The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence
暂无分享,去创建一个
R. Sederoff | Hairong Wei | Xingtan Zhang | R. Ming | J. Ralph | J. Wen | Quanzi Li | F. Lu | Hoon Kim | Li‐Yaung Kuo | Ya-long Guo | Hansheng Zhao | Gongke Zhou | Wenling Wang | Su Chen | Zhenyang Liao | Shuai Chen | Xiong Huang | Wenqi Wu | P. Zhu | Ting Gong | Changjiang Yu | Song Chen | David A Wickell | Fay-Wei Li | Wei Fan | Hui Li | Xiuqi Bao | Li Li | Dan Zhang | Longyu Jiang | Xiaojing Yan | Xiu-Qi Bao | Suting Chen | David Wickell
[1] Xinren Dai,et al. Investigation Into Different Wood Formation Mechanisms Between Angiosperm and Gymnosperm Tree Species at the Transcriptional and Post-transcriptional Level , 2021, Frontiers in Plant Science.
[2] Jue Ruan,et al. The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution , 2021, Nature Plants.
[3] P. Bork,et al. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..
[4] P. Szövényi,et al. Charting the genomic landscape of seed-free plants , 2021, Nature Plants.
[5] Yun-Xin Fu,et al. Stairway Plot 2: demographic history inference with folded SNP frequency spectra , 2020, Genome Biology.
[6] N. S. Allen,et al. Contrasting bacteriome of the hornwort Leiosporoceros dussii in two nearby sites with emphasis on the hornwort-cyanobacterial symbiosis , 2020, Symbiosis.
[7] H. Schneider,et al. Allopolyploid speciation accompanied by gene flow in a tree fern. , 2020, Molecular biology and evolution.
[8] Cédric Feschotte,et al. RepeatModeler2 for automated genomic discovery of transposable element families , 2020, Proceedings of the National Academy of Sciences.
[9] L. Forrest,et al. Extremely low genetic diversity in the European clade of the model bryophyte Anthoceros agrestis , 2020, Plant Systematics and Evolution.
[10] Michael S. Barker,et al. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts , 2020, Nature Plants.
[11] Y. van de Peer,et al. The hornwort genome and early land plant evolution , 2020, Nature Plants.
[12] L. Mandrich,et al. Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects. , 2019, Protein and peptide letters.
[13] T. Demura,et al. Involvement of VNS NAC-domain transcription factors in tracheid formation in Pinus taeda. , 2019, Tree physiology.
[14] D. Soltis,et al. The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly , 2019, Scientific Reports.
[15] C. Feng,et al. Nuclear loci developed from multiple transcriptomes yield high resolution in phylogeny of scaly tree ferns (Cyatheaceae) from China and Vietnam. , 2019, Molecular phylogenetics and evolution.
[16] D. Silvestro,et al. Slowly but surely: gradual diversification and phenotypic evolution in the hyper-diverse tree fern family Cyatheaceae , 2019, Annals of botany.
[17] J. Der,et al. Expression Level Dominance and Homeolog Expression Bias in Recurrent Origins of the Allopolyploid Fern Polypodium hesperium , 2019, American Fern Journal.
[18] Alexey M. Kozlov,et al. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference , 2019, Bioinform..
[19] Alexey M. Kozlov,et al. ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models , 2019, bioRxiv.
[20] Davide Heller,et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses , 2018, Nucleic Acids Res..
[21] Yves Van de Peer,et al. wgd—simple command line tools for the analysis of ancient whole-genome duplications , 2018, Bioinform..
[22] David Sankoff,et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. , 2018, Nature Genetics.
[23] Y. Hu,et al. A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. , 2018, Molecular phylogenetics and evolution.
[24] Shujun Ou,et al. Assessing genome assembly quality using the LTR Assembly Index (LAI) , 2018, Nucleic acids research.
[25] Shifeng Cheng,et al. Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing , 2018, PloS one.
[26] Dongxiao Liu,et al. Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus , 2018, BMC Genomics.
[27] Emmanuel Paradis,et al. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..
[28] Michael S. Barker,et al. Fern genomes elucidate land plant evolution and cyanobacterial symbioses , 2018, Nature Plants.
[29] Y. An,et al. Dynamic DNA Methylation in Plant Growth and Development , 2018, International journal of molecular sciences.
[30] C. Delwiche,et al. The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization , 2018, Cell.
[31] Y. Li,et al. Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance. , 2018, Molecular plant.
[32] Lixi Jiang,et al. Arabidopsis thaliana NOP10 is required for gametophyte formation. , 2018, Journal of integrative plant biology.
[33] Liying Kuo,et al. Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales) , 2018, Front. Plant Sci..
[34] Timothy R. Fallon,et al. The biosynthetic origin of psychoactive kavalactones in kava , 2018, bioRxiv.
[35] S. Dong,et al. On the Recognition of Gymnosphaera As a Distinct Genus in Cyatheaceae1 , 2018, Annals of the Missouri Botanical Garden.
[36] Michael S. Barker,et al. Multiple large-scale gene and genome duplications during the evolution of hexapods , 2018, Proceedings of the National Academy of Sciences.
[37] Mark N. Puttick,et al. The timescale of early land plant evolution , 2018, Proceedings of the National Academy of Sciences.
[38] Charlie Longtine,et al. Antimicrobial activity of ethanolic and aqueous extracts of medicinally used tree ferns Alsophila cuspidata and Cyathea microdonta , 2018 .
[39] Richard D. Hayes,et al. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. , 2018, The Plant journal : for cell and molecular biology.
[40] Ping Liu,et al. A genome for gnetophytes and early evolution of seed plants , 2018, Nature Plants.
[41] Yuehong Yan,et al. Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns , 2017, GigaScience.
[42] T. Demura,et al. Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation1[OPEN] , 2017, Plant Physiology.
[43] Christian R. Boehm,et al. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome , 2017, Cell.
[44] L. Berke,et al. The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves , 2017, Genome biology and evolution.
[45] Heng Li,et al. Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..
[46] Heng Li,et al. Minimap2: fast pairwise alignment for long DNA sequences , 2017 .
[47] J. Ralph,et al. Hydroxystilbenes Are Monomers in Palm Fruit Endocarp Lignins1[OPEN] , 2017, Plant Physiology.
[48] S. Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[49] Neva C. Durand,et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds , 2016, Science.
[50] Michael A. Sundue,et al. A 4000-species dataset provides new insight into the evolution of ferns. , 2016, Molecular phylogenetics and evolution.
[51] D. R. Farrar,et al. A community‐derived classification for extant lycophytes and ferns , 2016 .
[52] Neva C. Durand,et al. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.
[53] Daisy E. Pagete. An end-to-end assembly of the Aedes aegypti genome , 2016, 1605.04619.
[54] James W. Clark,et al. Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny. , 2016, The New phytologist.
[55] Robert J. Schmitz,et al. On the origin and evolutionary consequences of gene body DNA methylation , 2016, Proceedings of the National Academy of Sciences.
[56] B. Gaut,et al. Evolutionary patterns of genic DNA methylation vary across land plants , 2016, Nature Plants.
[57] James B. Beck,et al. Searching for Diamonds in the Apomictic Rough: A Case Study Involving Boechera lignifera (Brassicaceae) , 2015 .
[58] Haibao Tang,et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum , 2015, Nature.
[59] C. Delwiche,et al. The Evolutionary Origin of a Terrestrial Flora , 2015, Current Biology.
[60] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[61] S. Kelly,et al. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.
[62] C. N. Stewart,et al. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. , 2015, American journal of botany.
[63] Steven L Salzberg,et al. HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.
[64] Qing-Yong Yang,et al. De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. , 2015, Molecular plant.
[65] Anders Albrechtsen,et al. ANGSD: Analysis of Next Generation Sequencing Data , 2014, BMC Bioinformatics.
[66] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[67] Wei Chen,et al. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism , 2014, Nature Genetics.
[68] Nature Plants , 2014, Nature Genetics.
[69] D. Penny,et al. Two New Fern Chloroplasts and Decelerated Evolution Linked to the Long Generation Time in Tree Ferns , 2014, Genome biology and evolution.
[70] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[71] T. Demura,et al. Contribution of NAC Transcription Factors to Plant Adaptation to Land , 2014, Science.
[72] Charles-Elie Rabier,et al. Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. , 2014, Molecular biology and evolution.
[73] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[74] Amborella Genome. The Amborella Genome and the Evolution of Flowering Plants , 2013, Science.
[75] Xiangshan Zhou,et al. Engineered fungal polyketide biosynthesis in Pichia pastoris: a potential excellent host for polyketide production , 2013, Microbial Cell Factories.
[76] Nikolaos S. Alachiotis,et al. SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes , 2013, Molecular biology and evolution.
[77] Xun Xu,et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads , 2013, Bioinform..
[78] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[79] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[80] Zhengwei Zhu,et al. CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..
[81] S. Aubourg,et al. Structural, Functional, and Evolutionary Analysis of the Unusually Large Stilbene Synthase Gene Family in Grapevine1[W] , 2012, Plant Physiology.
[82] S. Mansfield,et al. Whole plant cell wall characterization using solution-state 2D NMR , 2012, Nature Protocols.
[83] Pablo Cingolani,et al. © 2012 Landes Bioscience. Do not distribute. , 2022 .
[84] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[85] Jeremy D. DeBarry,et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.
[86] M. Bunzel,et al. Chemical characterization of Klason lignin preparations from plant-based foods. , 2011, Journal of agricultural and food chemistry.
[87] Sean R. Eddy,et al. Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..
[88] L. Lucia,et al. Chemical and spatial differentiation of syringyl and guaiacyl lignins in poplar wood via time-of-flight secondary ion mass spectrometry. , 2011, Analytical chemistry.
[89] J. Weng,et al. Independent Recruitment of an O-Methyltransferase for Syringyl Lignin Biosynthesis in Selaginella moellendorffii[W] , 2011, Plant Cell.
[90] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[91] Michael S. Barker,et al. The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants , 2011, Science.
[92] N. Friedman,et al. Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .
[93] Felix Krueger,et al. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..
[94] Hasan Jameel,et al. Down-regulation of glycosyltransferase 8D genes in Populus trichocarpa caused reduced mechanical strength and xylan content in wood. , 2011, Tree physiology.
[95] P. Visscher,et al. GCTA: a tool for genome-wide complex trait analysis. , 2011, American journal of human genetics.
[96] K. Pryer,et al. ABRUPT DECELERATION OF MOLECULAR EVOLUTION LINKED TO THE ORIGIN OF ARBORESCENCE IN FERNS , 2010, Evolution; international journal of organic evolution.
[97] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[98] M. Lynch. Evolution of the mutation rate. , 2010, Trends in genetics : TIG.
[99] T. Demura,et al. VASCULAR-RELATED NAC-DOMAIN6 and VASCULAR-RELATED NAC-DOMAIN7 Effectively Induce Transdifferentiation into Xylem Vessel Elements under Control of an Induction System1[W] , 2010, Plant Physiology.
[100] D. Zilberman,et al. Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation , 2010, Science.
[101] L. F. Viccini,et al. Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus. , 2010, The New phytologist.
[102] J. Weng,et al. Convergent Evolution of Syringyl Lignin Biosynthesis via Distinct Pathways in the Lycophyte Selaginella and Flowering Plants[C][W] , 2010, Plant Cell.
[103] J. Dean,et al. An Improved Method of RNA Isolation from Loblolly Pine (P. taeda L.) and Other Conifer Species , 2010, Journal of visualized experiments : JoVE.
[104] David H. Alexander,et al. Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.
[105] Toni Gabaldón,et al. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..
[106] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[107] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[108] Nansheng Chen,et al. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.
[109] F. Pomar,et al. The presence of sinapyl lignin in Ginkgo biloba cell cultures changes our views of the evolution of lignin biosynthesis. , 2009, Physiologia plantarum.
[110] J. Ralph,et al. Solution-state 2D NMR of Ball-milled Plant Cell Wall Gels in DMSO-d6 , 2008, BioEnergy Research.
[111] Manuel A. R. Ferreira,et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.
[112] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[113] T. Demura,et al. SND1, a NAC Domain Transcription Factor, Is a Key Regulator of Secondary Wall Synthesis in Fibers of Arabidopsis[W] , 2006, The Plant Cell Online.
[114] Nello Cristianini,et al. CAFE: a computational tool for the study of gene family evolution , 2006, Bioinform..
[115] Tetsuro Mimura,et al. Transcription switches for protoxylem and metaxylem vessel formation. , 2005, Genes & development.
[116] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[117] G. Evanno,et al. Detecting the number of clusters of individuals using the software structure: a simulation study , 2005, Molecular ecology.
[118] R. Durbin,et al. GeneWise and Genomewise. , 2004, Genome research.
[119] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[120] Michael J. Sanderson,et al. R8s: Inferring Absolute Rates of Molecular Evolution, Divergence times in the Absence of a Molecular Clock , 2003, Bioinform..
[121] Ziheng Yang,et al. PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..
[122] Bernard R. Baum,et al. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components , 1997, Plant Molecular Biology Reporter.
[123] B. A. Thomas,et al. DISTRIBUTION OF LIGNIN DERIVATIVES IN PLANTS , 1985 .
[124] H. Fukuda,et al. Vascular tissue development in plants. , 2019, Current topics in developmental biology.
[125] T. Demura,et al. Evolution of plant conducting cells: perspectives from key regulators of vascular cell differentiation , 2017, Journal of experimental botany.
[126] He Xingjin,et al. Isolation of three chemical constituents from Alsophila spinulosa stalks for the first time. , 2011 .
[127] Gong Jia-wen. Primary Discussion on the Bacteriostatic Activity of Alsophila spinulosa Leaves and Stems , 2007 .
[128] Amie D. Sluiter,et al. Determination of Structural Carbohydrates and Lignin in Biomass , 2004 .
[129] G. Benson,et al. Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.
[130] C. Lapierre,et al. New insights into the molecular architecture of hardwood lignins by chemical degradative methods , 1995 .
[131] N. Nakato. Cytological studies on the genus Cyathea in Japan. , 1989 .