Signatures of the evolution of parthenogenesis and cryptobiosis in panagrolaimid nematodes

[1]  K. Panter,et al.  Mechanism of Action , 1967, Antibiotics.

[2]  PhD Anthony Oro MD,et al.  Molecular Analysis , 2020, Definitions.

[3]  Philipp H. Schiffer,et al.  The gene regulatory program of Acrobeloides nanus reveals conservation of phylum-specific expression , 2018, Proceedings of the National Academy of Sciences.

[4]  Matthew W. Hahn,et al.  Gene-tree reconciliation with MUL-trees to resolve polyploidy events , 2016, bioRxiv.

[5]  E. Danchin,et al.  Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life , 2017, Genes.

[6]  Philipp H. Schiffer,et al.  Differences in the genetic control of early egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus , 2017, EvoDevo.

[7]  M. Blaxter,et al.  KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences , 2017, G3: Genes, Genomes, Genetics.

[8]  Philipp H. Schiffer,et al.  Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction , 2017, BMC Genomics.

[9]  E. Danchin,et al.  Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes , 2017, PLoS genetics.

[10]  F. Li,et al.  DEAD-box RNA helicase , 2017 .

[11]  M. Tomita,et al.  Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus , 2017, bioRxiv.

[12]  Yutaka Suzuki,et al.  Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein , 2016, Nature Communications.

[13]  Henning Redestig,et al.  Homoeologs: What Are They and How Do We Infer Them? , 2016, Trends in plant science.

[14]  Leszek P. Pryszcz,et al.  Redundans: an assembly pipeline for highly heterozygous genomes , 2016, Nucleic Acids Research.

[15]  D. Fontaneto,et al.  Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex , 2016, Current Biology.

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

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

[18]  W. Vermeulen,et al.  Tissue specific response to DNA damage: C. elegans as role model. , 2015, DNA repair.

[19]  Olivier Gascuel,et al.  FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program , 2015, Molecular biology and evolution.

[20]  M. Meselson,et al.  Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers , 2015, Genetics.

[21]  Bernhard Haubold,et al.  andi: Fast and accurate estimation of evolutionary distances between closely related genomes , 2015, Bioinform..

[22]  M. Félix,et al.  Anhydrobiosis and Freezing-Tolerance: Adaptations That Facilitate the Establishment of Panagrolaimus Nematodes in Polar Habitats , 2015, PloS one.

[23]  Olivier Poch,et al.  OrthoInspector 2.0: Software and database updates , 2015, Bioinform..

[24]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[25]  James Wasmuth,et al.  Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes , 2014, Bioinform..

[26]  Alexander S. Mikheyev,et al.  Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge , 2014, Nature Communications.

[27]  M. Thorne,et al.  Molecular Analysis of the Cold Tolerant Antarctic Nematode, Panagrolaimus davidi , 2014, PloS one.

[28]  I. Feussner,et al.  The Reductase Activity of the Arabidopsis Caleosin RESPONSIVE TO DESSICATION20 Mediates Gibberellin-Dependent Flowering Time, Abscisic Acid Sensitivity, and Tolerance to Oxidative Stress1[W] , 2014, Plant Physiology.

[29]  R. Koszul,et al.  Gateway to genetic exchange? DNA double‐strand breaks in the bdelloid rotifer Adineta vaga submitted to desiccation , 2014, Journal of evolutionary biology.

[30]  E. Danchin,et al.  Parasitic success without sex – the nematode experience , 2014, Journal of evolutionary biology.

[31]  Philipp H. Schiffer,et al.  Developmental variations among Panagrolaimid nematodes indicate developmental system drift within a small taxonomic unit , 2014, Development Genes and Evolution.

[32]  A. Laroche,et al.  Characterization of the caleosin gene family in the Triticeae , 2014, BMC Genomics.

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

[34]  M. Blaxter,et al.  Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots , 2013, Front. Genet..

[35]  J. Harrow,et al.  Systematic evaluation of spliced alignment programs for RNA-seq data , 2013, Nature Methods.

[36]  Corinne Da Silva,et al.  Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga , 2013, Nature.

[37]  Cristobal Uauy,et al.  Separating homeologs by phasing in the tetraploid wheat transcriptome , 2013, Genome Biology.

[38]  Paul W. Sternberg,et al.  The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle , 2013, Genetics.

[39]  Alan Edelman,et al.  Julia: A Fast Dynamic Language for Technical Computing , 2012, ArXiv.

[40]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

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

[42]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[43]  M. Blaxter,et al.  A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags , 2012, BMC Research Notes.

[44]  Alejandro Sanchez-Flores,et al.  Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus , 2011, PLoS pathogens.

[45]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[46]  Aaron R. Quinlan,et al.  BamTools: a C++ API and toolkit for analyzing and managing BAM files , 2011, Bioinform..

[47]  Elaine R. Mardis,et al.  The draft genome of the parasitic nematode Trichinella spiralis , 2011, Nature Genetics.

[48]  Steven Salzberg,et al.  Mugsy: fast multiple alignment of closely related whole genomes , 2010, Bioinform..

[49]  K. Mita,et al.  Identification of Anhydrobiosis-related Genes from an Expressed Sequence Tag Database in the Cryptobiotic Midge Polypedilum vanderplanki (Diptera; Chironomidae) , 2010, The Journal of Biological Chemistry.

[50]  P. Baumann,et al.  Sister Chromosome Pairing Maintains Heterozygosity in Parthenogenetic Lizards , 2010, Nature.

[51]  Serban Nacu,et al.  Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..

[52]  D. Murphy,et al.  Roles of a membrane-bound caleosin and putative peroxygenase in biotic and abiotic stress responses in Arabidopsis. , 2009, Plant physiology and biochemistry : PPB.

[53]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[54]  M. Lynch,et al.  Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family. , 2009, Molecular biology and evolution.

[55]  D. Denver,et al.  Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P. davidi , 2009, BMC Evolutionary Biology.

[56]  Varghese P. Thomas,et al.  Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism , 2008, Proceedings of the National Academy of Sciences.

[57]  D. Lunt,et al.  Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins , 2008, BMC Evolutionary Biology.

[58]  M. Meselson,et al.  Massive Horizontal Gene Transfer in Bdelloid Rotifers , 2008, Science.

[59]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[60]  A. Cutter Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. , 2008, Molecular biology and evolution.

[61]  D. Hincha,et al.  Functional Divergence of Former Alleles in an Ancient Asexual Invertebrate , 2007, Science.

[62]  R. O. Schill,et al.  Induction of Hsp70 by desiccation, ionising radiation and heat-shock in the eutardigrade Richtersius coronifer. , 2007, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[63]  Nan Wang,et al.  AgBase: a functional genomics resource for agriculture , 2006, BMC Genomics.

[64]  D. Fitzpatrick,et al.  The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus (Nematoda, Panagrolaimidae) , 2005, Journal of Experimental Biology.

[65]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[66]  M. P. Cummings PHYLIP (Phylogeny Inference Package) , 2004 .

[67]  M. Archetti Recombination and loss of complementation: a more than two‐fold cost for parthenogenesis , 2004, Journal of evolutionary biology.

[68]  Mario Stanke,et al.  Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.

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

[70]  James O. McInerney,et al.  CRANN: detecting adaptive evolution in protein-coding DNA sequences , 2003, Bioinform..

[71]  T. Yamashita,et al.  Insect diapause-specific peptide from the leaf beetle has consensus with a putative iridovirus peptide , 2003, Peptides.

[72]  N. C. Price,et al.  The FAR Protein Family of the Nematode Caenorhabditis elegans , 2003, The Journal of Biological Chemistry.

[73]  J. Doležel,et al.  Nuclear DNA content and genome size of trout and human. , 2003, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[74]  E. Schierenberg,et al.  Comparative and experimental embryogenesis of Plectidae (Nematoda) , 2003, Development Genes and Evolution.

[75]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[76]  Mark L. Blaxter,et al.  A molecular evolutionary framework for the phylum Nematoda , 1998, Nature.

[77]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[78]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[79]  M. Lynch,et al.  The mutational meltdown in asexual populations. , 1993, The Journal of heredity.

[80]  G. Sancar,et al.  DNA photolyases: physical properties, action mechanism, and roles in dark repair. , 1990, Mutation research.

[81]  P. Feldman Evolution of sex , 1975, Nature.

[82]  J. Felsenstein The evolutionary advantage of recombination. , 1974, Genetics.

[83]  J. Haldane,et al.  Sex ratio and unisexual sterility in hybrid animals , 1922, Journal of Genetics.

[84]  H. Kowarzyk Structure and Function. , 1910, Nature.

[85]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[86]  C. Kaminski,et al.  Intrinsically disordered proteins as molecular shields. , 2012, Molecular bioSystems.

[87]  Ole Tange,et al.  GNU Parallel: The Command-Line Power Tool , 2011, login Usenix Mag..

[88]  D. Maddison,et al.  Mesquite: a modular system for evolutionary analysis. Version 2.6 , 2009 .

[89]  J. Avise Clonality: The Genetics, Ecology, and Evolution of Sexual Abstinence in Vertebrate Animals , 2008 .

[90]  M. Arnold,et al.  Genetics and the fitness of hybrids. , 2001, Annual review of genetics.

[91]  Dannie Durand,et al.  NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees , 2000, J. Comput. Biol..

[92]  S. Hapugoda,et al.  Evidence for the Evolution of Bdelloid Rotifers Without Sexual Reproduction or Genetic Exchange , 2000 .

[93]  S. Yoshida,et al.  Abscisic acid-induced secretory proteins in suspension-cultured cells of winter wheat. , 1999, Plant & cell physiology.

[94]  A. Coomans,et al.  Generation times of some free-living nematodes cultured at three temperatures , 1999 .