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Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes

BIOMOLECULES (2023)

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Article Plant Sciences

Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)

Huijuan Zhou et al.

Summary: Walnut (Juglans) species, including eastern black walnut (Juglans nigra), are globally important nut crops. In this study, a high-quality genome assembly of J. nigra was generated using various technologies. Resequencing analysis revealed population decline in J. nigra during the glacial maximum, and a whole-genome duplication event was identified. Comparative genomics identified genes related to walnut husk and shell development, as well as seed oil synthesis. This work provides valuable insights into fatty acid bioaccumulation and disease resistance in nut crops, and serves as a crucial resource for walnut breeding.

HORTICULTURE RESEARCH (2023)

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Review Biotechnology & Applied Microbiology

Methods to improve the accuracy of next-generation sequencing

Chu Cheng et al.

Summary: Next-generation sequencing (NGS) is widely used in life science research and clinical diagnosis. However, its high error rate poses challenges for detecting SNPs and low-abundance mutations, limiting its clinical applications. Sanger sequencing is still considered the gold standard and is used to verify the results of NGS in practice. Improvements have been made in template preparation, sequencing strategy, and data processing to ensure high-quality NGS data. Challenges and future development of NGS in clinical application are also discussed.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2023)

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Article Biochemistry & Molecular Biology

Large haplotypes highlight a complex age structure within the maize pan-genome

Jianing Liu et al.

Summary: Through analyzing 26 complete maize genomes, it was found that haplotype divergence in low recombination regions, such as centromeres, occurred as far back as 450 thousand years ago, indicating the presence of ancient diversity in maize populations.

GENOME RESEARCH (2023)

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Article Biochemistry & Molecular Biology

KEGG for taxonomy-based analysis of pathways and genomes

Minoru Kanehisa et al.

Summary: KEGG is a manually curated database resource that integrates various biological objects classified into systems, genomic, chemical, and health information. Through the KEGG identifier and URL links, users can retrieve and browse information for different biological objects, including pathway maps, hierarchy, and genomes. KEGG has also improved KO assignment annotation and included more eukaryotic genomes for better representation of organisms in the taxonomic tree. The taxonomy mapping enables analysis of the conservation of functional and physical links among genes in different organism groups.

NUCLEIC ACIDS RESEARCH (2023)

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Article Biochemistry & Molecular Biology

Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

Shangkun Jin et al.

Summary: This study constructs a pan-genome based on structural variations in cotton and demonstrates their association with important agronomic traits through population structure analysis and genome-wide association studies. The findings highlight the importance of structural variations in speciation, domestication, and improvement of cultivated crop species.

MOLECULAR PLANT (2023)

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Editorial Material Biochemistry & Molecular Biology

Long-read sequencing (method of the year 2022): The way forward for plant omics research

Sunil Kumar Sahu et al.

MOLECULAR PLANT (2023)

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Letter Biochemistry & Molecular Biology

Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes

Bosen Zhang et al.

MOLECULAR PLANT (2023)

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Article Genetics & Heredity

Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet

Haidong Yan et al.

Summary: A graph-based pan-genome, developed from ten pearl millet chromosomal genomes and one existing assembly, identifies 424,085 genomic structural variations. Comparative genomics and transcriptomics analyses highlight the role of RWP-RK transcription factors and endoplasmic reticulum (ER)-related genes in heat tolerance. Overexpression of an RWP-RK gene enhances plant heat tolerance and activates ER-related genes, indicating their importance in heat tolerance. Structural variations influence gene expression associated with heat tolerance and contribute to the adaptation of pearl millet during domestication. This study provides a comprehensive genomic resource for understanding heat tolerance and improving crop resilience to changing climates.

NATURE GENETICS (2023)

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Article Genetics & Heredity

A graph-based genome and pan-genome variation of the model plant Setaria

Qiang He et al.

Summary: By assembling 110 representative genomes, we established the pan-genome of Setaria italica and identified 73,528 gene families. The pan-genome contains core genes, soft core genes, dispensable genes, and private genes. We also detected nonredundant structural variants and found their importance in domestication and improvement of foxtail millet. Additionally, large-scale genetic studies across different environments identified potential genes for millet improvement at different geographic sites.

NATURE GENETICS (2023)

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Article Genetics & Heredity

Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

Ning Li et al.

Summary: Researchers constructed a tomato super-pangenome using chromosome-scale genomes of nine wild species and two cultivated accessions, revealing the genomic diversity and structural variation across wild and cultivated tomatoes.

NATURE GENETICS (2023)

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Editorial Material Multidisciplinary Sciences

Harnessing crop diversity

Susan R. McCouch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)

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Article Agronomy

Photoperiod and gravistimulation-associated Tiller Angle Control 1 modulates dynamic changes in rice plant architecture

Hong Wang et al.

Summary: TAC1 regulates rice dynamic plant architecture by affecting endogenous auxin distribution in response to photoperiodic and gravitropic cues, which may explain its widespread distribution in indica rice.

THEORETICAL AND APPLIED GENETICS (2023)

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Article Plant Sciences

Grapevine genome analysis demonstrates the role of gene copy number variation in the formation of monoterpenes

Robin Nicole Bosman et al.

Summary: Volatile organic compounds, such as terpenes, play a vital role in influencing the quality parameters of grapevine through their contribution to the flavor and aroma profile of grapes. The biosynthesis of these compounds is complex and controlled by multiple genes, many of which are unidentified. By analyzing volatile metabolic data from a grapevine mapping population, researchers identified several significant genomic regions associated with terpene modulation in grape berries. These findings provide insights into the molecular mechanisms of terpene accumulation and offer potential applications in developing grape cultivars with desired terpene profiles.

FRONTIERS IN PLANT SCIENCE (2023)

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Article Genetics & Heredity

The Gene Ontology knowledgebase in 2023

Suzi A. Aleksander et al.

Summary: The Gene Ontology (GO) knowledgebase is a comprehensive resource that provides information about the functions of genes and gene products. It covers a wide range of organisms and receives updates from a consortium of scientists. The knowledgebase consists of three components: GO, which describes gene functionality; GO annotations, which provide evidence-supported statements about gene products; and GO-CAMs, which are models of molecular pathways. The knowledgebase is continuously updated and reviewed, and guidance is provided to users on how to make the best use of the data.

GENETICS (2023)

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Article Plant Sciences

Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)

Sushma Naithani et al.

Summary: Modeling biological processes and genetic-regulatory networks using in silico approaches is valuable for understanding how genes and variations result in specific traits. This study constructed a network of 57 transcription factors to explore gene-gene interactions in seed germination and coleoptile elongation under submergence. The network incorporates co-expression data and experimental evidence, and is publicly accessible to facilitate re-analysis of OMICs data and accelerate crop improvement.

PLANTS-BASEL (2023)

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Article Genetics & Heredity

The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes

Lior Glick et al.

Genome Biology and Evolution (2023)

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Article Biotechnology & Applied Microbiology

Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa

Matthew Huff et al.

Summary: This study assembled and annotated the genome of a muscadine grape cultivar 'Carlos' that is resistant to Xfsf, and found an expansion of resistance (R) genes in 'Carlos'. Transcriptome sequencing of 'Carlos' infected with Xfsf revealed different gene expression and identified seven differentially expressed R genes. The results support the utility of a pan-genome approach to identify candidate genes for disease resistance and reveal differences between grape cultivars.

BMC GENOMICS (2023)

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Article Biochemical Research Methods

Efficient short read mapping to a pangenome that is represented by a graph of ED strings

Thomas Buechler et al.

Summary: The research focuses on developing graph-based models of pangenomes to improve read mapping efficiency and reduce memory requirements by encoding simple variations in the sequence.

BIOINFORMATICS (2023)

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Article Biotechnology & Applied Microbiology

A pangenome analysis pipeline provides insights into functional gene identification in rice

Jian Wang et al.

Summary: The researchers developed a novel strategy and analysis pipeline for constructing a plant pangenome and identifying the position information of genetic variants. They successfully constructed a high-quality rice pangenome and identified causal structural variations related to rice grain weight and plant height. This study provides valuable genomic resources for rice genomics research and improvement.

GENOME BIOLOGY (2023)

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Article Biochemistry & Molecular Biology

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Andrew D. Yates et al.

Summary: Ensembl Genomes provides access to non-vertebrate genomes complementing the vertebrate resources developed by the Ensembl project, creating one of the most comprehensive genomic resources globally. They are focused on reducing genome redundancy and improving gene annotation, pangenome analysis, data dissemination speed, and support for the microbial research community.

NUCLEIC ACIDS RESEARCH (2022)

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Article Plant Sciences

SorghumBase: a web-based portal for sorghum genetic information and community advancement

Nicholas Gladman et al.

Summary: SorghumBase is a web portal that provides resources for sorghum researchers. It hosts a wide range of sorghum genomic information and is built with a modular framework and open-source software to create a sustainable platform. It offers improved data collation and access for sorghum researchers to support genomics-assisted breeding.

PLANTA (2022)

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Review Biotechnology & Applied Microbiology

Reap the crop wild relatives for breeding future crops

Abhishek Bohra et al.

Summary: Crop wild relatives (CWRs) have played a crucial role in providing important traits or genes for crop improvement and global agricultural production. Advances in breeding, genomics, and gene-editing tools have accelerated the identification and transformation of CWRs into future ideal crops. Data-driven germplasm collection and management strategies, along with policy support, are equally important for improving access to CWRs and ensuring their sustainable use in meeting food and nutrition security targets.

TRENDS IN BIOTECHNOLOGY (2022)

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Article Multidisciplinary Sciences

Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber

Hongbo Li et al.

Summary: We report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies, and identify approximately 4.3 million genetic variants, including 56,214 structural variants. These findings provide valuable resources for studying agronomic traits and breeding of cucumber.

NATURE COMMUNICATIONS (2022)

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Article Biochemical Research Methods

ODGI: understanding pangenome graphs

Andrea Guarracino et al.

Summary: Pangenome graphs provide a complete representation of genomic diversity, but analyzing large-scale genome data using existing tools is challenging. Optimized Dynamic Genome/Graph Implementation (ODGI) is a new tool suite with efficient in-memory representation and support for various operations and visualization. Its parallel execution helps answer complex biological questions quickly.

BIOINFORMATICS (2022)

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Article Biochemical Research Methods

InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm

Emma Persson et al.

Summary: This paper presents an updated version of the InParanoid algorithm, which uses the faster tool DIAMOND instead of BLAST for orthology search. It reduces the runtime by 94% while maintaining similar performance in the Quest for Orthologs benchmark.

BIOINFORMATICS (2022)

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Article Genetics & Heredity

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Jana Ebler et al.

Summary: PanGenie is an alignment-free, k-mer-based tool that uses a haplotype-resolved pangenome reference and k-mer counts from short-read sequencing data to perform fast and accurate genotyping of a wide range of genetic variants. It outperforms mapping-based approaches in terms of speed and genotype concordance, especially for large insertions and variants in repetitive regions.

NATURE GENETICS (2022)

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Article Plant Sciences

Wheat Panache: A pangenome graph database representing presence-absence variation across sixteen bread wheat genomes

Philipp E. Bayer et al.

Summary: Bread wheat is a vital crop with a complex genome, making genomic approaches for improvement challenging. To address this, a wheat pangenome graph database has been developed for visualization and comparison of wheat genomes.

PLANT GENOME (2022)

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Article Plant Sciences

Pan-Genome Analysis Reveals the Abundant Gene Presence/Absence Variations Among Different Varieties of Melon and Their Influence on Traits

Yang Sun et al.

Summary: In this study, a melon pan-genome was constructed, revealing abundant genetic variations among different melon groups and identifying genes associated with fruit traits. In addition, novel gene sequences and genes were discovered.

FRONTIERS IN PLANT SCIENCE (2022)

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Article Plant Sciences

Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo)

Elad Oren et al.

Summary: Linking genotype with phenotype is a fundamental goal in biology, and recent advances in plant-genome sequencing have facilitated this process. In this study, we developed a multi-parental framework for trait dissection in melon and constructed a pan-genome for this crop. The framework combined genomic variation with phenotypic characterization to analyze various traits in melon. This integrated resource has the potential to enhance genetic dissection and accelerate breeding of this important crop.

PLANT JOURNAL (2022)

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Article Biochemical Research Methods

PanTools v3: functional annotation, classification and phylogenomics

Eef M. Jonkheer et al.

Summary: This article presents the latest update of PanTools, which enables the construction and comparative analysis of pangenomes, as well as the integration of functional annotations and phylogenetic analysis.

BIOINFORMATICS (2022)

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Article Multidisciplinary Sciences

Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon

Justin N. Vaughn et al.

Summary: This study examines the benefits of complete genomic information based on long-read assemblies in a biparental mapping experiment on melons. The research shows that a graph-based approach using both parental genomes can detect more variants across the population and reduce error rates compared to using a single reference genome. It also reveals the significant role of structural variations in shaping disease resistance loci.

NATURE COMMUNICATIONS (2022)

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Review Plant Sciences

Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies

Soodeh Tirnaz et al.

Summary: Global agricultural industries are facing pressure to meet future food demand, but the existing crop genetic diversity may not be sufficient. However, advances in genome sequencing technologies and discovery of genetic diversity in crop wild relatives (CWRs) offer potential for crop improvement. There are various ex-situ and in-situ resources holding rare and valuable wild species, which carry agronomically important traits. The availability and use of CWR genomic resources, as well as modern breeding experimental approaches and computational methods, can contribute to crop adaptability and yield improvement.

FRONTIERS IN PLANT SCIENCE (2022)

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Review Biochemistry & Molecular Biology

Plant pan-genomics: recent advances, new challenges, and roads ahead

Wei Li et al.

Summary: Pan-genomics is a powerful tool for studying genetic diversity, genomic evolution, and species domestication, as well as providing information for plant improvement. However, challenges such as computational complexity, high costs, and data integration remain. This review summarizes the definition and recent achievements of plant pan-genomics and discusses challenges and perspectives for future studies.

JOURNAL OF GENETICS AND GENOMICS (2022)

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Article Biochemistry & Molecular Biology

High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement

Changyou Liu et al.

Summary: This study analyzed the genomic diversity of mung bean based on a high-quality reference genome and pan-genome. The results showed differences in population structure between Chinese and non-Chinese accessions, indicating that mung bean was domesticated in South Asia and introduced to East Asia possibly through the Silk Road. The study also identified genetic variations involved in flowering regulation and associated SNPs and genes with agronomic traits. These findings provide insights into mung bean breeding.

PLANT COMMUNICATIONS (2022)

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Letter Biochemistry & Molecular Biology

Citrus Pan-Genome to Breeding Database (CPBD): A comprehensive genome database for citrus breeding

Hanmingzi Liu et al.

MOLECULAR PLANT (2022)

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Article Plant Sciences

The banana genome hub: a community database for genomics in the Musaceae

Gaetan Droc et al.

Summary: The Banana Genome Hub provides centralized access for genome assemblies, annotations, and various omics resources related to bananas and their relatives. It offers a range of tools and interfaces for comparative analysis, gene search, gene family analysis, and genome structure comparison. It aims to support basic, translational, and applied research in the banana scientific community.

HORTICULTURE RESEARCH (2022)

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Article Biology

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Weihong Qi et al.

Summary: This study demonstrates the use of high-fidelity sequencing reads and a specific assembler to achieve a high-resolution assembly of the cassava genome. The resulting assembly is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly to date. The study also identifies novel gene loci and explores the differential expression of transcripts. Additionally, the researchers use the assembly to build a cassava pan-genome, highlighting its importance for further research and breeding.

GIGASCIENCE (2022)

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Article Biotechnology & Applied Microbiology

A pan-Zea genome map for enhancing maize improvement

Songtao Gui et al.

Summary: Our study provides a comprehensive pan-Zea genome and genetic variation map for maize breeding. We identified a large number of dispensable genes in the pan-Zea population and discovered common structural variations associated with maize domestication. By integrating genetic analyses with multi-omics data, we demonstrated the potential utilization of structural variants in crop improvement.

GENOME BIOLOGY (2022)

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Article Cell Biology

A super pan-genomic landscape of rice

Lianguang Shang et al.

Summary: By studying the pan-genomes of large natural populations, we can uncover the genetic diversity and complexity of rice. We have created a super pan-genome of rice using long-read assembly and identified extensive structural variations and gene presence/absence variations. Additionally, we have discovered genetic variants associated with various traits in rice and identified a common set of genes that have played a role in adaptation and domestication in Asian and African rice.

CELL RESEARCH (2022)

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Letter Biotechnology & Applied Microbiology

BnPIR: Brassica napus pan-genome information resource for 1689 accessions

Jia-Ming Song et al.

PLANT BIOTECHNOLOGY JOURNAL (2021)

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Article Biochemical Research Methods

Panache: a web browser-based viewer for linearized pangenomes

Eloi Durant et al.

Summary: Pangenomics has evolved to study all sequences available, with linear representations being a suitable option for user-friendliness. Panache is a tool for visualizing gene-based and sequence-based pangenomes, using a linear layout similar to genome browsers.

BIOINFORMATICS (2021)

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Review Genetics & Heredity

Building pan-genome infrastructures for crop plants and their use in association genetics

Murukarthick Jayakodi et al.

Summary: Pan-genomic studies aim to represent the entire sequence diversity within a species for evolutionary studies, functional genomics, and breeding of cultivated plants. Advances in sequencing technology and assembly algorithms have made it possible to create multiple reference genomes and catalogue genetic variations in plant species with large and complex genomes.

DNA RESEARCH (2021)

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Article Biochemistry & Molecular Biology

GreenPhylDB v5: a comparative pangenomic database for plant genomes

Guignon Valentin et al.

Summary: Comparative genomics is the analysis of genomic relationships among different species, with GreenPhylDB providing a database for exploring gene families and homologous relationships among plant genomes. By harnessing multiple genome sequences by species, GreenPhylDBv5 introduces the concept of comparative pangenomics to predict homologous relationships and support community curation efforts.

NUCLEIC ACIDS RESEARCH (2021)

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Article Multidisciplinary Sciences

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Rajeev K. Varshney et al.

Summary: By studying the genetic diversity of chickpea, the research team estimated the divergence of Cicer over the last 21 million years and identified chromosomal locations of deleterious mutations in elite germplasm. They also found targets for purging deleterious alleles through genomics-assisted breeding and proposed three crop breeding strategies.

NATURE (2021)

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Article Multidisciplinary Sciences

Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

Qin Qiao et al.

Summary: Strawberry has become a model system for various research, with genomes of five different species sequenced in recent years. A study reported chromosome-scale reference genomes for five strawberry species, along with genome resequencing data for 128 additional accessions, providing valuable resources for future studies. The research also identified a new diploid species and explored the evolutionary dynamics of gene families, pointing out mutations associated with white pigmented fruit in different strawberry species.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Biochemical Research Methods

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

Haoyu Cheng et al.

Summary: hifiasm is a novel assembler that utilizes long high-fidelity sequence reads to accurately represent haplotype information, outperforming existing tools in haplotype-resolved assembly on various datasets, including a hexaploid genome dataset.

NATURE METHODS (2021)

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Article Plant Sciences

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

Lillian K. Padgitt-Cobb et al.

Summary: The draft phased assembly of the Cascade cultivar genome of hop provides a comprehensive representation of the hop genome, revealing genes with greater sequence divergence enriched for stress-response, growth, and flowering functions. The study also identified a high level of repetitive sequences in hop, along with a homolog of cannabidiolic acid synthase (CBDAS) expressed in multiple tissues, contributing to a deeper understanding of the genomic landscape of hop.

PLANT GENOME (2021)

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Article Plant Sciences

The Copy Number Variation of OsMTD1 Regulates Rice Plant Architecture

Qing Liu et al.

Summary: Copy number variation (CNV) can affect plant architecture and traits by altering gene expression levels, with a CNV in rice identified to modulate tiller number and leaf angle. This CNV influences traits through both dosage and position effects on specific genes, suggesting its potential importance in molecular breeding in rice.

FRONTIERS IN PLANT SCIENCE (2021)

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Article Biochemical Research Methods

The BioCyc Metabolic Network Explorer

Suzanne Paley et al.

Summary: The Metabolic Network Explorer is a user-friendly web-based software tool that allows users to specify a starting metabolite of interest and explore its immediate metabolic neighborhood interactively in either or both directions, providing dynamic control over which connections to follow.

BMC BIOINFORMATICS (2021)

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Article Biotechnology & Applied Microbiology

The pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content

Davoud Torkamaneh et al.

Summary: The construction of a pan-genome for cultivated soybean reveals a significant amount of novel genes, with over 90.6% of genes in the core genome shared by 99% of accessions. The PanSoy represents a major advancement in capturing the extent of genetic variation in cultivated soybean, serving as a valuable resource for soybean genomics research and breeding.

PLANT BIOTECHNOLOGY JOURNAL (2021)

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Article Plant Sciences

Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding

Lorenzo Barchi et al.

Summary: Eggplant is an important horticultural crop with a wide genetic diversity. A study on the eggplant pan-genome revealed additional genes compared to the reference genome, with selective sweeps related to fruit color, prickliness, and fruit shape driving the evolution from wild ancestors to present-day cultivars. Candidate genes underlying these selective sweeps were identified, suggesting a common set of orthologous genes in tomato and eggplant for fruit size and shape traits.

PLANT JOURNAL (2021)

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Article Multidisciplinary Sciences

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

Sushma Naithani et al.

Summary: The poorly characterized SDRLK subfamily in plants is being studied through manual bio-curation, leading to corrected gene annotations and identification of candidate genes involved in plant development, pathogen resistance, and abiotic stress tolerance. The study highlights the importance of manual annotation in improving the quality and contents of public databases.

PEERJ (2021)

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Article Plant Sciences

Genome wide association study of agronomic and seed traits in a world collection of proso millet (Panicum miliaceum L.)

Sameh Boukail et al.

Summary: The study investigated the genomic and phenotypic diversity of a global proso millet collection, identifying 13 MTAs for key agronomic and seed traits with potential for application in breeding programs.

BMC PLANT BIOLOGY (2021)

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Article Plant Sciences

A pan-genomic approach to genome databases using maize as a model system

Margaret R. Woodhouse et al.

Summary: MaizeGDB introduces a pan-genomic approach to hosting genomic data, allowing researchers to easily track the structural and functional differences of a locus and its orthologs across maize. This framework is believed to be unique and can serve as a template for other genomic databases hosting large-scale pan-genomic data.

BMC PLANT BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae

Charles Hawkins et al.

Summary: The research team created metabolic pathway databases of 126 plant and algal genomes, improving quality through a semi-automated validation process. They compared metabolic content across organisms, identifying distinct metabolic groups, and demonstrated the utility of the resource in plant biology research.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2021)

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Review Plant Sciences

Plant lectins and their many roles: Carbohydrate-binding and beyond

Sushma Naithani et al.

Summary: Lectins are proteins that bind to specific carbohydrates and function as readers of the sugar code. They play important roles in plant growth, development, and responses to various stimuli, showing structural diversity and evolutionary expansion with distinct signatures in different clades. Understanding their structure and function can potentially improve agricultural productivity through genetic manipulation and regulation of metabolic pathways.

JOURNAL OF PLANT PHYSIOLOGY (2021)

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Article Plant Sciences

Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development

Parul Gupta et al.

Summary: This study conducted a comprehensive transcriptome atlas of Chia using RNA sequencing, identifying a large number of gene transcripts and analyzing their expression patterns in different tissues and growth stages. Potential genetic markers were also discovered from the analysis of the transcripts. This provides important genomic resources for basic research and genetic breeding of Chia.

FRONTIERS IN PLANT SCIENCE (2021)

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Article Plant Sciences

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

Pradeep Ruperao et al.

Summary: The study constructed the sorghum pan-genome, revealing its structural and functional characteristics, and analyzing its role in genetic gain and drought adaptation. Results showed that the sorghum genome has rich gene diversity that can be utilized in crop improvement.

FRONTIERS IN PLANT SCIENCE (2021)

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Review Biotechnology & Applied Microbiology

Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes

Nazarul Hasan et al.

Summary: The use of DNA markers in plant breeding through marker-assisted selection has significantly sped up the development and market release of new crop varieties. It has also contributed to advancements in genetic diversity and breeding tools for crop plants.

JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY (2021)

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Article Plant Sciences

Extensive variation within the pan-genome of cultivated and wild sorghum

Yongfu Tao et al.

Summary: A study on the sorghum pan-genome sheds light on the genetic diversity and gene content variation within the sorghum primary gene pool. The research suggests that dispensable genes play a crucial role in sorghum adaptation, and reveals that genetic variation is influenced by recombination rate and transposable element content.

NATURE PLANTS (2021)

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Article Biotechnology & Applied Microbiology

Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

Jianying Li et al.

Summary: The research constructed a comprehensive genomic variome, identified loci associated with domestication and improvement selection signals, and analyzed genes related to agronomic traits. Additionally, pan-genome analysis revealed a large number of non-reference genes lost from the reference genomes, and showed the presence/absence variation, indicating genetic diversity changes driven by locus selection.

GENOME BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Marcela K. Tello-Ruiz et al.

Summary: Gramene is a knowledge-base focused on comparative functional analyses of genomic and pathway data for model plants and major crops, supporting agricultural researchers worldwide. They are committed to open access and reproducible science, continuously updating and expanding their content.

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Review Biotechnology & Applied Microbiology

How the pan-genome is changing crop genomics and improvement

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GENOME BIOLOGY (2021)

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Letter Biotechnology & Applied Microbiology

The nf-core framework for community-curated bioinformatics pipelines

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PLANT BIOTECHNOLOGY JOURNAL (2020)

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ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, VOL 21, 2020 (2020)

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PLOS ONE (2020)

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FRONTIERS IN PLANT SCIENCE (2020)

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Copy number variation of TdDof controls solid-stemmed architecture in wheat

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Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication

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ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline

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Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes

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Assembly of long, error-prone reads using repeat graphs

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The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

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NATURE GENETICS (2019)

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

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NATURE GENETICS (2019)

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African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops

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PLANTA (2019)

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Sequence tube maps: making graph genomes intuitive to commuters

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BIOINFORMATICS (2019)

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cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs

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BIOINFORMATICS (2019)

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Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat

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BMC GENETICS (2019)

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BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Dmitry Meleshko et al.

GENOME RESEARCH (2019)

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The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

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FRONTIERS IN PLANT SCIENCE (2019)

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Article Biochemical Research Methods

MoMI-G: modular multi-scale integrated genome graph browser

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BMC BIOINFORMATICS (2019)

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Editorial Material Plant Sciences

Pan-Genomic Illumination of Tomato Identifies Novel Gene-Trait Interactions

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TRENDS IN PLANT SCIENCE (2019)

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Article Biochemical Research Methods

GfaViz: flexible and interactive visualization of GFA sequence graphs

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BIOINFORMATICS (2019)

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SGTK: a toolkit for visualization and assessment of scaffold graphs

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BIOINFORMATICS (2019)

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Review Biochemistry & Molecular Biology

Exploring and Exploiting Pan-genomics for Crop Improvement

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MOLECULAR PLANT (2019)

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Fast and accurate genomic analyses using genome graphs

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NATURE GENETICS (2019)

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Article Biotechnology & Applied Microbiology

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

Jingyin Yu et al.

PLANT BIOTECHNOLOGY JOURNAL (2019)

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Article Biology

The draft genomes of five agriculturally important African orphan crops

Yue Chang et al.

GIGASCIENCE (2019)

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OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

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Article Biochemical Research Methods

Sequence Alignment on Directed Graphs

Vaddadi Naga Sai Kavya et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2019)

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Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance

Sariel Hubner et al.

NATURE PLANTS (2019)

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Article Biochemistry & Molecular Biology

Gramene 2018: unifying comparative genomics and pathway resources for plant research

Marcela K. Tello-Ruiz et al.

NUCLEIC ACIDS RESEARCH (2018)

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Trends in plant research using molecular markers

Jose Antonio Garrido-Cardenas et al.

PLANTA (2018)

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Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

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Letter Biotechnology & Applied Microbiology

KBase: The United States Department of Energy Systems Biology Knowledgebase

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NATURE BIOTECHNOLOGY (2018)

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Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

Qiang Zhao et al.

NATURE GENETICS (2018)

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Accurate detection of complex structural variations using single-molecule sequencing

Fritz J. Sedlazeck et al.

NATURE METHODS (2018)

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SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

Hartmut Foerster et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)

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MUMmer4: A fast and versatile genome alignment system

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PLOS COMPUTATIONAL BIOLOGY (2018)

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Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Wensheng Wang et al.

NATURE (2018)

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

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NATURE BIOTECHNOLOGY (2018)

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A universal SNP and small-indel variant caller using deep neural networks

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NATURE BIOTECHNOLOGY (2018)

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

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NEW PHYTOLOGIST (2018)

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Article Mathematical & Computational Biology

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

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DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)

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Current Strategies of Polyploid Plant Genome Sequence Assembly

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FRONTIERS IN PLANT SCIENCE (2018)

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RPAN: rice pan-genome browser for ∼3000 rice genomes

Chen Sun et al.

NUCLEIC ACIDS RESEARCH (2017)

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Plant Reactome: a resource for plant pathways and comparative analysis

Sushma Naithani et al.

NUCLEIC ACIDS RESEARCH (2017)

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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)

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Graphtyper enables population-scale genotyping using pangenome graphs

Hannes P. Eggertsson et al.

NATURE GENETICS (2017)

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The pangenome of hexaploid bread wheat

Juan D. Montenegro et al.

PLANT JOURNAL (2017)

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Article Biotechnology & Applied Microbiology

Hybrid assembly with long and short reads improves discovery of gene family expansions

Jason R. Miller et al.

BMC GENOMICS (2017)

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Article Biochemical Research Methods

A graph extension of the positional Burrows-Wheeler transform and its applications

Adam M. Novak et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2017)

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Review Biotechnology & Applied Microbiology

Towards plant pangenomics

Agnieszka A. Golicz et al.

PLANT BIOTECHNOLOGY JOURNAL (2016)

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Review Biotechnology & Applied Microbiology

Genomics of crop wild relatives: expanding the gene pool for crop improvement

Marta Brozynska et al.

PLANT BIOTECHNOLOGY JOURNAL (2016)

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Article Multidisciplinary Sciences

The pangenome of an agronomically important crop plant Brassica oleracea

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FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

Sushma Naithani et al.

Frontiers in Plant Science (2016)

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Review Plant Sciences

Towards an open grapevine information system

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HORTICULTURE RESEARCH (2016)

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Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

Ryan R. Wick et al.

BIOINFORMATICS (2015)

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Article Biochemical Research Methods

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Dinghua Li et al.

BIOINFORMATICS (2015)

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Copy number variation at the GL7 locus contributes to grain size diversity in rice

Yuexing Wang et al.

NATURE GENETICS (2015)

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SpeedSeq: ultra-fast personal genome analysis and interpretation

Colby Chiang et al.

NATURE METHODS (2015)

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Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)

Richard Durbin

BIOINFORMATICS (2014)

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The genome of Eucalyptus grandis

Alexander A. Myburg et al.

NATURE (2014)

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Article Biotechnology & Applied Microbiology

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

Ying-hui Li et al.

NATURE BIOTECHNOLOGY (2014)

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Article Biochemistry & Molecular Biology

Insights into the Maize Pan-Genome and Pan-Transcriptome

Candice N. Hirsch et al.

PLANT CELL (2014)

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A Roadmap for Functional Structural Variants in the Soybean Genome

Justin E. Anderson et al.

G3-GENES GENOMES GENETICS (2014)

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VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)

Sushma Naithani et al.

FRONTIERS IN PLANT SCIENCE (2014)

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Article Multidisciplinary Sciences

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

Lyza G. Maron et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

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Maize Metabolic Network Construction and Transcriptome Analysis

Marcela K. Monaco et al.

PLANT GENOME (2013)

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The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Angelique D'Hont et al.

NATURE (2012)

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Article Biotechnology & Applied Microbiology

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

Xun Xu et al.

NATURE BIOTECHNOLOGY (2012)

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Article Biochemical Research Methods

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

Martin T. Swain et al.

NATURE PROTOCOLS (2012)

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Article Biochemistry & Molecular Biology

Phytozome: a comparative platform for green plant genomics

David M. Goodstein et al.

NUCLEIC ACIDS RESEARCH (2012)

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Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

David E. Cook et al.

SCIENCE (2012)

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Article Genetics & Heredity

The genome of woodland strawberry (Fragaria vesca)

Vladimir Shulaev et al.

NATURE GENETICS (2011)

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Article Biotechnology & Applied Microbiology

Expansion and subfunctionalisation of flavonoid 3′, 5′-hydroxylases in the grapevine lineage

Luigi Falginella et al.

BMC GENOMICS (2010)

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Article Genetics & Heredity

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

Hon-Ming Lam et al.

NATURE GENETICS (2010)

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Article Agronomy

CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals

Andrea K. Knox et al.

THEORETICAL AND APPLIED GENETICS (2010)

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Article Multidisciplinary Sciences

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

Kenneth L. McNally et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

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Article Genetics & Heredity

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Nathan M. Springer et al.

PLOS GENETICS (2009)

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Article Plant Sciences

TAC1, a major quantitative trait locus controlling tiller angle in rice

Baisheng Yu et al.

PLANT JOURNAL (2007)

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Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:: Implications for the microbial pan-genome

H Tettelin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

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Article Biotechnology & Applied Microbiology

Simple sequence repeat diversity in diploid and tetraploid Coffea species

P Moncada et al.

GENOME (2004)

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Article Biochemistry & Molecular Biology

OrthoMCL: Identification of ortholog groups for eukaryotic genomes

L Li et al.

GENOME RESEARCH (2003)

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Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica

R Papa et al.

THEORETICAL AND APPLIED GENETICS (2003)

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