Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla

[1]  Shujun Ou,et al.  LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons1[OPEN] , 2017, Plant Physiology.

[2]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[3]  E. Schijlen,et al.  A footprint of desiccation tolerance in the genome of Xerophyta viscosa , 2017, Nature Plants.

[4]  Shin-Han Shiu,et al.  Evolution of Gene Duplication in Plants1[OPEN] , 2016, Plant Physiology.

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

[6]  Robert J. Schmitz,et al.  Widespread natural variation of DNA methylation within angiosperms , 2016, Genome Biology.

[7]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[8]  Michael S. Barker,et al.  The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution , 2016, Genome biology and evolution.

[9]  Ann A. Ferguson,et al.  What makes up plant genomes: The vanishing line between transposable elements and genes. , 2016, Biochimica et biophysica acta.

[10]  B. Gaut,et al.  Evolutionary patterns of genic DNA methylation vary across land plants , 2016, Nature Plants.

[11]  I. Xenarios,et al.  UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. , 2016, Methods in molecular biology.

[12]  Xiuren Zhang,et al.  Trehalose Accumulation Triggers Autophagy during Plant Desiccation , 2015, PLoS genetics.

[13]  Haibao Tang,et al.  Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum , 2015, Nature.

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

[15]  S. Kelly,et al.  OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.

[16]  S. Magallón,et al.  A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. , 2015, The New phytologist.

[17]  Xinhua Yang,et al.  The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration , 2015, Proceedings of the National Academy of Sciences.

[18]  T. Michael,et al.  Progress, challenges and the future of crop genomes. , 2015, Current opinion in plant biology.

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

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

[21]  T. Michael.  Plant genome size variation: bloating and purging DNA. , 2014, Briefings in functional genomics.

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

[23]  D. Bartels,et al.  Desiccation tolerance in resurrection plants: new insights from transcriptome, proteome and metabolome analysis , 2013, Front. Plant Sci..

[24]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[25]  Sergio Alan Cervantes-Pérez,et al.  Architecture and evolution of a minute plant genome , 2013, Nature.

[26]  Takayuki Tohge,et al.  Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis , 2012, Cellular and Molecular Life Sciences.

[27]  Francine E. Garrett-Bakelman,et al.  methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.

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

[29]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[30]  Mark Yandell,et al.  MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects , 2011, BMC Bioinformatics.

[31]  Zhiyong Lu,et al.  The gene normalization task in BioCreative III , 2011, BMC Bioinformatics.

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

[33]  Claude W. dePamphilis,et al.  Ancestral polyploidy in seed plants and angiosperms , 2011, Nature.

[34]  Michael S. Barker,et al.  The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants , 2011, Science.

[35]  Michaël Bekaert,et al.  Two-Phase Resolution of Polyploidy in the Arabidopsis Metabolic Network Gives Rise to Relative and Absolute Dosage Constraints[W] , 2011, Plant Cell.

[36]  Felix Krueger,et al.  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..

[37]  D. Bartels,et al.  Plant Desiccation Tolerance , 2011 .

[38]  Susan R. Wessler,et al.  MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences , 2010, Nucleic acids research.

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

[40]  D. Zilberman,et al.  Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation , 2010, Science.

[41]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[42]  J. Banks.  Selaginella and 400 million years of separation. , 2009, Annual review of plant biology.

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

[44]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

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

[46]  M. Freeling,et al.  How to usefully compare homologous plant genes and chromosomes as DNA sequences. , 2008, The Plant journal : for cell and molecular biology.

[47]  Sofia M. C. Robb,et al.  MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.

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

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

[50]  Zhao Xu,et al.  LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..

[51]  R. Veitia,et al.  The Gene Balance Hypothesis: From Classical Genetics to Modern Genomics , 2007, The Plant Cell Online.

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

[53]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[54]  D. Soltis,et al.  Evolution of DNA amounts across land plants (embryophyta). , 2005, Annals of botany.

[55]  Jianxin Ma,et al.  Rapid recent growth and divergence of rice nuclear genomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Nansheng Chen,et al.  Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.

[57]  B. Mishler,et al.  The evolution of vegetative desiccation tolerance in land plants , 2000, Plant Ecology.

[58]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[59]  Nicolae Moise,et al.  Early light-induced proteins protect Arabidopsis from photooxidative stress , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[61]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

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

[63]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[64]  A. Paterson,et al.  Preparation of megabase‐size DNA from plant nuclei , 1995 .

[65]  B. A. Thomas,et al.  Paleozoic Herbaceous Lycopsids and the Beginnings of Extant Lycopodium Sens Lat. And Selaginella Sens. Lat , 1992 .

[66]  M. Proctor.  The physiological basis of bryophyte production , 1990 .

[67]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.