Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom.


:We conducted a comprehensive analysis of codon usage bias (CUB) based on the available non-redundant full-length cDNA (nrFLcDNA) and expressed sequence tags (ESTs) data of cultivar Micro-Tom and evaluated the associations of observed CUB and measurements of transcriptional and translational effectiveness. The analysis presented in our study suggests a correlation, which is negative but highly correlated between Axis 1 and GC3s (r=-0.827, P<0.01), indicating that mutational bias has a significant and dominant repressive role to the choices of GC3. We also observed a strong positive correlation between codon adaptation index (CAI) and translational adaptation index (tAIg) (0.407, P<0.01), which demonstrates the facilitation of efficient translation by the optimal codon usage patterns of the highly expressed genes. We believe that the complete set of optimal codon usage patterns detected in this study will serve as a model to enhance the transgenesis in the studied cultivar of Solanum lycopersicum.






Sablok G,Wu X,Kuo J,Nayak KC,Baev V,Varotto C,Zhou F




Has Abstract


2013-05-01 00:00:00
















  • Comparative genomic analysis of two brucellaphages of distant origins.

    abstract::Here, we present the first complete genome sequence of brucellaphage Tbilisi (Tb) and compared it with that of Pr, a broad host-range brucellaphage recently isolated in Mexico. The genomes consist of 41,148 bp (Tb) and 38,253 bp (Pr), they differ mainly in the region encoding structural proteins, in which the genome o...


    pub_type: 杂志文章


    authors: Flores V,López-Merino A,Mendoza-Hernandez G,Guarneros G

    更新日期:2012-04-01 00:00:00

  • Structure, chromosomal locus, and promoter of mouse Hes2 gene, a homologue of Drosophila hairy and Enhancer of split.

    abstract::Hes2 encodes a mammalian basic helix-loop-helix transcriptional repressor homologous to the products of Drosophila hairy and Enhancer of split. Here, we isolated and characterized the mouse Hes2 gene. This gene consists of four exons, and all the introns are located within the protein-coding region at positions homolo...


    pub_type: 杂志文章


    authors: Nishimura M,Isaka F,Ishibashi M,Tomita K,Tsuda H,Nakanishi S,Kageyama R

    更新日期:1998-04-01 00:00:00

  • Isolation of a human chromosome 14-only somatic cell hybrid: analysis using Alu and LINE-based PCR.

    abstract::Interspecific somatic cell hybrids containing single human chromosomes are valuable reagents for localization of cloned genes and DNA fragments to specific chromosomes, for the development of chromosome-specific libraries, and for generation of hybrid cell lines containing subchromosomal regions. A CHO somatic cell hy...


    pub_type: 杂志文章


    authors: Mares A Jr,Ledbetter SA,Ledbetter DH,Roberts R,Hejtmancik JF

    更新日期:1991-09-01 00:00:00

  • Structure of the gene encoding the murine protein kinase CK2 beta subunit.

    abstract::The mouse protein kinase CK2 beta subunit gene (Csnk2b) is composed of seven exons contained within 7874 bp. The exon and intron lengths extend from 76 to 321 and 111 to 1272 bp, respectively. The lengths of the murine coding exons correspond exactly to the lengths of the exons in the human CK2 beta gene. Both genes c...


    pub_type: 杂志文章


    authors: Boldyreff B,Issinger OG

    更新日期:1995-09-01 00:00:00

  • Transposition, amplification, and divergence in the origin of the DNF15 loci, a polymorphic repetitive sequence family on chromosomes 1 and 3.

    abstract::The loci DNF15S1 and DNF15S2 are members of a small repetitive sequence family at discrete chromosomal locations, namely, 1p36 and 3p21, respectively. Studies of the structure, arrangement, and interrelations of the family suggest that the single copy on chromosome 3 is the original member and that this gave rise to t...


    pub_type: 杂志文章


    authors: Welch HM,Darby JK,Pilz AJ,Ko CM,Carritt B

    更新日期:1989-10-01 00:00:00

  • Genomic structure and chromosome location of the human mutT homologue gene MTH1 encoding 8-oxo-dGTPase for prevention of A:T to C:G transversion.

    abstract::8-Oxo-dGTP (8-oxo-7,8-dihydrodeoxyguanosine triphosphate) is produced by active oxygen species in the nucleotide pool of the cell and can be incorporated into cellular DNA. Human cells contain enzyme activity that hydrolyzes 8-oxo-dGTP to 8-oxo-dGMP, thereby preventing occurrence of mutations, caused by misincorporati...


    pub_type: 杂志文章


    authors: Furuichi M,Yoshida MC,Oda H,Tajiri T,Nakabeppu Y,Tsuzuki T,Sekiguchi M

    更新日期:1994-12-01 00:00:00

  • Isolation of a novel human homologue of the gene coding for echinoderm microtubule-associated protein (EMAP) from the Usher syndrome type 1a locus at 14q32.

    abstract::Usher syndrome type 1 (USH1) is an autosomal recessive, genetically heterogeneous disorder causing severe congenital deafness, retinitis pigmentosa, and vestibular dysfunction. The USHla locus located on 14q32 has been linked to the genetic markers D14S250 and D14S78. Using D14S250 and D14S78, we have isolated two non...


    pub_type: 杂志文章


    authors: Eudy JD,Ma-Edmonds M,Yao SF,Talmadge CB,Kelley PM,Weston MD,Kimberling WJ,Sumegi J

    更新日期:1997-07-01 00:00:00

  • Genetic manipulations in crops: Challenges and opportunities.

    abstract::An alarming increase in the human population necessitates doubling the world food production in the next few decades. Although a number of possible biotechnological measures are under consideration, central to these efforts is the development of transgenic crops to produce more food, and the traits with which plants c...


    pub_type: 杂志文章,评审


    authors: Ahmad N,Mukhtar Z

    更新日期:2017-10-01 00:00:00

  • Analysis of exon/intron structure and 400 kb of genomic sequence surrounding the 5'-promoter and 3'-terminal ends of the human glypican 3 (GPC3) gene.

    abstract::GPC3, the gene modified in the Simpson-Golabi-Behmel gigantism/overgrowth syndrome (SGBS), is shown to span more than 500 kb of genomic sequence, with the transcript beginning 197 bp 5' of the translational start site. The Xq26.1 region containing GPC3 as the only known gene has been extended to > 900 kb by sequence a...


    pub_type: 杂志文章


    authors: Huber R,Crisponi L,Mazzarella R,Chen CN,Su Y,Shizuya H,Chen EY,Cao A,Pilia G

    更新日期:1997-10-01 00:00:00

  • Mapping of the human CENP-B gene to chromosome 20 and the CENP-C gene to chromosome 12 by a rapid cycle DNA amplification procedure.

    abstract::By optimizing the primer-annealing temperature in a rapid air cycling procedure, two human DNA sequences encoding centromere proteins B and C (CENP-B and CENP-C) were specifically amplified without any detectable amplification of highly homologous rodent DNA sequences. Using a panel of rodent/human hybrid DNA, the gen...


    pub_type: 杂志文章


    authors: Sugimoto K,Yata H,Himeno M

    更新日期:1993-07-01 00:00:00

  • Identifying new candidate genes for hereditary facial paresis on chromosome 3q21-q22 by RNA in situ hybridization in mouse.

    abstract::Hereditary congenital facial paresis (HCFP) belongs to the family of congenital cranial dysinnervation disorders and is characterized by an isolated dysfunction of the facial nerve (nVII). While genetic defects have been identified for several members of this disease family, genes underlying congenital facial paresis ...


    pub_type: 杂志文章


    authors: van der Zwaag B,Burbach JP,Scharfe C,Oefner PJ,Brunner HG,Padberg GW,van Bokhoven H

    更新日期:2005-07-01 00:00:00

  • Physical map and characterization of transcripts in the candidate interval for familial chondrocalcinosis at chromosome 5p15.1.

    abstract::The gene for familial chondrocalcinosis (MIM 118600; gene symbol CCAL2) has been localized to a 0.8-cM interval on the short arm of chromosome 5, between the polymorphic microsatellite markers D5S416 and D5S2114. We have undertaken the physical and transcript mapping of this interval, as well as regions telomeric to t...


    pub_type: 杂志文章


    authors: Rojas K,Serrano de la Peña L,Gallardo T,Simmons A,Nyce K,McGrath R,Considine E,Vasko AJ,Peterson E,Grady D,Cox R,Andrew LJ,Lovett M,Overhauser J,Williams CJ

    更新日期:1999-12-01 00:00:00

  • Comparative transcriptome analysis of diploid and triploid hybrid groupers (Epinephelus coioides♀ × E. lanceolatus♂) reveals the mechanism of abnormal gonadal development in triploid hybrids.

    abstract::In our previous studies, diploid and triploid hybrids have been detected from the hybridization of Epinephelus coioides♀ × E. lanceolatus♂. The triploid groupers have been found to be delayed in gonadal development, but the mechanism remains poorly understood. In this study, we examined the gonadal development, assaye...


    pub_type: 杂志文章


    authors: Xiao L,Wang D,Guo Y,Tang Z,Liu Q,Li S,Zhang Y,Lin H

    更新日期:2019-05-01 00:00:00

  • Human type I pituitary adenylate cyclase activating polypeptide receptor (ADCYAP1R): localization to chromosome band 7p14 and integration into the cytogenetic, physical, and genetic map of chromosome 7.

    abstract::The gene encoding the human type I pituitary adenylate cyclase activating polypeptide receptor (ADCYAP1R1) was mapped to chromosome 7 by PCR analysis of genomic DNA from a human/rodent somatic cell hybrid mapping panel. This assignment was confirmed and the gene localized to chromosome band 7p14 by fluorescence in sit...


    pub_type: 杂志文章


    authors: Stoffel M,Espinosa R 3rd,Trabb JB,Le Beau MM,Bell GI

    更新日期:1994-10-01 00:00:00

  • Solh, the mouse homologue of the Drosophila melanogaster small optic lobes gene: organization, chromosomal mapping, and localization of gene product to the olfactory bulb.

    abstract::The Drosophila melanogaster small optic lobes gene (sol) is required for normal development of the neuropiles of the medulla and lobula complexes of the adult optic lobes. The predicted protein products of sol and its human homologue SOLH contain zinc-finger-like repeats, a calpain-like protease domain, and a C-termin...


    pub_type: 杂志文章


    authors: Kamei M,Webb GC,Heydon K,Hendry IA,Young IG,Campbell HD

    更新日期:2000-02-15 00:00:00

  • Minimum error calibration and normalization for genomic copy number analysis.

    abstract:BACKGROUND:Copy number variations (CNV) are regional deviations from the normal autosomal bi-allelic DNA content. While germline CNVs are a major contributor to genomic syndromes and inherited diseases, the majority of cancers accumulate extensive "somatic" CNV (sCNV or CNA) during the process of oncogenetic transforma...


    pub_type: 杂志文章


    authors: Gao B,Baudis M

    更新日期:2020-09-01 00:00:00

  • The mouse Laf4 gene: exon/intron organization, cDNA sequence, alternative splicing, and expression during central nervous system development.

    abstract::The cerebral cortex is a tissue with a high degree of neuronal diversity. It consists of six cell layers with a unique set of neuronal subtypes. A crucial step in the process of cortical differentiation is the transition from a mitotically active neuroblast to a postmitotic young neuron. To identify genes involved in ...


    pub_type: 杂志文章


    authors: Britanova O,Lukyanov S,Gruss P,Tarabykin V

    更新日期:2002-07-01 00:00:00

  • Isolation of human and murine homologues of the Drosophila minibrain gene: human homologue maps to 21q22.2 in the Down syndrome "critical region".

    abstract::The presence of an extra copy of human chromosome 21 (trisomy 21), especially region 21q22.2, causes many phenotypes in Down syndrome, including mental retardation. To study genes potentially responsible for some of these phenotypes, we cloned a human candidate gene (DYRK) from 21q22.2 and its murine counterpart (Dyrk...


    pub_type: 杂志文章


    authors: Song WJ,Sternberg LR,Kasten-Sportès C,Keuren ML,Chung SH,Slack AC,Miller DE,Glover TW,Chiang PW,Lou L,Kurnit DM

    更新日期:1996-12-15 00:00:00

  • The gene mutated in cocoa mice, carrying a defect of organelle biogenesis, is a homologue of the human Hermansky-Pudlak syndrome-3 gene.

    abstract::Hermansky-Pudlak syndrome (HPS) is a group of human disorders of organelle biogenesis characterized by defective synthesis of melanosomes, lysosomes, and platelet dense granules. In the mouse, at least 15 loci are associated with mutant phenotypes similar to human HPS. We have identified the gene mutated in cocoa (coa...


    pub_type: 杂志文章


    authors: Suzuki T,Li W,Zhang Q,Novak EK,Sviderskaya EV,Wilson A,Bennett DC,Roe BA,Swank RT,Spritz RA

    更新日期:2001-11-01 00:00:00

  • Assignment of defensin gene(s) to human chromosome 8p23.

    abstract::A relatively abundant component of the polymorphonuclear leukocyte granulocytes has been recently isolated and called defensin. Defensins have antimicrobial activity against gram-positive and gram-negative bacteria and enveloped viruses. A cDNA insert for defensin HNP-1 (DEF1) has been used to map the gene(s) to human...


    pub_type: 杂志文章


    authors: Sparkes RS,Kronenberg M,Heinzmann C,Daher KA,Klisak I,Ganz T,Mohandas T

    更新日期:1989-08-01 00:00:00

  • The alpha-fetoprotein promoter is the target of Afr1-mediated postnatal repression.

    abstract::The alpha-fetoprotein (AFP) gene is transcribed at high levels in the fetal liver and is repressed at birth, leading to low but detectable levels of AFP mRNA in the adult liver. This repression is regulated, in part, by a locus that is unlinked to AFP called Alpha-fetoprotein regulator 1 (Afr1). Previous studies showe...


    pub_type: 杂志文章


    authors: Peyton DK,Huang MC,Giglia MA,Hughes NK,Spear BT

    更新日期:2000-01-15 00:00:00

  • Database and analyses of known alternatively spliced genes in plants.

    abstract::Alternative splicing is an important cellular mechanism that increases the diversity of gene products. The number of alternatively spliced genes reported so far in plants is much smaller than that in mammals, but is increasing as a result of the explosive growth of available EST and genomic sequences. We have searched...


    pub_type: 杂志文章


    authors: Zhou Y,Zhou C,Ye L,Dong J,Xu H,Cai L,Zhang L,Wei L

    更新日期:2003-12-01 00:00:00

  • Ranking analysis of correlation coefficients in gene expressions.

    abstract::Development of statistical methods has become very necessary for large-scale correlation analysis in the current "omic" data. We propose ranking analysis of correlation coefficients (RAC) based on transforming correlation matrix into correlation vector and conducting a "locally ranking" strategy that significantly red...


    pub_type: 杂志文章


    authors: Tan YD

    更新日期:2011-01-01 00:00:00

  • The complete nucleotide sequence of murine beta-glucuronidase mRNA and its deduced polypeptide.

    abstract::The complete nucleotide sequence of murine beta-glucuronidase (GUS) mRNA has been compiled from three overlapping cloned cDNAs and a single GUS-specific genomic clone. The sequence is composed of 2455 nucleotides, exclusive of the poly(A) tail. The 5' and 3' untranslated regions contain 12 and 499 bases, respectively,...


    pub_type: 杂志文章


    authors: Gallagher PM,D'Amore MA,Lund SD,Ganschow RE

    更新日期:1988-04-01 00:00:00

  • A mutation in apolipoprotein A-I in the Iowa type of familial amyloidotic polyneuropathy.

    abstract::Immunoblotting of isoelectric focusing gels of plasma and direct genomic DNA sequencing have been used to characterize a mutation in apolipoprotein A-I associated with the familial amyloidotic polyneuropathy originally described by Van Allen in an Iowa kindred. An arginine for glycine substitution in apolipoprotein A-...


    pub_type: 杂志文章


    authors: Nichols WC,Gregg RE,Brewer HB Jr,Benson MD

    更新日期:1990-10-01 00:00:00

  • Rapid restriction mapping of cosmids by sequence-specific triple-helix-mediated affinity capture.

    abstract::A simple and rapid strategy for restriction mapping based on sequence-specific triple-helix affinity capture (TAC) was developed. The strategy was applied to the analysis of cosmid clones by the construction of a new cosmid vector, ScosTriplex-II, containing two different triple-helix-forming sequences flanking the cl...


    pub_type: 杂志文章


    authors: Ji H,Francisco T,Smith LM,Guilfoyle RA

    更新日期:1996-01-15 00:00:00

  • Drug response prediction by ensemble learning and drug-induced gene expression signatures.

    abstract::Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recently, considerable amount of drug-induced gene expression data has become publicly available, in addition to cytotoxicity databases. These large sets of data provided a...


    pub_type: 杂志文章


    authors: Tan M,Özgül OF,Bardak B,Ekşioğlu I,Sabuncuoğlu S

    更新日期:2019-09-01 00:00:00

  • Human tryptophan oxygenase localized to 4q31: possible implications for alcoholism and other behavioral disorders.

    abstract::A human tryptophan oxygenase clone was isolated by screening a liver cDNA library with a rat tryptophan oxygenase cDNA clone. Analysis showed extensive homology between the rat and the human DNA and protein sequences. The combined use of cell hybrids and in situ hydridization indicated that human tryptophan oxygenase ...


    pub_type: 杂志文章


    authors: Comings DE,Muhleman D,Dietz GW Jr,Donlon T

    更新日期:1991-02-01 00:00:00

  • Genomic mapping by anchoring random clones: a mathematical analysis.

    abstract::A complete physical map of the DNA of an organism, consisting of overlapping clones spanning the genome, is an extremely useful tool for genomic analysis. Various methods for the construction of such physical maps are available. One approach is to assemble the physical map by "fingerprinting" a large number of random ...


    pub_type: 杂志文章


    authors: Arratia R,Lander ES,Tavaré S,Waterman MS

    更新日期:1991-12-01 00:00:00

  • MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

    abstract::A key challenge in analyzing metagenomics data pertains to assembly of sequenced DNA fragments (i.e. reads) originating from various microbes in a given environmental sample. Several existing methodologies can assemble reads originating from a single genome. However, these methodologies cannot be applied for efficient...


    pub_type: 杂志文章


    authors: Reddy RM,Mohammed MH,Mande SS

    更新日期:2014-02-01 00:00:00