Comparative transcriptome analyses on silk glands of six silkmoths imply the genetic basis of silk structure and coloration

[1]  Z. Jia.  Bionomics of Antheraea assamensis , 2013 .

[2]  Y. Sima,et al.  Green cocoons in silkworm Bombyx mori resulting from the quercetin 5-O-glucosyltransferase of UGT86, is an evolved response to dietary toxins , 2013, Molecular Biology Reports.

[3]  L. Dai,et al.  The complete mitochondrial genome of the wild silkworm moth, Actias selene. , 2012, Gene.

[4]  B. Yao,et al.  Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing , 2012, PloS one.

[5]  G. Lubec,et al.  Mass spectrometrical analysis of bilin‐binding protein from the wing of Hebomoia glaucippe (Linnaeus, 1758) (Lepidoptera: Pieridae) , 2012, Electrophoresis.

[6]  C. Holland,et al.  Comparing the rheology of mulberry and “wild” silkworm spinning dopes , 2012, Biopolymers.

[7]  Joydip Kundu,et al.  Invited review nonmulberry silk biopolymers. , 2012, Biopolymers.

[8]  Jiahai Zhang,et al.  N-Terminal domain of Bombyx mori fibroin mediates the assembly of silk in response to pH decrease. , 2012, Journal of molecular biology.

[9]  Randolph V Lewis,et al.  Silkworms transformed with chimeric silkworm/spider silk genes spin composite silk fibers with improved mechanical properties , 2012, Proceedings of the National Academy of Sciences.

[10]  Zhong Wang,et al.  Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.

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

[12]  Siu-Ming Yiu,et al.  T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome - (Extended Abstract) , 2011, RECOMB.

[13]  Steven J. M. Jones,et al.  De novo assembly and analysis of RNA-seq data , 2010, Nature Methods.

[14]  G. Tsujimoto,et al.  The silkworm Green b locus encodes a quercetin 5-O-glucosyltransferase that produces green cocoons with UV-shielding properties , 2010, Proceedings of the National Academy of Sciences.

[15]  Yaopeng Zhang,et al.  Antheraea pernyi Silk Fiber: A Potential Resource for Artificially Biospinning Spider Dragline Silk , 2010, Journal of biomedicine & biotechnology.

[16]  Suvankar Ghorai,et al.  Analysis of Transcripts Expressed in One-Day-Old Larvae and Fifth Instar Silk Glands of Tasar Silkworm, Antheraea mylitta , 2010, Comparative and functional genomics.

[17]  Guangwu Guo,et al.  Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing , 2010, Nucleic acids research.

[18]  Y. Takasu,et al.  Identification of Ser2 proteins as major sericin components in the non-cocoon silk of Bombyx mori. , 2010, Insect biochemistry and molecular biology.

[19]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

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

[21]  Ruiqiang Li,et al.  SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology , 2009, Nucleic Acids Res..

[22]  F. Sehnal,et al.  Structure and expression of the silk adhesive protein Ser2 in Bombyx mori. , 2009, Insect biochemistry and molecular biology.

[23]  H. Sezutsu,et al.  Leucine-rich fibroin gene of the Japanese wild silkmoth, Rhodinia fugax (Lepidoptera: Saturniidae) , 2008 .

[24]  Ruiqiang Li,et al.  SOAP: short oligonucleotide alignment program , 2008, Bioinform..

[25]  Toru Shimada,et al.  WildSilkbase: An EST database of wild silkmoths , 2008, BMC Genomics.

[26]  K. Mita,et al.  Identification and characterization of a novel sericin gene expressed in the anterior middle silk gland of the silkworm Bombyx mori. , 2007, Insect biochemistry and molecular biology.

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

[28]  Matthew A. Collin,et al.  Blueprint for a High-Performance Biomaterial: Full-Length Spider Dragline Silk Genes , 2007, PloS one.

[29]  H. Sezutsu,et al.  Carotenoid silk coloration is controlled by a carotenoid-binding protein, a product of the Yellow blood gene , 2007, Proceedings of the National Academy of Sciences.

[30]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[31]  F. Vollrath,et al.  Spider and mulberry silkworm silks as compatible biomaterials , 2007 .

[32]  Paul M. Choate,et al.  Evolution of the Insects , 2006 .

[33]  Lin Fang,et al.  WEGO: a web tool for plotting GO annotations , 2006, Nucleic Acids Res..

[34]  S. Kundu,et al.  Isolation, purification and characterization of silk protein sericin from cocoon peduncles of tropical tasar silkworm, Antheraea mylitta. , 2006, International journal of biological macromolecules.

[35]  David L. Kaplan,et al.  Role of pH and charge on silk protein assembly in insects and spiders , 2006 .

[36]  Tao Liu,et al.  TreeFam: a curated database of phylogenetic trees of animal gene families , 2005, Nucleic Acids Res..

[37]  F. Sehnal,et al.  The Design of Silk Fiber Composition in Moths Has Been Conserved for More Than 150 Million Years , 2006, Journal of Molecular Evolution.

[38]  Y. Kato,et al.  Green colouration of cocoons in Antheraea yamamai (Lepidoptera: Saturniidae): light-induced production of blue bilin in the larval haemolymph. , 2004, Journal of insect physiology.

[39]  Tae-Won Goo,et al.  Cloning of the fibroin gene from the oak silkworm, Antheraea yamamai and its complete sequence , 2001, Biotechnology Letters.

[40]  F. Sehnal,et al.  Correlation between Fibroin Amino Acid Sequence and Physical Silk Properties* , 2003, Journal of Biological Chemistry.

[41]  John Quackenbush,et al.  TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets , 2003, Bioinform..

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

[43]  Fumio Arisaka,et al.  Silk Fibroin of Bombyx mori Is Secreted, Assembling a High Molecular Mass Elementary Unit Consisting of H-chain, L-chain, and P25, with a 6:6:1 Molar Ratio* , 2000, The Journal of Biological Chemistry.

[44]  Hideki Sezutsu,et al.  Dynamic Rearrangement Within the Antheraea pernyi Silk Fibroin Gene Is Associated with Four Types of Repetitive Units , 2000, Journal of Molecular Evolution.

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

[46]  G. Deléage,et al.  Structure and organization of the Bombyx mori sericin 1 gene and of the sericins 1 deduced from the sequence of the Ser 1B cDNA. , 1997, Insect biochemistry and molecular biology.

[47]  B. Meier,et al.  Local Structure in Spider Dragline Silk Investigated by Two-Dimensional Spin-Diffusion Nuclear Magnetic Resonance† , 1996 .

[48]  D. Ginzinger,et al.  Silk Properties Determined by Gland-Specific Expression of a Spider Fibroin Gene Family , 1996, Science.

[49]  T. Shimada,et al.  Phylogenetic relationship of silkmoths inferred from sequence data of the arylphorin gene. , 1995, Molecular phylogenetics and evolution.

[50]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[51]  Y. Katō.  Cocoon coloration and its determination factor in Rhodinia fugax. , 1994 .

[52]  T. Shimada,et al.  Diapause of the inter-specific F1 hybrids between Antheraea yamamai (Guerin-Meneville) and A. pernyi (G.-M.) (Lepidoptera: Saturniidae). , 1988 .

[53]  R. Huber,et al.  Crystallization, crystal structure analysis and preliminary molecular model of the bilin binding protein from the insect Pieris brassicae. , 1987, Journal of molecular biology.

[54]  M. Denny,et al.  The structure and properties of spider silk , 1986 .

[55]  J. Felsenstein.  Phylogenies and the Comparative Method , 1985, The American Naturalist.