Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

The Genetic Basis of Tomato Aroma

(2021) Matteo Martina et al.   Genes

Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)

(2021) Xuewen Wang et al.   GigaScience

Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment

(2021) Nur Shuhadah Mohd Saad et al.   Frontiers in Genetics

The complete molecular sequence of chloroplast genome of Lablab purpureus (L.) Sweet

(2021) Na Li et al.   Mitochondrial DNA Part B-Resources

Antiproliferative potential of Andean Berry ( Vacciniu m meridionale Swartz) juice in combination with Aspirin in human SW480 colon adenocarcinoma cells

(2021) Sandra S. Arango‐Varela et al.   JOURNAL OF FOOD BIOCHEMISTRY

The chromosome‐scale reference genome of safflower ( Carthamus tinctorius ) provides insights into linoleic acid and flavonoid biosynthesis

(2021) Zhihua Wu et al.   PLANT BIOTECHNOLOGY JOURNAL

Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics

(2021) Jacob I. Marsh et al.   THEORETICAL AND APPLIED GENETICS

Meta-GWAS for quantitative trait loci identification in soybean

(2021) Johnathon M Shook et al.   G3-Genes Genomes Genetics

Studying the Genetic Diversity of Yam Bean Using a New Draft Genome Assembly

(2021) Cassandria G. Tay Fernandez et al.   Agronomy-Basel

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

(2021) Peng Qin et al.   CELL

Mineral Content, Chemical Analysis, In Vitro Antidiabetic and Antioxidant Activities, and Antibacterial Power of Aqueous and Organic Extracts of Moroccan Leopoldia comosa (L.) Parl. Bulbs

(2021) Mohamed Boulfia et al.   Evidence-based Complementary and Alternative Medicine

Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes

(2021) Xiaohui Zhang et al.   Molecular Plant

The Chemical Composition of Oils and Cakes of Ochna serrulata (Ochnaceae) and Other Underutilized Traditional Oil Trees from Western Zambia

(2021) Adela Frankova et al.   MOLECULES

Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation

(2021) Haifei Hu et al.   NEW PHYTOLOGIST

Current status of structural variation studies in plants

(2021) Yuxuan Yuan et al.   PLANT BIOTECHNOLOGY JOURNAL

Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

(2021) Philipp E. Bayer et al.   PLANT BIOTECHNOLOGY JOURNAL

The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

(2021) Raquel Santos da Silva et al.   PLoS One

Fast-forward breeding for a food-secure world

(2021) Rajeev K. Varshney et al.   TRENDS IN GENETICS

The pangenome of banana highlights differences between genera and genomes

(2021) Habib Rijzaani et al.   Plant Genome

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

(2021) Philipp E. Bayer et al.   Plant Genome

The application of pangenomics and machine learning in genomic selection in plants

(2021) Philipp E. Bayer et al.   Plant Genome

Natural Genetic Diversity in Tomato Flavor Genes

(2021) Lara Pereira et al.   Frontiers in Plant Science

Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain

(2021) Pradeep Ruperao et al.   Frontiers in Plant Science

Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding

(2021) Sujata Thakur et al.   Frontiers in Plant Science

Comparative cytology combined with transcriptomic and metabolomic analyses of Solanum nigrum L. in response to Cd toxicity

(2021) Juncai Wang et al.   JOURNAL OF HAZARDOUS MATERIALS

Genome-wide imputation using the practical haplotype graph in the heterozygous crop cassava

(2021) Evan M Long et al.   G3-Genes Genomes Genetics

Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

(2021) Silvia F. Zanini et al.   Plant Genome

Climate change and the need for agricultural adaptation

(2020) Robyn Anderson et al.   CURRENT OPINION IN PLANT BIOLOGY

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

(2020) Oleksandr M. Maistrenko et al.   ISME Journal

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

Whole-genome sequencing of the NARO World Rice Core Collection (WRC) as the basis for diversity and association studies

(2020) N Tanaka et al.   PLANT AND CELL PHYSIOLOGY

Trait associations in the pangenome of pigeon pea ( Cajanus cajan )

(2020) Junliang Zhao et al.   PLANT BIOTECHNOLOGY JOURNAL

The genome of kenaf ( Hibiscus cannabinus L.) provides insights into bast fibre and leaf shape biogenesis

(2020) Liwu Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

(2020) Wen-Biao Jiao et al.   Nature Communications

Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus

(2020) Iulian Gabur et al.   Scientific Reports

Pangenome Graphs

(2020) Jordan M. Eizenga et al.   Annual Review of Genomics and Human Genetics

Plant pangenomics: approaches, applications and advancements

(2020) Monica Furaste Danilevicz et al.   CURRENT OPINION IN PLANT BIOLOGY

First report of Basella alba naturally infected with basella rugose mosaic virus in Hawaii

(2020) Xupeng Wang et al.   PLANT DISEASE

A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction

(2020) Sarah E. Jensen et al.   Plant Genome

RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars

(2020) Amandeep Mittal et al.   BMC GENOMICS

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

Dolichos Lablab-an underutilized crop with future potentials for food and nutrition security: a review

(2020) Josephine J. Minde et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Identifying barley pan-genome sequence anchors using genetic mapping and machine learning

(2020) Shang Gao et al.   THEORETICAL AND APPLIED GENETICS

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

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

The complete chloroplast genome sequence of the Canna edulis Ker Gawl. (Cannaceae)

(2020) Qianglong Zhu et al.   Mitochondrial DNA Part B-Resources

A chromosome‐level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava ( Psidium guajava )

(2020) Chen Feng et al.   PLANT BIOTECHNOLOGY JOURNAL

Hyacinth bean (Lablab purpureus L.) – An underutilised crop with future potential

(2020) M. Naeem et al.   SCIENTIA HORTICULTURAE

Small Millets for Enduring Food Security Amidst Pandemics

(2020) Mehanathan Muthamilarasan et al.   TRENDS IN PLANT SCIENCE

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

(2020) Michael Abrouk et al.   Nature Communications

The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development

(2020) Manosh Kumar Biswas et al.   Scientific Reports

Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives

(2020) Aldrin Y. Cantila et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Frontiers in Dissecting and Managing Brassica Diseases: From Reference-Based RGA Candidate Identification to Building Pan-RGAomes

(2020) Yueqi Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Edible Fruit Plant Species in the Amazon Forest Rely Mostly on Bees and Beetles as Pollinators

(2020) Fabricia Sousa Paz et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

The barley pan-genome reveals the hidden legacy of mutation breeding

(2020) Murukarthick Jayakodi et al.   NATURE

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense

(2020) Rasmita Rani Das et al.   Scientific Reports

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

The genome of broomcorn millet

(2019) Changsong Zou et al.   Nature Communications

Lateral transfers of large DNA fragments spread functional genes among grasses

(2019) Luke T. Dunning et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction of genetic linkage map and genome dissection of domestication-related traits of moth bean (Vigna aconitifolia), a legume crop of arid areas

(2019) Chutintorn Yundaeng et al.   MOLECULAR GENETICS AND GENOMICS

Rapid evolution of protein diversity by de novo origination in Oryza

(2019) Li Zhang et al.   Nature Ecology & Evolution

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

(2019) Lei Gao et al.   NATURE GENETICS

First report of genome size and ploidy of the underutilized leguminous tuber crop Yam Bean (Pachyrhizus erosus and P. tuberosus) by flow cytometry

(2019) Kalidas Pati et al.   Plant Genetic Resources-Characterization and Utilization

Role of Wetland Plants and Use of Ornamental Flowering Plants in Constructed Wetlands for Wastewater Treatment: A Review

(2019) Luis Sandoval et al.   Applied Sciences-Basel

Haplotype-aware graph indexes

(2019) Jouni Sirén et al.   BIOINFORMATICS

Subsets of NLR genes show differential signatures of adaptation during colonisation of new habitats

(2019) Remco Stam et al.   NEW PHYTOLOGIST

Complete chloroplast genome sequence of Carthamus tinctorius L. from PacBio Sequel Platform

(2019) Zhi-Hua Wu et al.   Mitochondrial DNA Part B-Resources

Long-read sequencing in deciphering human genetics to a greater depth

(2019) Mohit K. Midha et al.   HUMAN GENETICS

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

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

Characterisation of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

(2019) Aria Dolatabadian et al.   PLANT BIOTECHNOLOGY JOURNAL

Chemical Genomic Profiling Unveils the in Vitro and in Vivo Antiplasmodial Mechanism of Açaı́ (Euterpe oleracea Mart.) Polyphenols

(2019) Letícia T. Ferreira et al.   ACS Omega

Stay-Green Trait: A Prospective Approach for Yield Potential, and Drought and Heat Stress Adaptation in Globally Important Cereals

(2019) Kamal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits

(2019) Shaogui Guo et al.   NATURE GENETICS

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

(2019) Aamir W. Khan et al.   TRENDS IN PLANT SCIENCE

Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean

(2019) Yang Liu et al.   Frontiers in Genetics

Application of Near-Infrared Hyperspectral Imaging with Machine Learning Methods to Identify Geographical Origins of Dry Narrow-Leaved Oleaster (Elaeagnus angustifolia) Fruits

(2019) Pan Gao et al.   Foods

Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops

(2019) Elliott J. Price et al.   PLANT JOURNAL

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

(2019) Agnieszka A. Golicz et al.   TRENDS IN GENETICS

Identification by Molecular Docking ofHomoisoflavones from Leopoldia comosa as Ligands of Estrogen Receptors

(2018) Fedora Grande et al.   MOLECULES

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Transcriptome profiling of genes involved in photosynthesis in Elaeagnus angustifolia L. under salt stress

(2018) J. Lin et al.   PHOTOSYNTHETICA

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

(2018) Bhavna Hurgobin et al.   PLANT BIOTECHNOLOGY JOURNAL

Potential, constraints and applications of in vitro methods in improving grain legumes

(2018) Aditya Pratap et al.   PLANT BREEDING

MCRiceRepGP: A framework for the identification of sexual reproduction associated genes in rice

(2018) Agnieszka A Golicz et al.   PLANT JOURNAL

Growth performance, organ-level ionic relations and organic osmoregulation of Elaeagnus angustifolia in response to salt stress

(2018) Zhengxiang Liu et al.   PLoS One

Assessment of fruit aroma for twenty-seven guava ( Psidium guajava ) accessions through three fruit developmental stages

(2018) Pamela Moon et al.   SCIENTIA HORTICULTURAE

Identification of drought-inducible regulatory factors in Lablab purpureus by a comparative genomic approach

(2018) Biao Wang et al.   Crop & Pasture Science

Contribution of Schinziophyton rautanenii to Sustainable Diets, Livelihood Needs and Environmental Sustainability in Southern Africa

(2018) Alfred Maroyi   Sustainability

Chemical, antimicrobial, and molecular characterization of mortiño (Vaccinium floribundum Kunth) fruits and leaves

(2018) Susana Llivisaca et al.   Food Science & Nutrition

The complete chloroplast genome sequences of little millet (Panicum sumatrense Roth ex Roem. and Schult.) (Poaceae)

(2018) Raveendar Sebastin et al.   Mitochondrial DNA Part B-Resources

Recent advancement in modern genomic tools for adaptation of Lablab purpureus L to biotic and abiotic stresses: present mechanisms and future adaptations

(2018) Krishna Kumar Rai et al.   ACTA PHYSIOLOGIAE PLANTARUM

Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower

(2018) Jiang Chen et al.   BMC GENOMICS

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Pan-genome of cultivated pepper (Capsicum ) and its use in gene presence-absence variation analyses

(2018) Lijun Ou et al.   NEW PHYTOLOGIST

Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome

(2018) Philipp E Bayer et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome wide association mapping of agro-morphological traits among a diverse collection of finger millet (Eleusine coracana L.) genotypes using SNP markers

(2018) Divya Sharma et al.   PLoS One

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

(2018) et al.   SCIENCE

Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants

(2018) Xiaofang Liao et al.   Scientific Reports

Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species

(2018) Bárbara Regina Bazzo et al.   BMC PLANT BIOLOGY

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

(2018) Jingyin Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

QTL analysis of domestication syndrome in zombi pea (Vigna vexillata), an underutilized legume crop

(2018) Sujinna Dachapak et al.   PLoS One

The draft genomes of five agriculturally important African orphan crops

(2018) Yue Chang et al.   GigaScience

Enset in Ethiopia: a poorly characterized but resilient starch staple

(2018) James S Borrell et al.   ANNALS OF BOTANY

Genetic diversity in cultivated yam bean (Pachyrhizus spp.) evaluated through multivariate analysis of morphological and agronomic traits

(2017) A. Séraphin Zanklan et al.   GENETIC RESOURCES AND CROP EVOLUTION

Long-read genome sequencing identifies causal structural variation in a Mendelian disease

(2017) Jason D Merker et al.   GENETICS IN MEDICINE

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

Genetic Diversity in the Desert Watermelon Citrullus colocynthis and its Relationship with Citrullus Species as Determined by High-frequency Oligonucleotides-targeting Active Gene Markers

(2017) Amnon Levi et al.   JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

(2017) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

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

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

(2017) Sean P. Gordon et al.   Nature Communications

Unconventional vegetables collected in Brazil: chromosome number and description of nuclear DNA content

(2017) Luis Felipe Lima e Silva et al.   Crop Breeding and Applied Biotechnology

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

Karyotype and genome size in Euterpe Mart. (Arecaceae) species

(2016) Giovana Augusta Torres et al.   Comparative Cytogenetics

The pangenome of an agronomically important crop plant Brassica oleracea

(2016) Agnieszka A. Golicz et al.   Nature Communications

Genetic Mapping of Millions of SNPs in Safflower ( Carthamus tinctorius L.) via Whole-Genome Resequencing

(2016) John E. Bowers et al.   G3-Genes Genomes Genetics

Complete chloroplast genome sequence of Solanum nigrum and development of markers for the discrimination of S. nigrum

(2016) Kwang-Soo Cho et al.   Horticulture Environment and Biotechnology

Diversity of yam bean ( Pachyrhizus spp. Fabaceae) based on morphoagronomic traits in the Brazilian Amazon

(2016) Edinei Santos da SILVA et al.   ACTA AMAZONICA

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding

(2016) Javaid A. Bhat et al.   Frontiers in Genetics

Novel Genetic Resources in the Genus Vigna Unveiled from Gene Bank Accessions

(2016) Yu Takahashi et al.   PLoS One

Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt

(2015) Jie-Yin Chen et al.   BMC PLANT BIOLOGY

Disease Resistance Gene Analogs (RGAs) in Plants

(2015) Manoj Sekhwal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

De novo assembly of kenaf (Hibiscus cannabinus) transcriptome using Illumina sequencing for gene discovery and marker identification

(2015) Liwu Zhang et al.   MOLECULAR BREEDING

Towards plant pangenomics

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

Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

(2015) Rusama Marubodee et al.   PLoS One

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

(2015) Fei Lu et al.   Nature Communications

The whole chloroplast genome sequence of black nightshade plant (Solanum nigrum)

(2015) Abdur Rahim Khan et al.   Mitochondrial DNA Part A

SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips

(2014) Shoshana Marcus et al.   BIOINFORMATICS

Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana

(2014) Jingyin Yu et al.   BMC GENOMICS

Antioxidant Enzymes and Photosynthetic Responses to Drought Stress of Three Canna edulis Cultivars

(2014) Wen-E Zhang et al.   Korean Journal of Horticultural Science & Technology

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Analysis of the Citrullus colocynthis Transcriptome during Water Deficit Stress

(2014) Zhuoyu Wang et al.   PLoS One

A Draft Genome Sequence for Ensete ventricosum, the Drought-Tolerant “Tree Against Hunger”

(2014) James Harrison et al.   Agronomy-Basel

A new endornavirus species infecting Malabar spinach (Basella alba L.)

(2013) Ryo Okada et al.   ARCHIVES OF VIROLOGY

Identification of Key Drought Stress-Related Genes in the Hyacinth Bean

(2013) Lu-Ming Yao et al.   PLoS One

Yield Trends Are Insufficient to Double Global Crop Production by 2050

(2013) Deepak K. Ray et al.   PLoS One

Constituents from Vigna vexillata and Their Anti-Inflammatory Activity

(2012) Yann-Lii Leu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Comparative transcriptome analysis of cadmium responses in Solanum nigrum and Solanum torvum

(2012) Jin Xu et al.   NEW PHYTOLOGIST

The First Illumina-Based De Novo Transcriptome Sequencing and Analysis of Safflower Flowers

(2012) Huang Lulin et al.   PLoS One

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

(2010) Chad Laing et al.   BMC BIOINFORMATICS

Metabolic analysis of guava (Psidium guajava L.) fruits at different ripening stages using different data-processing approaches

(2010) Sarah Lee et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Genetic compatibility among domesticated and wild accessions of the tropical tuberous legumeVigna vexillata(L.) A. Rich.

(2010) F. Damayanti et al.   Crop & Pasture Science

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

(2010) Margaret R. Woodhouse et al.   PLOS BIOLOGY