The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype

(2023) Amandine Velt et al.   G3-Genes Genomes Genetics

‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)

(2022) Simone Maestri et al.   BMC GENOMICS

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Centromere Identity and the Regulation of Chromosome Segregation

(2022) Kousik Sundararajan et al.   Frontiers in Cell and Developmental Biology

Repeat-based holocentromeres influence genome architecture and karyotype evolution

(2022) Paulo G. Hofstatter et al.   CELL

A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

(2022) Yun Deng et al.   Molecular Plant

The telomere‐to‐telomere gap‐free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding

(2022) Yilin Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Assembly of complete diploid-phased chromosomes from draft genome sequences

(2022) Andrea Minio et al.   G3-Genes Genomes Genetics

Structural variation and parallel evolution of apomixis in citrus during domestication and diversification

(2022) Nan Wang et al.   National Science Review

Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis

(2022) Junyang Yue et al.   Horticulture Research

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

(2021) Noé Cochetel et al.   G3-Genes Genomes Genetics

Back to the Origins: Background and Perspectives of Grapevine Domestication

(2021) Fabrizio Grassi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Multiple independent recombinations led to hermaphroditism in grapevine

(2021) Cheng Zou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome design of hybrid potato

(2021) Chunzhi Zhang et al.   CELL

Rootstock influences the effect of grapevine leafroll‐associated viruses on berry development and metabolism via abscisic acid signalling

(2021) Amanda M. Vondras et al.   MOLECULAR PLANT PATHOLOGY

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

(2021) Bo Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

(2021) Caroline Belser et al.   Communications Biology

The genetic and epigenetic landscape of the Arabidopsis centromeres

(2021) Matthew Naish et al.   SCIENCE

TELOMERE- RELATED MARKERS FOR CANCER

(2020) Xiaotian Yuan et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

What makes a centromere?

(2020) Paul B. Talbert et al.   EXPERIMENTAL CELL RESEARCH

Telomeric Transcription and Telomere Rearrangements in Quiescent Cells

(2020) Stéphane Coulon et al.   JOURNAL OF MOLECULAR BIOLOGY

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

DeepTE: a computational method for de novo classification of transposons with convolutional neural network

(2020) Haidong Yan et al.   BIOINFORMATICS

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

The genetic basis of sex determination in grapes

(2020) Mélanie Massonnet et al.   Nature Communications

Evaluation of copper-induced DNA damage in Vitis vinifera L. using Comet-FISH

(2020) Cláudia Castro et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development

(2019) Andrea Minio et al.   G3-Genes Genomes Genetics

Diploid Genome Assembly of the Wine Grape Carménère

(2019) Andrea Minio et al.   G3-Genes Genomes Genetics

Meiotic recombination within plant centromeres

(2019) Joiselle B Fernandes et al.   CURRENT OPINION IN PLANT BIOLOGY

The complex allosteric and redox regulation of the fumarate hydratase and malate dehydratase reactions of Arabidopsis thaliana Fumarase 1 and 2 gives clues for understanding the massive accumulation of fumarate

(2018) Juan P. Zubimendi et al.   FEBS Journal

Comparison of Oryza sativa and Oryza brachyantha genomes reveals selection-driven gene escape from the centromeric regions

(2018) Yi Liao et al.   PLANT CELL

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

(2018) Michael J. Roach et al.   PLoS Genetics

New Approaches for Genome Assembly and Scaffolding

(2018) Edward S. Rice et al.   Annual Review of Animal Biosciences

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

(2017) Punna Ramu et al.   NATURE GENETICS

Evolutionary genomics of grape (Vitis viniferassp.vinifera) domestication

(2017) Yongfeng Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Chen-Shan Chin et al.   NATURE METHODS

Defects in Peroxisomal 6-Phosphogluconate Dehydrogenase IsoformPGD2Prevent Gametophytic Interaction inArabidopsis thaliana

(2016) Christian Hölscher et al.   PLANT PHYSIOLOGY

Evolutionary perspectives of telomerase RNA structure and function

(2016) Joshua D. Podlevsky et al.   RNA Biology

De Novo Centromere Formation and Centromeric Sequence Expansion in Wheat and its Wide Hybrids

(2016) Xiang Guo et al.   PLoS Genetics

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The molecular basis for centromere identity and function

(2015) Kara L. McKinley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

Holocentromeres are dispersed point centromeres localized at transcription factor hotspots

(2014) Florian A Steiner et al.   eLife

Arabidopsis ALTERED MERISTEM PROGRAM 1 negatively modulates plant responses to abscisic acid and dehydration stress

(2013) Haitao Shi et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

How does genome instability affect lifespan?

(2011) Takehiko Kobayashi   GENES TO CELLS

Quantitative Genetic Bases of Anthocyanin Variation in Grape (Vitis vinifera L. ssp. sativa) Berry: A Quantitative Trait Locus to Quantitative Trait Nucleotide Integrated Study

(2009) A. Fournier-Level et al.   GENETICS

High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

(2008) Akira Kawabe et al.   GENETICS

Fine-scale genetic mapping of two Pierce’s disease resistance loci and a major segregation distortion region on chromosome 14 of grape

(2008) S. Riaz et al.   THEORETICAL AND APPLIED GENETICS