the evolution of host adaptation and cytoplasmic incompatibility factor genes
por: Liu, Bo, et al.
Publicado: (2023)

Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
por: Shapiro, Jason W., et al.
Publicado: (2021)

The super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis
por: Noroy, Christophe, et al.
Publicado: (2021)

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights
por: Bosi, Emanuele, et al.
Publicado: (2017)

Crop pangenomes
por: Pronozin, A.Yu., et al.
Publicado: (2021)

A pangenome reference of 36 Chinese populations
por: Gao, Yang, et al.
Publicado: (2023)

Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
por: Zhou, Yang, et al.
Publicado: (2022)

Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks
por: Agarwal, Viplav, et al.
Publicado: (2023)

The human pangenome reference anticipates equitable and fundamental genomic insights
por: Frazer, Kelly A., et al.
Publicado: (2023)

Estimating Pangenomes with Roary
por: Sitto, Farrah, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_lq0ogfiaefj7nuibnuilp0n78f