Scallop genome provides insights into evolution of bilaterian karyotype and development

[1]  D. Weese,et al.  Phylogenomics of Lophotrochozoa with Consideration of Systematic Error , 2016, Systematic biology.

[2]  Ruiqiang Li,et al.  The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees , 2016, PLoS genetics.

[3]  Li Li,et al.  A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata) Using Genotyping-by-Sequencing , 2016, G3: Genes, Genomes, Genetics.

[4]  S. Watabe,et al.  Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle , 2016, Zoological Letters.

[5]  F. Ronquist,et al.  Xenacoelomorpha is the sister group to Nephrozoa , 2016, Nature.

[6]  N. Satoh,et al.  The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization , 2015, Nature Communications.

[7]  Ximing Guo,et al.  Immune and stress responses in oysters with insights on adaptation. , 2015, Fish & shellfish immunology.

[8]  Oleg Simakov,et al.  The octopus genome and the evolution of cephalopod neural and morphological novelties , 2015, Nature.

[9]  Sun Xiao.  Hox Genes and Their Expression Pattern in Early Development of Litopenaeus vannamei , 2015 .

[10]  M. A. Biscotti,et al.  Hox and ParaHox genes: A review on molluscs , 2014, Genesis.

[11]  Qiang Li,et al.  Genome sequence and genetic diversity of the common carp, Cyprinus carpio , 2014, Nature Genetics.

[12]  Shi Wang,et al.  High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker , 2014 .

[13]  K. Whoriskey,et al.  Systematic Differences in Eye Numbers between the Left and Right Valves of the Sea Scallop Placopecten magellanicus: an Evolutionary Response for Visualizing the Water Column? , 2014 .

[14]  W. Arthur,et al.  Evolving Animals: The Story of our Kingdom , 2014 .

[15]  Guojie Zhang,et al.  Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle , 2014, Nature Genetics.

[16]  Shi Wang,et al.  RADtyping: An Integrated Package for Accurate De Novo Codominant and Dominant RAD Genotyping in Mapping Populations , 2013, PloS one.

[17]  David E. K. Ferrier,et al.  Time is of the essence for ParaHox homeobox gene clustering , 2013, BMC Biology.

[18]  Nicholas H. Putnam,et al.  Insights into bilaterian evolution from three spiralian genomes , 2012, Nature.

[19]  F. Raible,et al.  Stable transgenesis in the marine annelid Platynereis dumerilii sheds new light on photoreceptor evolution , 2012, Proceedings of the National Academy of Sciences.

[20]  Shi Wang,et al.  Growth and Reproductive Performance of Triploid Yesso Scallops (Patinopecten yessoensis) Induced by Hypotonic Shock , 2012 .

[21]  Qiang Wang,et al.  The oyster genome reveals stress adaptation and complexity of shell formation , 2012, Nature.

[22]  D. Arendt,et al.  Molecular analysis of the amphioxus frontal eye unravels the evolutionary origin of the retina and pigment cells of the vertebrate eye , 2012, Proceedings of the National Academy of Sciences.

[23]  M. Matz,et al.  2b-RAD: a simple and flexible method for genome-wide genotyping , 2012, Nature Methods.

[24]  Dieter Deforce,et al.  Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination , 2011, Nucleic acids research.

[25]  P. Holland,et al.  Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization. , 2012, Molecular biology and evolution.

[26]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[27]  L. Moroz,et al.  Phylogenomics reveals deep molluscan relationships , 2011, Nature.

[28]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[29]  Shi Wang,et al.  Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX , 2011, PloS one.

[30]  D. Duboule,et al.  A regulatory 'landscape effect' over the HoxD cluster. , 2011, Developmental biology.

[31]  Stefano Lonardi,et al.  Accurate Construction of Consensus Genetic Maps via Integer Linear Programming , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[32]  Le Kang,et al.  De Novo Analysis of Transcriptome Dynamics in the Migratory Locust during the Development of Phase Traits , 2010, PloS one.

[33]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[34]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[35]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[36]  A. Ivantsov.  New reconstruction of Kimberella, problematic Vendian metazoan , 2009 .

[37]  K. Yau,et al.  Phototransduction Motifs and Variations , 2009, Cell.

[38]  M. Martindale,et al.  Coordinated spatial and temporal expression of Hox genes during embryogenesis in the acoel Convolutriloba longifissura , 2009, BMC Biology.

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

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

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

[42]  E. Seaver,et al.  Genomic Organization and Expression Demonstrate Spatial and Temporal Hox Gene Colinearity in the Lophotrochozoan Capitella sp. I , 2008, PloS one.

[43]  D. Eernisse,et al.  Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution , 2008, Evolution: Education and Outreach.

[44]  P. Holland,et al.  HomeoDB: a database of homeobox gene diversity , 2008, Evolution & development.

[45]  D. Blackburn,et al.  Isolation and expression of Pax6 and atonal homologues in the American horseshoe crab, Limulus polyphemus , 2008, Developmental dynamics : an official publication of the American Association of Anatomists.

[46]  Nicholas H. Putnam,et al.  The amphioxus genome illuminates vertebrate origins and cephalochordate biology. , 2008, Genome research.

[47]  Nicholas H. Putnam,et al.  The amphioxus genome and the evolution of the chordate karyotype , 2008, Nature.

[48]  G. Budd.  The earliest fossil record of the animals and its significance , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[49]  Z. Kozmík.  The role of Pax genes in eye evolution , 2008, Brain Research Bulletin.

[50]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[51]  Gerard Talavera,et al.  Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.

[52]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[53]  Denis Duboule,et al.  The rise and fall of Hox gene clusters , 2007, Development.

[54]  Shi Wang,et al.  Fosmid Library Construction and Initial Analysis of End Sequences in Zhikong Scallop (Chlamys farreri) , 2007, Marine Biotechnology.

[55]  Rolf Apweiler,et al.  InterPro and InterProScan , 2007 .

[56]  N. Mulder,et al.  InterPro and InterProScan: tools for protein sequence classification and comparison. , 2007, Methods in molecular biology.

[57]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[58]  Russell D. Fernald,et al.  Casting a Genetic Light on the Evolution of Eyes , 2006, Science.

[59]  William McGinnis,et al.  Genomic Evolution of Hox Gene Clusters , 2006, Science.

[60]  A. Zhan,et al.  Cloning and characterization of tryptophan 2,3‐dioxygenase gene of Zhikong scallop Chlamys farreri (Jones and Preston 1904) , 2006 .

[61]  L. Wilkens.  Chapter 5 Neurobiology and behaviour of the scallop , 2006 .

[62]  R. P. Kostyuchenko,et al.  Hox gene expression in larval development of the polychaetes Nereis virens and Platynereis dumerilii (Annelida, Lophotrochozoa) , 2006, Development Genes and Evolution.

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

[64]  Jordi Garcia-Fernàndez,et al.  The genesis and evolution of homeobox gene clusters , 2005, Nature Reviews Genetics.

[65]  David Posada,et al.  ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..

[66]  Thomas Ludwig,et al.  RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees , 2005, Bioinform..

[67]  James A. MacLean,et al.  Rhox: A New Homeobox Gene Cluster , 2005, Cell.

[68]  Steven Salzberg,et al.  TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..

[69]  N. Satoh,et al.  Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[70]  S Miyano,et al.  Open source clustering software. , 2004, Bioinformatics.

[71]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[72]  M. Akam,et al.  The Hox gene complement of acoel flatworms, a basal bilaterian clade , 2004, Evolution & development.

[73]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[74]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[75]  D. Ferrier,et al.  Evolution of the Hox/ParaHox gene clusters. , 2003, The International journal of developmental biology.

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

[77]  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.

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

[79]  V. Gremigni,et al.  The genetic network of prototypic planarian eye regeneration is Pax6 independent. , 2002, Development.

[80]  D. Arendt,et al.  Development of pigment-cup eyes in the polychaete Platynereis dumerilii and evolutionary conservation of larval eyes in Bilateria. , 2002, Development.

[81]  Catherine Thiriot-Ouievreux.  Review of the literature on bivalve cytogenetics in the last ten years , 2002 .

[82]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[83]  D. Massa,et al.  Devonian and carboniferous brachiopods and bivalves of the Djado sub-basin (North Niger, SW Libya) , 2001 .

[84]  J. Jurka.  Repbase update: a database and an electronic journal of repetitive elements. , 2000, Trends in genetics : TIG.

[85]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[86]  K Ikeo,et al.  Pax 6: mastering eye morphogenesis and eye evolution. , 1999, Trends in genetics : TIG.

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

[88]  W. Gehring,et al.  Isolation and developmental expression of the amphioxus Pax-6 gene (AmphiPax-6): insights into eye and photoreceptor evolution. , 1998, Development.

[89]  M. Fedonkin,et al.  The Late Precambrian fossil Kimberella is a mollusc-like bilaterian organism , 1997, Nature.

[90]  P. Callaerts,et al.  Squid Pax-6 and eye development. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[91]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[92]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[93]  W. Gehring,et al.  Homology of the eyeless gene of Drosophila to the Small eye gene in mice and Aniridia in humans. , 1994, Science.

[94]  P. Stam,et al.  Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. , 1993 .

[95]  C. Richardson.  Scallops: biology, ecology and aquaculture: edited by S.E. Shumway; Elsevier; 1991; 116 pp.; NLG 300.00; ISBN 0-444-88954-X , 1992 .

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

[97]  H. Sambrook.  Molecular cloning : a laboratory manual. Cold Spring Harbor, NY , 1989 .

[98]  L. Thim,et al.  J. Gen. Appl. Microbiol , 2020 .

[99]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .