A global assembly of cotton ESTs Material Supplemental

[1]  A. Skovsted Cytological studies in cotton , 1937, Journal of Genetics.

[2]  D. Llewellyn,et al.  A quick and easy method for isolating good-quality RNA from cotton (Gossypium hirsutum L.) tissues , 2002, Plant Molecular Biology Reporter.

[3]  Hee-Jin Kim,et al.  A novel expression assay system for fiber-specific promoters in developing cotton fibers , 2002, Plant Molecular Biology Reporter.

[4]  W. McCombie,et al.  Differential methylation of genes and repeats in land plants. , 2005, Genome research.

[5]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[6]  C. Wilkerson,et al.  Biotechnological improvement of cotton fibre maturity , 2005 .

[7]  Weisheng Wu,et al.  Identification and characterization of differentially expressed ESTs of Gossypium barbadense infected by Verticillium dahliae with suppression subtractive hybridization , 2005, Molecular Biology.

[8]  Trung B. Nguyen,et al.  QTL Analysis of Cotton Fiber Quality Using Multiple Gossypium hirsutum × Gossypium barbadense Backcross Generations , 2005 .

[9]  A. Hughes,et al.  Expression Patterns of Duplicate Genes in the Developing Root in Arabidopsis thaliana , 2005, Journal of Molecular Evolution.

[10]  Jonathan F Wendel,et al.  Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid , 2004, Genetics.

[11]  Patrick S. Schnable,et al.  Picky: oligo microarray design for large genomes , 2004, Bioinform..

[12]  Miftahudin,et al.  Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivum L.) , 2004, Genetics.

[13]  Jessica A Schlueter,et al.  Mining EST databases to resolve evolutionary events in major crop species. , 2004, Genome.

[14]  G. Martin,et al.  ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. , 2004, The Plant journal : for cell and molecular biology.

[15]  I. Wilson,et al.  Gene expression profile changes in cotton root and hypocotyl tissues in response to infection with Fusarium oxysporum f. sp. vasinfectum. , 2004, Molecular plant-microbe interactions : MPMI.

[16]  D. Galbraith,et al.  Methods for Transcriptional Profiling in Plants. Be Fruitful and Replicate , 2004, Plant Physiology.

[17]  Michael D. Gonzales,et al.  Functional genomics of cell elongation in developing cotton fibers , 2004, Plant Molecular Biology.

[18]  Rod A Wing,et al.  A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age1 , 2004, Plant Physiology.

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

[20]  G. Fincher,et al.  Members of a New Group of Chitinase-Like Genes are Expressed Preferentially in Cotton Cells with Secondary Walls , 2004, Plant Molecular Biology.

[21]  Vipin K. Rastogi,et al.  A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium) , 2004, Genetics.

[22]  J. Wendel,et al.  Evolution and expression of MYB genes in diploid and polyploid cotton , 2003, Plant Molecular Biology.

[23]  Robert D. Finn,et al.  The Pfam protein families database , 2004, Nucleic Acids Res..

[24]  J. Laroche,et al.  Large-scale statistical analysis of secondary xylem ESTs in pine , 2004, Plant Molecular Biology.

[25]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[26]  Emily Dimmer,et al.  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology , 2004, Nucleic Acids Res..

[27]  P. Arruda,et al.  Collection for Tropical Crop Sugarcane Analysis and Functional Annotation of an Expressed Sequence Tag , 2006 .

[28]  Yongbiao Xue,et al.  Identification of GhMYB109 encoding a R2R3 MYB transcription factor that expressed specifically in fiber initials and elongating fibers of cotton (Gossypium hirsutum L.). , 2003, Biochimica et biophysica acta.

[29]  C. V. Jongeneel,et al.  Modeling sequencing errors by combining Hidden Markov models , 2003, ECCB.

[30]  Christopher D Town,et al.  Annotation of the Arabidopsis Genome1 , 2003, Plant Physiology.

[31]  Srinivas Aluru,et al.  Efficient clustering of large EST data sets on parallel computers. , 2003, Nucleic acids research.

[32]  Yuxian Zhu,et al.  Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. , 2003, Nucleic acids research.

[33]  A. Paterson,et al.  Rate variation among nuclear genes and the age of polyploidy in Gossypium. , 2003, Molecular biology and evolution.

[34]  Jonathan F. Wendel,et al.  Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[35]  G. Pertea,et al.  Comparative Analyses of Potato Expressed Sequence Tag Libraries1 , 2003, Plant Physiology.

[36]  J. Wendel,et al.  Polyploidy and the Evolutionary History of Cotton , 2003 .

[37]  Y. Yamazaki,et al.  Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags , 2003, Molecular Genetics and Genomics.

[38]  Jian-wei Liu,et al.  Molecular Characterization of the Cotton GhTUB1 Gene That Is Preferentially Expressed in Fiber1 , 2002, Plant Physiology.

[39]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[40]  R. Van der Hoeven,et al.  Identification, Analysis, and Utilization of Conserved Ortholog Set Markers for Comparative Genomics in Higher Plants Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010479. , 2002, The Plant Cell Online.

[41]  J. Wendel,et al.  Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). , 2002, Molecular biology and evolution.

[42]  Jin-yuan Liu,et al.  Isolation of a cotton RGP gene: a homolog of reversibly glycosylated polypeptide highly expressed during fiber development. , 2002, Biochimica et biophysica acta.

[43]  J. Wendel,et al.  Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. , 2002, American journal of botany.

[44]  G. Robinson,et al.  Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. , 2002, Genome research.

[45]  W. Michalek,et al.  EST analysis in barley defines a unigene set comprising 4,000 genes , 2002, Theoretical and Applied Genetics.

[46]  Hui-Hsien Chou,et al.  DNA sequence quality trimming and vector removal , 2001, Bioinform..

[47]  Hong Wang,et al.  Gene Expression Profiles during the Initial Phase of Salt Stress in Rice , 2001, Plant Cell.

[48]  The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[49]  J. Ohlrogge,et al.  Arabidopsis microarray service facilities. , 2000, Plant physiology.

[50]  D. Stekel,et al.  The comparison of gene expression from multiple cDNA libraries. , 2000, Genome research.

[51]  J. Wendel,et al.  Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium l., malvaceae). , 2000, Molecular phylogenetics and evolution.

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

[53]  J. Claverie,et al.  Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. , 1999, Genome research.

[54]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[55]  C. V. Jongeneel,et al.  ESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences , 1999, ISMB.

[56]  J. Timmis,et al.  Characterisation of a cotton gene expressed late in fibre cell elongation , 1999, Theoretical and Applied Genetics.

[57]  L. Greller,et al.  Detecting selective expression of genes and proteins. , 1999, Genome research.

[58]  J. Claverie Computational methods for the identification of differential and coordinated gene expression. , 1999, Human molecular genetics.

[59]  K. El-Zik,et al.  D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel avenues for evolution. , 1998, Genetics.

[60]  J. Timmis,et al.  Specific expression of an expansin gene during elongation of cotton fibres. , 1998, Biochimica et biophysica acta.

[61]  K. El-Zik,et al.  Polyploid formation created unique avenues for response to selection in Gossypium (cotton). , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[62]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[63]  E. Turcotte,et al.  Genetics, cytology and evolution of Gossypium. , 1985 .