Current Strategies of Polyploid Plant Genome Sequence Assembly

BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach

(2018) Anqi Wang et al.   BIOINFORMATICS

The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis

(2018) Qian Shen et al.   Molecular Plant

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

(2018) Amanda M. Hulse-Kemp et al.   Horticulture Research

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

Recent Advances in Experimental Whole Genome Haplotyping Methods

(2017) Mengting Huang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genomic innovation for crop improvement

(2017) Michael W. Bevan et al.   NATURE

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy

(2017) John M. Bell et al.   NUCLEIC ACIDS RESEARCH

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

The pangenome of hexaploid bread wheat

(2017) Juan D. Montenegro et al.   PLANT JOURNAL

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

(2017) Tianying Lan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genome of wild olive and the evolution of oil biosynthesis

(2017) Turgay Unver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dense and accurate whole-chromosome haplotyping of individual genomes

(2017) David Porubsky et al.   Nature Communications

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

(2017) Bing Cheng et al.   GigaScience

Polyploidy: Pitfalls and paths to a paradigm

(2016) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Computational pan-genomics: status, promises and challenges

(2016)   BRIEFINGS IN BIOINFORMATICS

Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions

(2016) Naoya Urasaki et al.   DNA RESEARCH

Sequencing and comparative analyses of the genomes of zoysiagrasses

(2016) Hidenori Tanaka et al.   DNA RESEARCH

Genome analysis ofHibiscus syriacusprovides insights of polyploidization and indeterminate flowering in woody plants

(2016) Yong-Min Kim et al.   DNA RESEARCH

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

(2016) Jinghua Yang et al.   NATURE GENETICS

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

(2016) David John Bertioli et al.   NATURE GENETICS

Novel proteases from the genome of the carnivorous plantDrosera capensis: Structural prediction and comparative analysis

(2016) Carter T. Butts et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Homoeologs: What Are They and How Do We Infer Them?

(2016) Natasha M. Glover et al.   TRENDS IN PLANT SCIENCE

Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus

(2016) Wei Wu et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming

(2015) Shreepriya Das et al.   BMC GENOMICS

Progress, challenges and the future of crop genomes

(2015) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

High-resolution genetic mapping of maize pan-genome sequence anchors

(2015) Fei Lu et al.   Nature Communications

SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops

(2015) Josh P. Clevenger et al.   G3-Genes Genomes Genetics

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

(2015) Gabriel R. A. Margarido et al.   PLoS Computational Biology

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

(2014) Gina Cannarozzi et al.   BMC GENOMICS

Karyotype analysis of Santalum album L.

(2014) Zhang Xin-Hua et al.   CARYOLOGIA

Genome sequence of the cultivated cotton Gossypium arboreum

(2014) Fuguang Li et al.   NATURE GENETICS

Karyological analysis of bitter gourd (Momordica charantia L., Cucurbitaceae) from Southeast Asian countries

(2014) Nadia Kausar et al.   Plant Genetic Resources-Characterization and Utilization

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure

(2014) Sateesh Kagale et al.   Nature Communications

The tobacco genome sequence and its comparison with those of tomato and potato

(2014) Nicolas Sierro et al.   Nature Communications

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

(2014) Emily Berger et al.   PLoS Computational Biology

Haplotype assembly in polyploid genomes and identical by descent shared tracts

(2013) Derek Aguiar et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics

(2013) Rajeev K. Varshney et al.   BIOTECHNOLOGY ADVANCES

HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids

(2013) Aziz Mithani et al.   BMC GENOMICS

Sugar beet (Beta vulgarisL.) growth at different ploidy levels

(2013) Ramazan Beyaz et al.   CARYOLOGIA

Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

(2013) H. Hirakawa et al.   DNA RESEARCH

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

Draft genome of the kiwifruit Actinidia chinensis

(2013) Shengxiong Huang et al.   Nature Communications

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

(2013) Kentaro Yoshida et al.   eLife

HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data

(2012) Derek Aguiar et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Wheat TILLING Mutants Show That the Vernalization Gene VRN1 Down-Regulates the Flowering Repressor VRN2 in Leaves but Is Not Essential for Flowering

(2012) Andrew Chen et al.   PLoS Genetics

Size matters in Triticeae polyploids: larger genomes have higher remodeling

(2011) Miguel Bento et al.   GENOME

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Comparing De Novo Genome Assembly: The Long and Short of It

(2011) Giuseppe Narzisi et al.   PLoS One

Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.

(2010) S. Sato et al.   DNA RESEARCH

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

(2010) Frédéric Choulet et al.   PLANT CELL

Genomic aspects of research involving polyploid plants

(2010) Xiaohan Yang et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Molecular mechanisms of polyploidy and hybrid vigor

(2010) Z. Jeffrey Chen   TRENDS IN PLANT SCIENCE

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

(2010) Nynke L. van Berkum et al.   Jove-Journal of Visualized Experiments

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Polyploidy and genome restructuring: a variety of outcomes

(2009) Andrew L Hufton et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

An efficient high-throughput flow cytometric method for estimating DNA ploidy level in plants

(2009) A. Cousin et al.   CYTOMETRY PART A

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

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

(2008) V. Bansal et al.   BIOINFORMATICS

Polyploid and Hybrid Origins of Pacific Island Sandalwoods (Santalum, Santalaceae) Inferred from Low‐Copy Nuclear and Flow Cytometry Data

(2008) Danica T. Harbaugh   INTERNATIONAL JOURNAL OF PLANT SCIENCES

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

(2008) Ray Ming et al.   NATURE