Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

[1]  James C. Schnable,et al.  Linked read technology for assembling large complex and polyploid genomes , 2018, BMC Genomics.

[2]  P. Schnable,et al.  Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes , 2018, Nature Genetics.

[3]  L. Mao,et al.  The Aegilops tauschii genome reveals multiple impacts of transposons , 2017, Nature Plants.

[4]  Karl G. Kugler,et al.  Genome sequence of the progenitor of the wheat D genome Aegilops tauschii , 2017, Nature.

[5]  Jian-Kang Zhu,et al.  A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value , 2017, Cell Research.

[6]  N. Nagarajan,et al.  The draft genome of tropical fruit durian (Durio zibethinus) , 2017, Nature Genetics.

[7]  O. P. Yadav,et al.  Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments , 2017, Nature Biotechnology.

[8]  Han Fang,et al.  GenomeScope: Fast reference-free genome profiling from short reads , 2016, bioRxiv.

[9]  Yan Li,et al.  Sequencing and de novo assembly of a near complete indica rice genome , 2017, Nature Communications.

[10]  John K. McCooke,et al.  A chromosome conformation capture ordered sequence of the barley genome , 2017, Nature.

[11]  Kevin L. Schneider,et al.  Improved maize reference genome with single-molecule technologies , 2017, Nature.

[12]  Ge Gao,et al.  PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants , 2016, Nucleic Acids Res..

[13]  Ute Roessner,et al.  The genome of Chenopodium quinoa , 2017, Nature.

[14]  E. Kellogg,et al.  The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes , 2016, Genome Biology.

[15]  Rod A Wing,et al.  Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63 , 2016, Proceedings of the National Academy of Sciences.

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

[17]  M. Schatz,et al.  Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.

[18]  Siyan Liu,et al.  Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.) , 2016, BMC Genomics.

[19]  D. Santra,et al.  Mapping QTLs for morpho-agronomic traits in proso millet (Panicum miliaceum L.) , 2016, Molecular Breeding.

[20]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[21]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

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

[23]  Lei Fang,et al.  Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement , 2015, Nature Biotechnology.

[24]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[25]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

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

[27]  C. Howe,et al.  Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum , 2014, Journal of experimental botany.

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

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

[30]  Anushya Muruganujan,et al.  Large-scale gene function analysis with the PANTHER classification system , 2013, Nature Protocols.

[31]  O. Panaud,et al.  Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution , 2013, Genome biology and evolution.

[32]  Robert J. Elshire,et al.  Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol , 2013, PLoS genetics.

[33]  Alan Bridge,et al.  New and continuing developments at PROSITE , 2012, Nucleic Acids Res..

[34]  Glenn Tesler,et al.  Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory , 2012, BMC Bioinformatics.

[35]  Jian Wang,et al.  Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential , 2012, Nature Biotechnology.

[36]  Justin N. Vaughn,et al.  Reference genome sequence of the model plant Setaria , 2012, Nature Biotechnology.

[37]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[38]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[39]  J. Batley,et al.  Accessing complex crop genomes with next-generation sequencing , 2012, Theoretical and Applied Genetics.

[40]  Yan He,et al.  Chromosome Organization and Dynamics during Interphase, Mitosis, and Meiosis in Plants1 , 2011, Plant Physiology.

[41]  C. Howe,et al.  Genetic diversity and phylogeography of broomcorn millet (Panicum miliaceum L.) across Eurasia , 2011, Molecular ecology.

[42]  J. Poulain,et al.  The genome of the mesopolyploid crop species Brassica rapa , 2011, Nature Genetics.

[43]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[44]  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.

[45]  T. Sakurai,et al.  Genome sequence of the palaeopolyploid soybean , 2010, Nature.

[46]  Chunguang Du,et al.  The polychromatic Helitron landscape of the maize genome , 2009, Proceedings of the National Academy of Sciences.

[47]  Lixing Yang,et al.  Distribution, diversity, evolution, and survival of Helitrons in the maize genome , 2009, Proceedings of the National Academy of Sciences.

[48]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[49]  Kam‐biu Liu,et al.  Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago , 2009, Proceedings of the National Academy of Sciences.

[50]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[51]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[52]  E. Kellogg,et al.  A Phylogeny of Setaria (Poaceae, Panicoideae, Paniceae) and Related Genera Based on the Chloroplast Gene ndhF , 2009, International Journal of Plant Sciences.

[53]  Stefan Kurtz,et al.  LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons , 2008, BMC Bioinformatics.

[54]  Patrice Koehl,et al.  Plant NBS-LRR proteins: adaptable guards , 2006, Genome Biology.

[55]  David A. Lee,et al.  Gene3D: modelling protein structure, function and evolution , 2005, Nucleic Acids Res..

[56]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[57]  Jonathan F Wendel,et al.  Polyploidy and Genome Evolution in Plants This Review Comes from a Themed Issue on Genome Studies and Molecular Genetics Edited , 2022 .

[58]  Jianxin Ma,et al.  Close split of sorghum and maize genome progenitors. , 2004, Genome research.

[59]  P. Belton,et al.  Sorghum and millets: protein sources for Africa , 2004 .

[60]  R. Newton,et al.  Expression analysis of a gene family in loblolly pine (Pinus taeda L.) induced by water deficit stress , 1997, Plant Molecular Biology.

[61]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[62]  Jianzhi Zhang Evolution by gene duplication: an update , 2003 .

[63]  The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[64]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[65]  Phillip SanMiguel,et al.  The paleontology of intergene retrotransposons of maize , 1998, Nature Genetics.