Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

[1]  R. Varshney,et al.  High resolution mapping of restoration of fertility (Rf) by combining large population and high density genetic map in pigeonpea [Cajanus cajan (L.) Millsp] , 2020, BMC Genomics.

[2]  S. Cannon,et al.  Evaluating two different models of peanut’s origin , 2020, Nature Genetics.

[3]  A. Paterson,et al.  Reply to: Evaluating two different models of peanut’s origin , 2020, Nature Genetics.

[4]  Xiyin Wang,et al.  Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology , 2020, Frontiers in Genetics.

[5]  S. DiFazio,et al.  Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica) , 2020, Molecular ecology resources.

[6]  J. Batley,et al.  Trait associations in the pangenome of pigeon pea (Cajanus cajan) , 2020, Plant biotechnology journal.

[7]  J. Bennetzen,et al.  5Gs for crop genetic improvement , 2020, Current opinion in plant biology.

[8]  Jinpu Jin,et al.  PlantRegMap: charting functional regulatory maps in plants , 2019, Nucleic Acids Res..

[9]  Claire Yik-Lok Chung,et al.  Construction and comparison of three reference-quality genome assemblies for soybean. , 2019, The Plant journal : for cell and molecular biology.

[10]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[11]  H. Liu,et al.  Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement. , 2019, Molecular Plant.

[12]  L. F. V. Ferrão,et al.  How can a high-quality genome assembly help plant breeders? , 2019, GigaScience.

[13]  Xingtan Zhang,et al.  The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication , 2019, Nature Genetics.

[14]  Erez Lieberman Aiden,et al.  The genome sequence of segmental allotetraploid peanut Arachis hypogaea , 2019, Nature Genetics.

[15]  Patricia P. Chan,et al.  tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes , 2019, bioRxiv.

[16]  Hongkun Zheng,et al.  Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense , 2018, Nature Genetics.

[17]  S. Kelly,et al.  OrthoFinder: phylogenetic orthology inference for comparative genomics , 2019, Genome Biology.

[18]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[19]  T. Mockler,et al.  A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome , 2018, GigaScience.

[20]  Christophe Klopp,et al.  D-GENIES: dot plot large genomes in an interactive, efficient and simple way , 2018, PeerJ.

[21]  Alex Bateman,et al.  Non‐Coding RNA Analysis Using the Rfam Database , 2018, Current protocols in bioinformatics.

[22]  P. Wincker,et al.  The Rosa genome provides new insights into the domestication of modern roses , 2018, Nature Genetics.

[23]  Sanjit S. Batra,et al.  The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 , 2018, bioRxiv.

[24]  T. Liu,et al.  An Overlooked Paleotetraploidization in Cucurbitaceae , 2017, Molecular biology and evolution.

[25]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[26]  Jihun Kim,et al.  Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits , 2017, Nature Genetics.

[27]  Bernardo J. Clavijo,et al.  Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. , 2017, Genome research.

[28]  A. Paterson,et al.  Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform1[OPEN] , 2017, Plant Physiology.

[29]  Jianping Wang,et al.  Transcriptome profiles reveal gene regulation of peanut (Arachis hypogaea L.) nodulation , 2017, Scientific Reports.

[30]  S. Isobe,et al.  Draft genome sequence of subterranean clover, a reference for genus Trifolium , 2016, Scientific Reports.

[31]  Yan Liang,et al.  Neglecting legumes has compromised human health and sustainable food production , 2016, Nature Plants.

[32]  James T. Robinson,et al.  Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. , 2016, Cell systems.

[33]  S. Cloutier,et al.  RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants , 2016, BMC Genomics.

[34]  Daisy E. Pagete An end-to-end assembly of the Aedes aegypti genome , 2016, 1605.04619.

[35]  Juliane C. Dohm,et al.  Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes , 2016, Genome Biology.

[36]  Wei Huang,et al.  The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut , 2016, Nature Genetics.

[37]  Zhiwu Zhang,et al.  Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies , 2016, PLoS genetics.

[38]  M. Libault,et al.  Comprehensive Comparative Genomic and Transcriptomic Analyses of the Legume Genes Controlling the Nodulation Process , 2016, Front. Plant Sci..

[39]  Haibao Tang,et al.  Comparative genomic de-convolution of the cotton genome revealed a decaploid ancestor and widespread chromosomal fractionation. , 2016, The New phytologist.

[40]  Dave Kudrna,et al.  Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement , 2015, Scientific Reports.

[41]  Tim Sutton,et al.  Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.) , 2015, Scientific Reports.

[42]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[43]  O. Kohany,et al.  Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.

[44]  A. Paterson,et al.  Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events. , 2015, Molecular plant.

[45]  He Zhang,et al.  Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution , 2015, Nature Biotechnology.

[46]  Qing-Yong Yang,et al.  De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. , 2015, Molecular plant.

[47]  Rajeev K. Varshney,et al.  Draft genome sequence of adzuki bean, Vigna angularis , 2015, Scientific Reports.

[48]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[49]  Rajeev K. Varshney,et al.  Genome sequence of mungbean and insights into evolution within Vigna species , 2014, Nature Communications.

[50]  Corinne Da Silva,et al.  Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome , 2014, Science.

[51]  M. Mascher,et al.  Genetic anchoring of whole-genome shotgun assemblies , 2014, Front. Genet..

[52]  J. Bennetzen,et al.  The contributions of transposable elements to the structure, function, and evolution of plant genomes. , 2014, Annual review of plant biology.

[53]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[54]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[55]  Sumeet Singh,et al.  Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.) , 2013, Theoretical and Applied Genetics.

[56]  Andrew C. Adey,et al.  Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions , 2013, Nature Biotechnology.

[57]  Sean R. Eddy,et al.  Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..

[58]  Mira V. Han,et al.  Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. , 2013, Molecular biology and evolution.

[59]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[60]  James K. Hane,et al.  Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement , 2013, Nature Biotechnology.

[61]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[62]  Yeting Zhang,et al.  A genome triplication associated with early diversification of the core eudicots , 2012, Genome Biology.

[63]  Huanming Yang,et al.  Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers , 2011, Nature Biotechnology.

[64]  Alvaro J. González,et al.  The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses , 2011, Nature.

[65]  James C. Schnable,et al.  Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss , 2011, Proceedings of the National Academy of Sciences.

[66]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[67]  Melissa D. Lehti-Shiu,et al.  Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice1[C][W][OA] , 2009, Plant Physiology.

[68]  Haibao Tang,et al.  Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses , 2009, Genome Biology.

[69]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[70]  H. Mori,et al.  Genome Structure of the Legume, Lotus japonicus , 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.

[71]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[72]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[73]  Zhe Li,et al.  Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice , 2006, BMC Bioinformatics.

[74]  Mark Gerstein,et al.  PseudoPipe: an automated pseudogene identification pipeline , 2006, Bioinform..

[75]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[76]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[77]  J. Bennetzen,et al.  A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[78]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

[79]  Hao Wu,et al.  R/qtl: QTL Mapping in Experimental Crosses , 2003, Bioinform..

[80]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[81]  M. Nei,et al.  Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.

[82]  Mario Stanke,et al.  Whole-Genome Annotation with BRAKER. , 2019, Methods in molecular biology.

[83]  D. D. Kosambi The estimation of map distances from recombination values. , 1943 .