A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

[1]  H. Adam,et al.  Insights from ANA-grade angiosperms into the early evolution of CUP-SHAPED COTYLEDON genes. , 2011, Annals of botany.

[2]  D. Soltis,et al.  T HE AGE AND DIVERSIFICATION OF THE ANGIOSPERMS RE - REVISITED 1 , 2010 .

[3]  J. Pires,et al.  Integration of Genetic, Physical, and Cytogenetic Maps for Brassica rapa Chromosome A7 , 2010, Cytogenetic and Genome Research.

[4]  S. Magallón Using fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms. , 2010, Systematic biology.

[5]  M. Donoghue,et al.  An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants , 2010, Proceedings of the National Academy of Sciences.

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

[7]  Haibao Tang,et al.  Angiosperm genome comparisons reveal early polyploidy in the monocot lineage , 2009, Proceedings of the National Academy of Sciences.

[8]  Sebastian Proost,et al.  The flowering world: a tale of duplications. , 2009, Trends in plant science.

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

[10]  Cristian Chaparro,et al.  Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome , 2009, PLoS genetics.

[11]  P. K. Wall,et al.  Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. , 2009, Molecular biology and evolution.

[12]  Itay Mayrose,et al.  The frequency of polyploid speciation in vascular plants , 2009, Proceedings of the National Academy of Sciences.

[13]  Suzanna Lewis,et al.  Apollo: a community resource for genome annotation editing , 2009, Bioinform..

[14]  J. Bennetzen,et al.  The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes , 2009, Plant Methods.

[15]  F. Zhou,et al.  MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. , 2009, Gene.

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

[17]  Enrique Blanco,et al.  Computational gene annotation in new genome assemblies using GeneID. , 2009, Methods in molecular biology.

[18]  D. Sankoff,et al.  Polyploidy and angiosperm diversification. , 2009, American journal of botany.

[19]  Jim Leebens-Mack,et al.  Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels , 2010, BMC Evolutionary Biology.

[20]  Haibao Tang,et al.  Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. , 2008, Genome research.

[21]  S. Kurtz,et al.  A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes , 2008, BMC Genomics.

[22]  Haibao Tang,et al.  Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids1[W] , 2008, Plant Physiology.

[23]  Miriam K. Konkel,et al.  Genome analysis of the platypus reveals unique signatures of evolution , 2008, Nature.

[24]  Andrew H. Paterson,et al.  Synteny and Collinearity in Plant Genomes , 2008, Science.

[25]  Stephen M. Mount,et al.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) , 2008, Nature.

[26]  Naomi S. Altman,et al.  The Amborella genome: an evolutionary reference for plant biology , 2008, Genome Biology.

[27]  Kai F. Müller,et al.  PlantTribes: a gene and gene family resource for comparative genomics in plants , 2007, Nucleic Acids Res..

[28]  Matthew D. Wilkerson,et al.  PlantGDB: a resource for comparative plant genomics , 2007, Nucleic Acids Res..

[29]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): gene structure and function annotation , 2007, Nucleic Acids Res..

[30]  James Leebens-Mack,et al.  Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns , 2007, Proceedings of the National Academy of Sciences.

[31]  Pamela S Soltis,et al.  Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms , 2007, Proceedings of the National Academy of Sciences.

[32]  C. Scutt,et al.  Functional conservation between CRABS CLAW orthologues from widely diverged angiosperms. , 2007, Annals of botany.

[33]  Andrea Zuccolo,et al.  Transposable element distribution, abundance and role in genome size variation in the genus Oryza , 2007, BMC Evolutionary Biology.

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

[35]  M. Donoghue,et al.  Towards a phylogenetic nomenclature of Tracheophyta , 2007 .

[36]  Pamela S Soltis,et al.  The ABC model and its applicability to basal angiosperms. , 2007, Annals of botany.

[37]  A. Farjon In defence of a conifer taxonomy which recognises evolution , 2007 .

[38]  S. Jackson,et al.  Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type) , 2007, Genetics.

[39]  Kanako O. Koyanagi,et al.  Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. , 2007, Genome research.

[40]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[41]  B. Roe,et al.  Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes , 2006, Proceedings of the National Academy of Sciences.

[42]  Rod A Wing,et al.  Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. , 2006, Genome research.

[43]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[44]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[45]  D. Soltis,et al.  Widespread genome duplications throughout the history of flowering plants. , 2006, Genome research.

[46]  Hong Ma,et al.  Conservation and divergence in the AGAMOUS subfamily of MADS‐box genes: evidence of independent sub‐ and neofunctionalization events , 2006, Evolution & development.

[47]  S. Jackson,et al.  The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. , 2005, Genome research.

[48]  Claude W. dePamphilis,et al.  A Genomics Approach to the Study of Ancient Polyploidy and Floral Developmental Genetics , 2006 .

[49]  Burkhard Morgenstern,et al.  Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources , 2006, BMC Bioinformatics.

[50]  Steven Maere,et al.  Genome duplication and the origin of angiosperms. , 2005, Trends in ecology & evolution.

[51]  Gene A. Brewer,et al.  Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Galina Fuks,et al.  Whole-Genome Validation of High-Information-Content Fingerprinting1 , 2005, Plant Physiology.

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

[54]  D. Soltis,et al.  Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. , 2005, The Plant journal : for cell and molecular biology.

[55]  李佩芳 International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. , 2005 .

[56]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[57]  Jim Leebens-Mack,et al.  Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. , 2005, Molecular biology and evolution.

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

[59]  J. Leebens-Mack,et al.  To B or Not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. , 2005, The Journal of heredity.

[60]  D. Soltis,et al.  The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history. , 2005, Genetics.

[61]  C. Dumas,et al.  Evidence that CRABS CLAW and TOUSLED have conserved their roles in carpel development since the ancestor of the extant angiosperms. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Yi Hu,et al.  Floral gene resources from basal angiosperms for comparative genomics research , 2005, BMC Plant Biology.

[63]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[64]  A. Paterson,et al.  Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[65]  T. Wetter,et al.  Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. , 2004, Genome research.

[66]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[67]  J. S. Heslop-Harrison,et al.  LINEs and gypsy-like retrotransposons in Hordeum species , 2002, Plant Molecular Biology.

[68]  T. Schmidt LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes , 1999, Plant Molecular Biology.

[69]  D. Smyth,et al.  An abundant LINE-like element amplified in the genome of Lilium speciosum , 1993, Molecular and General Genetics MGG.

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

[71]  Carolyn Thomas,et al.  High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. , 2003, Genomics.

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

[73]  V. Goremykin,et al.  Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm. , 2003, Molecular biology and evolution.

[74]  Brad A. Chapman,et al.  Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events , 2003, Nature.

[75]  R. Wing,et al.  An improved method for plant BAC library construction. , 2003, Methods in molecular biology.

[76]  I. Leitch,et al.  DNA C-values in seven families fill phylogenetic gaps in the basal angiosperms , 2002 .

[77]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[78]  M. Morgante,et al.  Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes , 2002, Nature Genetics.

[79]  Hui-Hsien Chou,et al.  DNA sequence quality trimming and vector removal , 2001, Bioinform..

[80]  C. Soderlund,et al.  Contigs built with fingerprints, markers, and FPC V4.7. , 2000, Genome research.

[81]  D. Soltis,et al.  Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology , 1999, Nature.

[82]  Mark W. Chase,et al.  The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes , 1999, Nature.

[83]  M. Donoghue,et al.  The root of angiosperm phylogeny inferred from duplicate phytochrome genes. , 1999, Science.

[84]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[85]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[86]  R. Durbin,et al.  A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. , 1995, Gene.

[87]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[88]  Yasuko Takahashi,et al.  Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events , 2022 .