Sex-linked regions in the guppy genome 1 Title : Improved reference genome uncovers novel sex-linked regions in the guppy ( Poecilia reticulata )

[1]  D. Charlesworth,et al.  Using GC content to compare recombination patterns on the sex chromosomes and autosomes of the guppy, Poecilia reticulata, and its close outgroup species , 2020, bioRxiv.

[2]  Marius Roesti,et al.  Widespread intersex differentiation across the stickleback genome – The signature of sexually antagonistic selection? , 2020, Molecular ecology.

[3]  J. Volff,et al.  Sex and the TEs: transposable elements in sexual development and function in animals , 2019, Mobile DNA.

[4]  P. S. Mitchell,et al.  The NLRP1 inflammasome: new mechanistic insights and unresolved mysteries. , 2019, Current opinion in immunology.

[5]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[6]  D. Charlesworth.  Young sex chromosomes in plants and animals. , 2019, The New phytologist.

[7]  Peter L. Ralph,et al.  Limits to Genomic Divergence Under Sexually Antagonistic Selection , 2019, G3: Genes, Genomes, Genetics.

[8]  D. Charlesworth,et al.  Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms , 2019, Proceedings of the National Academy of Sciences.

[9]  Mosè Manni,et al.  BUSCO: Assessing Genome Assembly and Annotation Completeness. , 2019, Methods in molecular biology.

[10]  J. Abbott,et al.  Why Do Sex Chromosomes Stop Recombining? , 2018, Trends in genetics : TIG.

[11]  D. Charlesworth.  The Guppy Sex Chromosome System and the Sexually Antagonistic Polymorphism Hypothesis for Y Chromosome Recombination Suppression , 2018, Genes.

[12]  Natasha I. Bloch,et al.  Shared and Species-Specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species , 2018, Genes.

[13]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[14]  Daniel Gautheret,et al.  DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition , 2017, Genome Biology.

[15]  Chang Liu,et al.  Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis , 2017, Nature Plants.

[16]  G. K. Sandve,et al.  NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences , 2017, BMC Bioinformatics.

[17]  S. Hatakeyama,et al.  TRIM Family Proteins: Roles in Autophagy, Immunity, and Carcinogenesis. , 2017, Trends in biochemical sciences.

[18]  Natasha I. Bloch,et al.  Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation , 2017, Nature Communications.

[19]  Markus J. Ankenbrand,et al.  AliTV-interactive visualization of whole genome comparisons , 2017, PeerJ Prepr..

[20]  D. Weigel,et al.  The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population , 2016, PloS one.

[21]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[22]  Davide Heller,et al.  eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences , 2015, Nucleic Acids Res..

[23]  Ana Conesa,et al.  Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data , 2015, Bioinform..

[24]  Katharina J. Hoff,et al.  BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS , 2016, Bioinform..

[25]  W. Davidson,et al.  Genomic Instability of the Sex-Determining Locus in Atlantic Salmon (Salmo salar) , 2015, G3: Genes, Genomes, Genetics.

[26]  Manfred Schartl,et al.  Transposable elements and early evolution of sex chromosomes in fish , 2015, Chromosome Research.

[27]  Hani Z. Girgis.  Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale , 2015, BMC Bioinformatics.

[28]  R. Phillips,et al.  Comparative Analysis of the Shared Sex-Determination Region (SDR) among Salmonid Fishes , 2015, Genome biology and evolution.

[29]  A. Lisachov,et al.  Sex chromosome synapsis and recombination in male guppies. , 2015, Zebrafish.

[30]  Noam Kaplan,et al.  The Hitchhiker's guide to Hi-C analysis: practical guidelines. , 2015, Methods.

[31]  D. Reznick,et al.  Population genomics of natural and experimental populations of guppies (Poecilia reticulata) , 2015, Molecular ecology.

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

[33]  B. Langmead,et al.  Lighter: fast and memory-efficient sequencing error correction without counting , 2014, Genome Biology.

[34]  M. Borodovsky,et al.  Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm , 2014, Nucleic acids research.

[35]  Stefan R. Henz,et al.  Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata , 2014, BMC Genomics.

[36]  M. Lercher,et al.  PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R , 2014, Molecular biology and evolution.

[37]  M. Schartl,et al.  Sex chromosome polymorphism in guppies , 2014, Chromosoma.

[38]  Wendy K Chung,et al.  Quantitative Analysis of Copy Number Variants Based on Real‐Time LightCycler PCR , 2014, Current protocols in human genetics.

[39]  D. Chalopin,et al.  A multicopy Y-chromosomal SGNH hydrolase gene expressed in the testis of the platyfish has been captured and mobilized by a Helitron transposon , 2014, BMC Genetics.

[40]  K. Hughes,et al.  Mating advantage for rare males in wild guppy populations , 2013, Nature.

[41]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[42]  Angel Amores,et al.  The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits , 2013, Nature Genetics.

[43]  D. Bachtrog,et al.  Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration , 2013, Nature Reviews Genetics.

[44]  Joaquín Dopazo,et al.  Qualimap: evaluating next-generation sequencing alignment data , 2012, Bioinform..

[45]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[46]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

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

[48]  D. Reznick,et al.  PREDATION‐ASSOCIATED DIFFERENCES IN SEX LINKAGE OF WILD GUPPY COLORATION , 2012, Evolution; international journal of organic evolution.

[49]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[50]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[51]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[52]  E. Eichler,et al.  Limitations of next-generation genome sequence assembly , 2011, Nature Methods.

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

[54]  Detlef Weigel,et al.  Genome‐wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies , 2010, Molecular ecology.

[55]  T. Miura,et al.  Spermatogenesis in fish. , 2010, General and comparative endocrinology.

[56]  M. Schartl,et al.  Transcriptional Rewiring of the Sex Determining dmrt1 Gene Duplicate by Transposable Elements , 2010, PLoS genetics.

[57]  J. D. Fry.  THE GENOMIC LOCATION OF SEXUALLY ANTAGONISTIC VARIATION: SOME CAUTIONARY COMMENTS , 2009, Evolution; international journal of organic evolution.

[58]  Scott J Emrich,et al.  Open Access Research Article Population-level Transcriptome Sequencing of Nonmodel Organisms Erynnis Propertius and Papilio Zelicaon , 2022 .

[59]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[60]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[61]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[62]  D. Weigel,et al.  Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation , 2009, Proceedings of the Royal Society B: Biological Sciences.

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

[64]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[65]  D. Weigel,et al.  Linkage Analysis Reveals the Independent Origin of Poeciliid Sex Chromosomes and a Case of Atypical Sex Inheritance in the Guppy (Poecilia reticulata) , 2009, Genetics.

[66]  David Haussler,et al.  Using native and syntenically mapped cDNA alignments to improve de novo gene finding , 2008, Bioinform..

[67]  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.

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

[69]  Robert Olendorf,et al.  Frequency-dependent survival in natural guppy populations , 2006, Nature.

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

[71]  A. Magurran.  Evolutionary Ecology: The Trinidadian Guppy , 2005 .

[72]  M. Schartl,et al.  Evolutionary Origin of the Medaka Y Chromosome , 2004, Current Biology.

[73]  J. Volff,et al.  Variability of genetic sex determination in poeciliid fishes , 2004, Genetica.

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

[75]  D. Bachtrog.  Accumulation of Spock and Worf, two novel non-LTR retrotransposons, on the neo-Y chromosome of Drosophila miranda. , 2003, Molecular biology and evolution.

[76]  Felix Breden,et al.  Sex Chromosomes and Sexual Selection in Poeciliid Fishes , 2002, The American Naturalist.

[77]  T. Iwamatsu,et al.  Fine Structure of the Storage Micropocket of Spermatozoa in the Ovary of the Guppy Poecilia reticulata , 2002, Zoological science.

[78]  J. Volff,et al.  Amplification of a long terminal repeat-like element on the Y chromosome of the platyfish, Xiphophorus maculatus , 2000, Chromosoma.

[79]  B. Charlesworth.  Measures of divergence between populations and the effect of forces that reduce variability. , 1998, Molecular biology and evolution.

[80]  J. Endler.  Multiple-trait coevolution and environmental gradients in guppies. , 1995, Trends in ecology & evolution.

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

[82]  W. Rice.  THE ACCUMULATION OF SEXUALLY ANTAGONISTIC GENES AS A SELECTIVE AGENT PROMOTING THE EVOLUTION OF REDUCED RECOMBINATION BETWEEN PRIMITIVE SEX CHROMOSOMES , 1987, Evolution; international journal of organic evolution.

[83]  M. Nei.  Molecular Evolutionary Genetics , 1987 .