Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding

Allele‐aware chromosome‐scale assembly of the allopolyploid genome of hexaploid Ma Bamboo ( Dendrocalamus latiflorus Munro)

(2022) Yushan Zheng et al.   Journal of Integrative Plant Biology

Genomic footprints of sorghum domestication and breeding selection for multiple end uses

(2022) Xiaoyuan Wu et al.   Molecular Plant

Pore‐C simultaneously captures genome‐wide multi‐way chromatin interaction and associated DNA methylation status in Arabidopsis

(2022) Zhuowen Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

(2022) Jessen V. Bredeson et al.   Nature Communications

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

A draft phased assembly of the diploid Cascade hop ( Humulus lupulus ) genome

(2021) Lillian K. Padgitt‐Cobb et al.   Plant Genome

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

(2021) Tingting Zhu et al.   PLANT JOURNAL

Jumpstarting evolution: How transposition can facilitate adaptation to rapid environmental changes

(2021) Pierre Baduel et al.   CURRENT OPINION IN PLANT BIOLOGY

Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution

(2021) Kui Li et al.   Molecular Plant

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

(2021) Matthew B. Hufford et al.   SCIENCE

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

Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning

(2021) Peng Ni et al.   Nature Communications

Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants

(2020) Zhichao Xu et al.   BMC BIOLOGY

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

(2020) Sean P. Gordon et al.   Nature Communications

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore

(2020) Dandan Lang et al.   GigaScience

Highly accurate long-read HiFi sequencing data for five complex genomes

(2020) Ting Hon et al.   Scientific Data

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats

(2019) Tihana Vondrak et al.   PLANT JOURNAL

A guide to sequence your favorite plant genomes

(2018) Fay-Wei Li et al.   Applications in Plant Sciences

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods

(2016) Guillaume Martin et al.   BMC GENOMICS

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

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

Evolution of gene duplication in plants

(2016) Nicholas Panchy et al.   PLANT PHYSIOLOGY

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)

(2013) Jana Čížková et al.   PLoS One

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Consensus generation and variant detection by Celera Assembler

(2008) G. Denisov et al.   BIOINFORMATICS

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE