The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms
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Jianquan Liu | Congcong Dong | Yongzhi Yang | Pengchuan Sun | Jianxiang Ma | Nawal Shrestha | Ying Li | Zhenyue Wang | Dandan Wang | W. Mu | Renping Xu | Ying Wu | Jiao Yang
[1] D. Soltis,et al. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome , 2021, Nature Plants.
[2] Ting Li,et al. WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes , 2021, bioRxiv.
[3] R. Dixon,et al. The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements , 2020, Genome biology.
[4] B. Liu,et al. The Phoebe genome sheds light on the evolution of magnoliids , 2020, Horticulture Research.
[5] Shuangxia Jin,et al. The chromosome-level wintersweet (Chimonanthus praecox) genome provides insights into floral scent biosynthesis and flowering in winter , 2020, Genome Biology.
[6] Diego F. Morales-Briones,et al. Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l , 2020, Systematic biology.
[7] Michael S. Barker,et al. The Chimonanthus salicifolius genome provides insight into magnoliids evolution and flavonoids biosynthesis. , 2020, The Plant journal : for cell and molecular biology.
[8] A. Lemmon,et al. The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales , 2020, bioRxiv.
[9] Dinesh A Nagegowda,et al. Advances in biosynthesis, regulation, and metabolic engineering of plant specialized terpenoids. , 2020, Plant science : an international journal of experimental plant biology.
[10] W. Tong,et al. The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into genome evolution and adaptation of tea plants. , 2020, Molecular plant.
[11] Y. van de Peer,et al. The Litsea genome and the evolution of the laurel family , 2020, Nature Communications.
[12] C. Davis,et al. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution , 2020, Nature Plants.
[13] Charles S. P. Foster,et al. Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling , 2020, Plant communications.
[14] Yang Liu,et al. The water lily genome and the early evolution of flowering plants , 2019, Nature.
[15] Chao Zhang,et al. ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy , 2019, bioRxiv.
[16] E. M. Friis,et al. The endothelium in seeds of early angiosperms. , 2019, The New phytologist.
[17] Jiang Hu,et al. NextPolish: a fast and efficient genome polishing tool for long-read assembly , 2019, Bioinform..
[18] Rui Fan,et al. The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis , 2019, Nature Communications.
[19] Xun Xu,et al. One thousand plant transcriptomes and the phylogenomics of green plants , 2019, Nature.
[20] P. Zerbe,et al. Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity , 2019, Front. Plant Sci..
[21] D. Sankoff,et al. The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation , 2019, Proceedings of the National Academy of Sciences.
[22] Pamela S Soltis,et al. Origin of angiosperms and the puzzle of the Jurassic gap , 2019, Nature Plants.
[23] T. Demura,et al. Creating vessel elements in vitro: Towards a comprehensive understanding of the molecular basis of xylem vessel element differentiation. , 2019, Plant biotechnology.
[24] E. M. Friis,et al. Hedyosmum-Like Fossils in the Early Cretaceous Diversification of Angiosperms , 2019, International Journal of Plant Sciences.
[25] Yu-Wei Wu,et al. Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution , 2019, Nature Plants.
[26] Haibin Xu,et al. Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation , 2018, Nature Plants.
[27] G. Tuskan,et al. Recent Advances in the Transcriptional Regulation of Secondary Cell Wall Biosynthesis in the Woody Plants , 2018, Front. Plant Sci..
[28] Wataru Iwasaki,et al. SonicParanoid: fast, accurate and easy orthology inference , 2018, Bioinform..
[29] J. Doyle,et al. Phylogenetic Analyses of Cretaceous Fossils Related to Chloranthaceae and their Evolutionary Implications , 2018, The Botanical Review.
[30] Siavash Mirarab,et al. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees , 2018, BMC Genomics.
[31] Chao Zhang,et al. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees , 2018, BMC Bioinformatics.
[32] R. Dixon,et al. Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses , 2018, Front. Plant Sci..
[33] Wen-Bin Yu,et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes , 2018, Genome Biology.
[34] Mark N. Puttick,et al. The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte , 2018, Current Biology.
[35] S. Kelly,et al. STAG: Species Tree Inference from All Genes , 2018, bioRxiv.
[36] Korbinian Schneeberger,et al. findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies , 2018, Bioinform..
[37] B. Rost,et al. LocText: relation extraction of protein localizations to assist database curation , 2018, BMC Bioinformatics.
[38] B. Trost,et al. Transcriptome analysis of response to Plasmodiophora brassicae infection in the Arabidopsis shoot and root , 2018, BMC Genomics.
[39] Shujun Ou,et al. LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons1[OPEN] , 2017, Plant Physiology.
[40] Paul Bastide,et al. PhyloNetworks: A Package for Phylogenetic Networks , 2017, Molecular biology and evolution.
[41] Siavash Mirarab,et al. DiscoVista: Interpretable visualizations of gene tree discordance. , 2017, Molecular phylogenetics and evolution.
[42] R. Buggs. The deepening of Darwin's abominable mystery , 2017, Nature Ecology &Evolution.
[43] Axel Fischer,et al. GeSeq – versatile and accurate annotation of organelle genomes , 2017, Nucleic Acids Res..
[44] Joseph W. Brown,et al. Phyx: phylogenetic tools for unix , 2017, Bioinform..
[45] G. Martin,et al. iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases. , 2016, Molecular plant.
[46] M. Christenhusz,et al. The number of known plants species in the world and its annual increase , 2016 .
[47] D. Soltis,et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV , 2016 .
[48] Jens Keilwagen,et al. Using intron position conservation for homology-based gene prediction , 2016, Nucleic acids research.
[49] R. Corlett. Plant diversity in a changing world: Status, trends, and conservation needs , 2016, Plant diversity.
[50] Frédéric Bouché,et al. FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana , 2015, Nucleic Acids Res..
[51] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[52] D. Dilcher,et al. Montsechia, an ancient aquatic angiosperm , 2015, Proceedings of the National Academy of Sciences.
[53] H. Endo,et al. NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants , 2015, Front. Plant Sci..
[54] Hongchuan Song,et al. Secondary Metabolites of Plants from the Genus Chloranthus: Chemistry and Biological Activities , 2015, Chemistry & biodiversity.
[55] Steven L Salzberg,et al. HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.
[56] B. M. Lange,et al. Functional analysis of (4S)-limonene synthase mutants reveals determinants of catalytic outcome in a model monoterpene synthase , 2015, Proceedings of the National Academy of Sciences.
[57] S. Salzberg,et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.
[58] Md. Shamsuzzoha Bayzid,et al. Statistical binning enables an accurate coalescent-based estimation of the avian tree , 2014, Science.
[59] A. von Haeseler,et al. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.
[60] Hong Ma,et al. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times , 2014, Nature Communications.
[61] Stephen A. Smith,et al. Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics , 2014, Molecular biology and evolution.
[62] A. Paterson,et al. Polyploidy-associated genome modifications during land plant evolution , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.
[63] Amborella Genome. The Amborella Genome and the Evolution of Flowering Plants , 2013, Science.
[64] Andrew C. Adey,et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions , 2013, Nature Biotechnology.
[65] S. Kikuchi,et al. Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants , 2013, Front. Microbiol..
[66] E. Vranová,et al. Network analysis of the MVA and MEP pathways for isoprenoid synthesis. , 2013, Annual review of plant biology.
[67] Joshua S. Yuan,et al. Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis , 2012, BMC Bioinformatics.
[68] K. Berthelot,et al. Isopentenyl diphosphate isomerase: A checkpoint to isoprenoid biosynthesis. , 2012, Biochimie.
[69] J. Doyle. Molecular and Fossil Evidence on the Origin of Angiosperms , 2012 .
[70] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[71] K. Vandepoele,et al. Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform1[W] , 2011, Plant Physiology.
[72] Carl Kingsford,et al. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..
[73] Naomi S. Altman,et al. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower , 2010, Proceedings of the National Academy of Sciences.
[74] Qian Gao,et al. Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa , 2010, BMC Plant Biology.
[75] Jeet Sukumaran,et al. DendroPy: a Python library for phylogenetic computing , 2010, Bioinform..
[76] G. Theißen,et al. On the origin of MADS-domain transcription factors. , 2010, Trends in genetics : TIG.
[77] Lili Yu,et al. Phybase: an R package for species tree analysis , 2010, Bioinform..
[78] Thomas L. Madden,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[79] Mark W. Chase,et al. A phylogenetic classification of the land plants to accompany APG III , 2009 .
[80] Naomi S. Altman,et al. Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae) , 2009, Proceedings of the National Academy of Sciences.
[81] B. Gaut,et al. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. , 2009, Genome research.
[82] T. Mailund,et al. SNPFile – A software library and file format for large scale association mapping and population genetics studies , 2008, BMC Bioinformatics.
[83] J. Martínez-Zapater,et al. Genome-Wide Analysis of MIKCC-Type MADS Box Genes in Grapevine1[W][OA] , 2008, Plant Physiology.
[84] Jonathan E. Allen,et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.
[85] 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.
[86] R. Jansen,et al. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). , 2007, Molecular phylogenetics and evolution.
[87] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[88] M. Donoghue,et al. Towards a phylogenetic nomenclature of Tracheophyta , 2007 .
[89] Ashutosh Kumar Singh,et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress , 2007, BMC Genomics.
[90] Zhao Xu,et al. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..
[91] K. Shinozaki,et al. NAC Transcription Factors, NST1 and NST3, Are Key Regulators of the Formation of Secondary Walls in Woody Tissues of Arabidopsis[W][OA] , 2007, The Plant Cell Online.
[92] Aili Li,et al. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa. , 2006, Gene.
[93] Peer Bork,et al. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..
[94] Burkhard Morgenstern,et al. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources , 2006, BMC Bioinformatics.
[95] E. Koonin. Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .
[96] K. Shinozaki,et al. The NAC Transcription Factors NST1 and NST2 of Arabidopsis Regulate Secondary Wall Thickenings and Are Required for Anther Dehiscencew⃞ , 2005, The Plant Cell Online.
[97] Steven Salzberg,et al. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..
[98] Stephen M. Mount,et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.
[99] C. Stoeckert,et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.
[100] Michael J. Sanderson,et al. R8s: Inferring Absolute Rates of Molecular Evolution, Divergence times in the Absence of a Molecular Clock , 2003, Bioinform..
[101] S. Polasky,et al. Agricultural sustainability and intensive production practices , 2002, Nature.
[102] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[103] H. Kong,et al. Floral organogenesis of Chloranthus sessilifolius, with special emphasis on the morphological nature of the androecium of Chloranthus (Chloranthaceae) , 2002, Plant Systematics and Evolution.
[104] E. M. Friis,et al. Early Evolution of Flowers , 2002, Plant Systematics and Evolution Supplement 8.
[105] Rolf Apweiler,et al. InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..
[106] M. Yanofsky,et al. Function and evolution of the plant MADS-box gene family , 2001, Nature Reviews Genetics.
[107] H. Kong,et al. Karyotypes of Sarcandra Gardn. and Chloranthus Swartz (Chloranthaceae) from China , 2000 .
[108] Mark W. Chase,et al. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes , 1999, Nature.
[109] S. Karlin,et al. Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.
[110] W. R. Anderson,et al. An Integrated System of Classification of Flowering Plants , 1982 .
[111] N. Friedman,et al. Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .
[112] Sébastien Tempel. Using and understanding RepeatMasker. , 2012, Methods in molecular biology.
[113] W. Friedman. The meaning of Darwin's 'abominable mystery'. , 2009, American journal of botany.
[114] A. Szkopińska,et al. Farnesyl diphosphate synthase; regulation of product specificity. , 2005, Acta biochimica Polonica.
[115] Jonathan Blumenthal Ma. INAUGURAL ARTICLES: Rapid recent growth and divergence of rice nuclear genomes , 2004 .
[116] J. Lundberg,et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants : APG II THE ANGIOSPERM PHYLOGENY GROUP * , 2003 .
[117] S. Eddy. Profile hidden Markov models , 1998, Bioinform..
[118] R. Bouckaert,et al. Bioinformatics Applications Note Phylogenetics Densitree: Making Sense of Sets of Phylogenetic Trees , 2022 .