4.7 Article

The Genome of Vitis zhejiang-adstricta Strengthens the Protection and Utilization of the Endangered Ancient Grape Endemic to China

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

Ze-Long Nie et al.

Summary: The north temperate region had a warm climate and a rich thermophilic flora before the Eocene, but the early diversifications of the temperate biome under global climate change and biome shift are not well understood. Hybridization/introgression is an important driving force of speciation in plant diversity. In this study, we analyzed genomic data from the New World Vitis, a temperate North American flora, and found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2023)

Article Multidisciplinary Sciences

Dual domestications and origin of traits in grapevine evolution

Yang Dong et al.

Summary: We investigate the evolution and domestication of grapevines by studying 3525 cultivated and wild varieties worldwide. Harsh climate in the Pleistocene led to the separation of wild grape ecotypes due to habitat fragmentation. Domestication occurred around 11,000 years ago in Western Asia and the Caucasus, giving rise to table and wine grapevines. The domesticates from Western Asia dispersed into Europe, hybridizing with ancient wild ecotypes and diversifying into muscat and unique western wine grape ancestries as human migration took place in the late Neolithic. Analysis of domestication traits also provides insights into the selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These findings demonstrate the significance of grapevines in the early development of agriculture across Eurasia.

SCIENCE (2023)

Article Biochemistry & Molecular Biology

PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process

Joan Calle Garcia et al.

Summary: The PRGdb database has been significantly expanded and upgraded, providing more data and tools, with a new section dedicated to collecting plant resistance transcriptomic experimental data. Additionally, the DRAGO3 tool has been improved in accuracy and sensitivity, leading to more reliable predictions.

NUCLEIC ACIDS RESEARCH (2022)

Article Plant Sciences

A genome for Cissus illustrates features underlying its evolutionary success in dry savannas

Haiping Xin et al.

Summary: This study provides a chromosomal-level assembly of Cissus rotundifolia and compares it with the grape genome, shedding light on the genome divergence within the ancient eudicot family. The findings highlight the genetic basis underlying C. rotundifolia's adaptation to arid environments and reveal the significant functional divergence from grape.

HORTICULTURE RESEARCH (2022)

Article Plant Sciences

The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine

Yi Wang et al.

Summary: Vitis amurensis (Shanputao), the most cold-tolerant species of grape, has a genome assembly revealing a common ancestor with V. vinifera and potential gene expansions contributing to cold tolerance. Transcriptome analysis identified 17 genes involved in cold signal transduction with different mechanisms for low temperature and freezing responses. A genome-wide association study highlighted a phosphoglycerate kinase gene implication in winter bud freezing resistance.

PLANT JOURNAL (2021)

Article Biotechnology & Applied Microbiology

The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

Zhongyu Du et al.

Summary: This study reported the complete chloroplast genome sequences of subg. Amygdalus, revealing a highly conserved genomic structure and estimating the divergence time of subg. Amygdalus species to be approximately 15.65 million years ago.

BMC GENOMICS (2021)

Article Genetics & Heredity

The complete chloroplast genome sequence of Garcinia anomala (Clusiaceae) from Yunnan Province, China

Biying Yue et al.

Summary: This study reported the complete chloroplast genome sequence of Garcinia anomala and investigated its phylogenetic relationship, placing it in a clade with four Garcinia taxa within clusioid clade of the Malpighiales.

MITOCHONDRIAL DNA PART B-RESOURCES (2021)

Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

Fast and accurate long-read assembly with wtdbg2

Jue Ruan et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

RepeatModeler2 for automated genomic discovery of transposable element families

Jullien M. Flynn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biotechnology & Applied Microbiology

Long-read-based human genomic structural variation detection with cuteSV

Tao Jiang et al.

GENOME BIOLOGY (2020)

Article Genetics & Heredity

Origin and evolution of the octoploid strawberry genome

Patrick P. Edger et al.

NATURE GENETICS (2019)

Article Multidisciplinary Sciences

Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

Zhenchang Liang et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

UniProt: a worldwide hub of protein knowledge

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content

Hue T. M. Tran et al.

PLANT BIOTECHNOLOGY JOURNAL (2018)

Article Horticulture

Morphological variability in leaves of Chinese wild Vitis species

Zhuo Min et al.

SCIENTIA HORTICULTURAE (2018)

Review Genetics & Heredity

The Third Revolution in Sequencing Technology

Erwin L. van Dijk et al.

TRENDS IN GENETICS (2018)

Article Biochemical Research Methods

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

Michael J. Roach et al.

BMC BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Expansion of the Gene Ontology knowledgebase and resources

S. Carbon et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

Article Biochemistry & Molecular Biology

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Jaime Huerta-Cepas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemical Research Methods

GenomeScope: fast reference-free genome profiling from short reads

Gregory W. Vurture et al.

BIOINFORMATICS (2017)

Article Biochemical Research Methods

Phased diploid genome assembly with single-molecule real-time sequencing

Chen-Shan Chin et al.

NATURE METHODS (2016)

Article Biochemistry & Molecular Biology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Biochemistry & Molecular Biology

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Agriculture, Multidisciplinary

The wild relatives of grape in China: diversity, conservation gaps and impact of climate change

Jianfu Jiang et al.

AGRICULTURE ECOSYSTEMS & ENVIRONMENT (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Review Plant Sciences

Gene duplication as a driver of plant morphogenetic evolution

Stefan A. Rensing

CURRENT OPINION IN PLANT BIOLOGY (2014)

Article Multidisciplinary Sciences

Genomic Signatures of Specialized Metabolism in Plants

Lee Chae et al.

SCIENCE (2014)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Genetics & Heredity

The draft genome of sweet orange (Citrus sinensis)

Qiang Xu et al.

NATURE GENETICS (2013)

Article Multidisciplinary Sciences

The tomato genome sequence provides insights into fleshy fruit evolution

Shusei Sato et al.

NATURE (2012)

Article Biochemical Research Methods

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

Guillaume Marcais et al.

BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Genetics & Heredity

The genome of Theobroma cacao

Xavier Argout et al.

NATURE GENETICS (2011)

Article Genetics & Heredity

The genome of the domesticated apple (Malus x domestica Borkh.)

Riccardo Velasco et al.

NATURE GENETICS (2010)

Article Genetics & Heredity

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

Dapeng Wang et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Morgan N. Price et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Review Genetics & Heredity

OPINION The evolutionary significance of ancient genome duplications

Yves Van de Peer et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Multidisciplinary Sciences

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

G. A. Tuskan et al.

SCIENCE (2006)

Article Biochemical Research Methods

CAFE: a computational tool for the study of gene family evolution

T De Bie et al.

BIOINFORMATICS (2006)

Article Computer Science, Information Systems

Engineering a software tool for gene structure prediction in higher organisms

G Gremme et al.

INFORMATION AND SOFTWARE TECHNOLOGY (2005)

Article Biochemistry & Molecular Biology

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints

M Stanke et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemical Research Methods

Gene finding in novel genomes

I Korf

BMC BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

OrthoMCL: Identification of ortholog groups for eukaryotic genomes

L Li et al.

GENOME RESEARCH (2003)

Article Multidisciplinary Sciences

A draft sequence of the rice genome (Oryza sativa L. ssp indica)

J Yu et al.

SCIENCE (2002)