Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle

[1]  M. Gerdol,et al.  The genome of the Pacific oyster Crassostrea gigas brings new insights on the massive expansion of the C1q gene family in Bivalvia. , 2015, Developmental and comparative immunology.

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

[3]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[4]  D. Funabara,et al.  Novel Genes Participating in the Formation of Prismatic and Nacreous Layers in the Pearl Oyster as Revealed by Their Tissue Distribution and RNA Interference Knockdown , 2014, PloS one.

[5]  Hiromichi Nagasawa,et al.  The Diversity of Shell Matrix Proteins: Genome-Wide Investigation of the Pearl Oyster, Pinctada fucata , 2013, Zoological science.

[6]  K. Matsuno,et al.  An In-silico Genomic Survey to Annotate Genes Coding for Early Development-Relevant Signaling Molecules in the Pearl Oyster, Pinctada fucata , 2013, Zoological science.

[7]  T. Kawashima,et al.  Initiating the Mollusk Genomics Annotation Community: Toward Creating the Complete Curated Gene-Set of the Japanese Pearl Oyster, Pinctada fucata , 2013, Zoological Science.

[8]  T. Abe,et al.  A Genome-Wide Survey of Genes Encoding Transcription Factors in Japanese Pearl Oyster Pinctada fucata: II. Tbx, Fox, Ets, HMG, NF&kgr;B, bZIP, and C2H2 Zinc Fingers , 2013, Zoological science.

[9]  N. Satoh,et al.  A Genome-Wide Survey of Genes Encoding Transcription Factors in the Japanese Pearl Oyster, Pinctada fucata: I. Homeobox Genes , 2013, Zoological science.

[10]  Kiyohito Nagai A History of the Cultured Pearl Industry , 2013, Zoological science.

[11]  D. Funabara,et al.  Genome-Wide Survey of Genes Encoding Muscle Proteins in the Pearl Oyster, Pinctada fucata , 2013, Zoological science.

[12]  N. Satoh,et al.  Reproduction-Related Genes in the Pearl Oyster Genome , 2013, Zoological science.

[13]  N. Satoh,et al.  Evolutionary Aspects of Variability in bHLH Orthologous Families: Insights from the Pearl Oyster, Pinctada fucata , 2013, Zoological science.

[14]  Anushya Muruganujan,et al.  Large-scale gene function analysis with the PANTHER classification system , 2013, Nature Protocols.

[15]  M. Arnone,et al.  Identification of an intact ParaHox cluster with temporal colinearity but altered spatial colinearity in the hemichordate Ptychodera flava , 2013, BMC Evolutionary Biology.

[16]  Felipe Aguilera,et al.  Rapid evolution of pearl oyster shell matrix proteins with repetitive, low-complexity domains , 2013, Journal of The Royal Society Interface.

[17]  Huan Zhang,et al.  A four-CRD C-type lectin from Chlamys farreri mediating nonself-recognition with broader spectrum and opsonization. , 2013, Developmental and comparative immunology.

[18]  Benjamin Marie,et al.  The shell‐forming proteome of Lottia gigantea reveals both deep conservations and lineage‐specific novelties , 2013, The FEBS journal.

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

[20]  Benjamin Marie,et al.  Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell , 2012, Proceedings of the National Academy of Sciences.

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

[22]  Mengqiang Wang,et al.  A novel C1qDC protein acting as pattern recognition receptor in scallop Argopecten irradians. , 2012, Fish & shellfish immunology.

[23]  Hideo Aoki,et al.  Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology , 2012, DNA research : an international journal for rapid publication of reports on genes and genomes.

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

[25]  Rongqing Zhang,et al.  Identification of Genes Directly Involved in Shell Formation and Their Functions in Pearl Oyster, Pinctada fucata , 2011, PloS one.

[26]  Kaoru Maeyama,et al.  Deep Sequencing of ESTs from Nacreous and Prismatic Layer Producing Tissues and a Screen for Novel Shell Formation-Related Genes in the Pearl Oyster , 2011, PloS one.

[27]  M. Gerdol,et al.  The C1q domain containing proteins of the Mediterranean mussel Mytilus galloprovincialis: a widespread and diverse family of immune-related molecules. , 2011, Developmental and comparative immunology.

[28]  Arul Marie,et al.  Coupling Proteomics and Transcriptomics for the Identification of Novel and Variant Forms of Mollusk Shell Proteins: A Study with P. margaritifera , 2011, Chembiochem : a European journal of chemical biology.

[29]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[30]  Sophie Arnaud-Haond,et al.  Evolutionary Patterns in Pearl Oysters of the Genus Pinctada (Bivalvia: Pteriidae) , 2011, Marine Biotechnology.

[31]  G. Lanfranchi,et al.  Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis , 2011, BMC Genomics.

[32]  Federico Plazzi,et al.  Towards a molecular phylogeny of Mollusks: bivalves' early evolution as revealed by mitochondrial genes. , 2010, Molecular phylogenetics and evolution.

[33]  Benjamin Marie,et al.  Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization , 2010, BMC Genomics.

[34]  Huan Zhang,et al.  AiC1qDC-1, a novel gC1q-domain-containing protein from bay scallop Argopecten irradians with fungi agglutinating activity. , 2010, Developmental and comparative immunology.

[35]  D. Weisblat,et al.  Evolutionary dynamics of the wnt gene family: a lophotrochozoan perspective. , 2010, Molecular biology and evolution.

[36]  Michael Kube,et al.  Parallel evolution of nacre building gene sets in molluscs. , 2010, Molecular biology and evolution.

[37]  Dawei Li,et al.  The sequence and de novo assembly of the giant panda genome , 2010, Nature.

[38]  Takashi Kato,et al.  An Acidic Matrix Protein, Pif, Is a Key Macromolecule for Nacre Formation , 2009, Science.

[39]  Huan Zhang,et al.  A novel C1q-domain-containing protein from Zhikong scallop Chlamys farreri with lipopolysaccharide binding activity. , 2008, Fish & shellfish immunology.

[40]  E. Loker,et al.  Expression profiling and binding properties of fibrinogen-related proteins (FREPs), plasma proteins from the schistosome snail host Biomphalaria glabrata , 2008, Innate immunity.

[41]  K. Muroga,et al.  Purification and antibacterial characterization of a novel isoform of the Manila clam lectin (MCL-4) from the plasma of the Manila clam, Ruditapes philippinarum. , 2008, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[42]  Hao Wang,et al.  A lectin (CfLec-2) aggregating Staphylococcus haemolyticus from scallop Chlamys farreri. , 2008, Fish & shellfish immunology.

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

[44]  A. Pallavicini,et al.  High sequence variability of myticin transcripts in hemocytes of immune-stimulated mussels suggests ancient host-pathogen interactions. , 2008, Developmental and comparative immunology.

[45]  Benjamin Marie,et al.  Molluscan shell proteins: primary structure, origin, and evolution. , 2008, Current topics in developmental biology.

[46]  Koichi Morimoto,et al.  A novel nacre protein N19 in the pearl oyster Pinctada fucata. , 2007, Biochemical and biophysical research communications.

[47]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[48]  S. Kuratani,et al.  EVOLUTION OF HOX GENES IN MOLLUSCS: A COMPARISON AMONG SEVEN MORPHOLOGICALLY DIVERSE CLASSES , 2006 .

[49]  Masato Yano,et al.  Shematrin: a family of glycine-rich structural proteins in the shell of the pearl oyster Pinctada fucata. , 2006, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[50]  Feng Chen,et al.  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups , 2005, Nucleic Acids Res..

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

[52]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[53]  M. A. Biscotti,et al.  Isolation of Hox and ParaHox genes in the bivalve Pecten maximus. , 2005, Gene.

[54]  Takeshi Takeuchi,et al.  Biphasic and Dually Coordinated Expression of the Genes Encoding Major Shell Matrix Proteins in the Pearl Oyster Pinctada fucata , 2005, Marine Biotechnology.

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

[56]  Jesper Givskov Sørensen,et al.  The evolutionary and ecological role of heat shock proteins , 2003 .

[57]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

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

[59]  Charles A. Janeway,et al.  Decoding the Patterns of Self and Nonself by the Innate Immune System , 2002, Science.

[60]  P. Holland Beyond the Hox: how widespread is homeobox gene clustering? , 2001, Journal of anatomy.

[61]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[62]  R. Miller,et al.  A family of fibrinogen-related proteins that precipitates parasite-derived molecules is produced by an invertebrate after infection. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[63]  T. Fujikawa,et al.  Structures of mollusc shell framework proteins , 1997, Nature.

[64]  T Morita,et al.  A carbonic anhydrase from the nacreous layer in oyster pearls. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[65]  F. Hartl Molecular chaperones in cellular protein folding , 1996, Nature.

[66]  Jerzy Jurka,et al.  Censor - a Program for Identification and Elimination of Repetitive Elements From DNA Sequences , 1996, Comput. Chem..

[67]  F. Hartl,et al.  Molecular chaperones in cellular protein folding. , 1994, Nature.

[68]  R. Newell,et al.  9 – Physiological Energetics of Marine Molluscs , 1983 .