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
















  • Expression analysis of a panel of long non-coding RNAs (lncRNAs) revealed their potential as diagnostic biomarkers in bladder cancer.

    abstract:INTRODUCTION:Long non-coding RNAs (lncRNAs) have fundamental roles in cell migration, proliferation, invasion and metastasis. METHODS:In the current study, we evaluated expression of a panel of lncRNAs in bladder cancer tissues, adjacent non-cancerous tissues (ANCTs) and normal bladder tissues to evaluate their diagno...


    pub_type: 杂志文章


    authors: Abdolmaleki F,Ghafoui-Fard S,Taheri M,Mordadi A,Afsharpad M,Varmazyar S,Nazparvar B,Oskooei VK,Omrani MD

    更新日期:2020-01-01 00:00:00

  • cDNA cloning and gene structure of a novel water channel expressed exclusively in human kidney: evidence for a gene cluster of aquaporins at chromosome locus 12q13.

    abstract::A 1.8-kb cDNA clone (designed hKID, gene symbol AQP2L) with homology to the aquaporins was isolated from a human kidney cDNA library. The longest open reading frame of 846 bp encoded a 282-amino-acid hydrophobic protein that contained the conserved NPA motifs of MIP family members. Cell-free translation produced a non...


    pub_type: 杂志文章


    authors: Ma T,Yang B,Kuo WL,Verkman AS

    更新日期:1996-08-01 00:00:00

  • Identification of INSL5, a new member of the insulin superfamily.

    abstract::A new member of the insulin gene superfamily (INSL5) was identified by searching EST databases for the presence of the conserved insulin B-chain cysteine motif. Human and murine INSL5 are both polypeptides of 135 amino acids, matching the classical signature of the insulin superfamily. Through the B- and A-chain regio...


    pub_type: 杂志文章


    authors: Conklin D,Lofton-Day CE,Haldeman BA,Ching A,Whitmore TE,Lok S,Jaspers S

    更新日期:1999-08-15 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

  • Cloning and gene mapping of the mouse homologue of the CBFA2T1 gene associated with human acute myeloid leukemia.

    abstract::The human CBFA2T1 (also known as MTG8) gene, on chromosome 8, has been identified through its involvement in the t(8;21) chromosomal translocation, frequently found in acute myeloid leukemia. We report here the isolation and characterization of the mouse homologue of the CBFA2T1 gene, Cbfa2t1h. Nucleotide sequence ana...


    pub_type: 杂志文章


    authors: Niwa-Kawakita M,Miyoshi H,Gotoh O,Matsushima Y,Nishimura M,Shisa H,Ohki M

    更新日期:1995-10-10 00:00:00

  • Primary structure of the goat beta-globin locus control region.

    abstract::The goat beta-globin cluster is composed of a triplicated four-gene set. A locus control region (LCR) containing elements homologous to 5'DNase I hypersensitive sites (HS) 1, 2, and 3 of the human beta-globin LCR has been identified at the 5' end of this locus. We determined 10.2 kb of nucleotide sequence from the goa...


    pub_type: 杂志文章


    authors: Li Q,Zhou B,Powers P,Enver T,Stamatoyannopoulos G

    更新日期:1991-03-01 00:00:00

  • Multipoint mapping of the central core disease locus.

    abstract::A linkage analysis with 12 DNA markers from proximal 19q was performed in eight families with central core disease (CCO). Two-point analysis gave a peak lod score of Z = 4.95 at theta = 0.00 for the anonymous marker D19S190 and of Z = 2.53 at theta = 0.00 for the ryanodine receptor (RYR1) candidate gene. Multipoint li...


    pub_type: 杂志文章


    authors: Schwemmle S,Wolff K,Palmucci LM,Grimm T,Lehmann-Horn F,Hübner C,Hauser E,Iles DE,MacLennan DH,Müller CR

    更新日期:1993-07-01 00:00:00

  • Genomic structure of the EWS gene and its relationship to EWSR1, a site of tumor-associated chromosome translocation.

    abstract::The EWS gene has been identified based on its location at the chromosome 22 breakpoint of the t(11;22)(q24;q12) translocation that characterizes Ewing sarcoma and related neuroectodermal tumors. The EWS gene spans about 40 kb of DNA and is encoded by 17 exons. The nucleotide sequence of the exons is identical to that ...


    pub_type: 杂志文章


    authors: Plougastel B,Zucman J,Peter M,Thomas G,Delattre O

    更新日期:1993-12-01 00:00:00

  • Developmental expression of p107 mRNA and evidence for alternative splicing of the p107 (RBL1) gene product.

    abstract::Expression of p107, a protein with homology to the retinoblastoma tumor suppressor (pRB), was monitored during murine development. Northern blot tissue surveys identified two transcripts of 4.9 and 2.4 kb that hybridized to a p107 cDNA clone. Expression of both transcripts was detected in fetal tissues, with particula...


    pub_type: 杂志文章


    authors: Kim KK,Soonpaa MH,Wang H,Field LJ

    更新日期:1995-08-10 00:00:00

  • Chromosomal localization of human genes required for G1 progression in mammalian cells.

    abstract::Specific probes derived from the human genes that complement the mutations of two independent temperature-sensitive (ts) mutants of the BHK-21 hamster cell line were used to determine the chromosomal locations of the loci in the human genome. The ts11 gene, which complements a mutation that blocks progression through ...


    pub_type: 杂志文章


    authors: Greco A,Ittmann M,Barletta C,Basilico C,Croce CM,Cannizzaro LA,Huebner K

    更新日期:1989-04-01 00:00:00

  • Fine-structure mapping of the murine IL-3 and GM-CSF genes by pulsed-field gel electrophoresis and molecular cloning.

    abstract::The hemopoietic growth factors interleukin-3 (IL-3, multi-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF) belong to a family of secreted glycoproteins that stimulate the proliferation and differentiation of hemopoietic progenitor cells. IL-3 and GM-CSF have overlapping biological activities and show...


    pub_type: 杂志文章


    authors: Lee JS,Young IG

    更新日期:1989-08-01 00:00:00

  • The generation of a library of PCR-analyzed microsatellite variants for genetic mapping of the mouse genome.

    abstract::Forty-three sequences containing simple sequence repeats or microsatellites were generated from an M13 library of total genomic mouse DNA. These sequences were analyzed for size variation using the polymerase chain reaction and gel electrophoresis without the need for radiolabeling. Seventy-two percent of the sequence...


    pub_type: 杂志文章


    authors: Cornall RJ,Aitman TJ,Hearne CM,Todd JA

    更新日期:1991-08-01 00:00:00

  • Positional cloning of the Ttc7 gene required for normal iron homeostasis and mutated in hea and fsn anemia mice.

    abstract::Genes playing essential roles in iron homeostasis have yet to be identified. We report the discovery of a strong candidate gene affecting iron homeostasis in two allelic anemia mouse mutants: hea (hereditary erythroblastic anemia) and fsn (flaky skin). To clone this novel gene positionally, we established a large back...


    pub_type: 杂志文章


    authors: White RA,McNulty SG,Nsumu NN,Boydston LA,Brewer BP,Shimizu K

    更新日期:2005-03-01 00:00:00

  • Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome.

    abstract::Mammalian sex chromosomes are the remnants of an ancient autosomal pair present in the ancestral mammalian karyotype. As a consequence of random decay and chromosome rearrangements over evolutionary time, Y chromosome gene repertoires differ between eutherian lineages. To investigate the gene repertoire and transcript...


    pub_type: 杂志文章


    authors: Pearks Wilkerson AJ,Raudsepp T,Graves T,Albracht D,Warren W,Chowdhary BP,Skow LC,Murphy WJ

    更新日期:2008-11-01 00:00:00

  • Mapping of human chromosome 5 microsatellite DNA polymorphisms.

    abstract::Thirteen moderately to highly informative microsatellite DNA polymorphisms based on (dC-dA)n.(dG-dT)n repeats were mapped to segments of human chromosome 5 using both linkage analysis and a panel of somatic cell hybrids which contained rearranged chromosomes. The markers were distributed throughout most of the length ...


    pub_type: 杂志文章


    authors: Weber JL,Polymeropoulos MH,May PE,Kwitek AE,Xiao H,McPherson JD,Wasmuth JJ

    更新日期:1991-11-01 00:00:00

  • A novel approach to detect differentially expressed genes from count-based digital databases by normalizing with housekeeping genes.

    abstract::Sequence tag count-based gene expression analysis is potent for the identification of candidate genes relevant to the cancerous phenotype. With the public availability of count-based data, the computational approaches for differentially expressed genes, which are mainly based on Binomial or beta-Binomial distribution,...


    pub_type: 杂志文章


    authors: Lü B,Yu J,Xu J,Chen J,Lai M

    更新日期:2009-09-01 00:00:00

  • Expression analysis of microRNAs and their target mRNAs of testes with high and low sperm motility in domestic pigeons (Columba livia).

    abstract::Sperm motility is one of the most important indicators to evaluate poultry fertility. In order to explore key molecular regulation roles related to sperm motility, we employed testicular RNA sequencing of pigeon. A total of 705 known and 385 novel microRNAs were identified. Compared with the low sperm motility group, ...


    pub_type: 杂志文章


    authors: Yin Z,Xu X,Tan Y,Cao H,Zhou W,Dong X,Mao H

    更新日期:2021-01-01 00:00:00

  • Functional analysis of bacterial artificial chromosomes in mammalian cells: mouse Cdc6 is associated with the mitotic spindle apparatus.

    abstract::Bacterial artificial chromosomes (BACs) provide a well-characterized resource for studying the functional organization of genes and other large chromosomal domains. To facilitate functional studies in cell cultures, we have developed a simple approach for generating stable cell lines with variable copy numbers of any ...


    pub_type: 杂志文章


    authors: Illenye S,Heintz NH

    更新日期:2004-01-01 00:00:00

  • Cytological characterization of the tandem repetitive sequences and their methylation status in the Antirrhinum majus genome.

    abstract::Tandem repetitive sequences are DNA motifs common in the genomes of eukaryotic species and are often embedded in heterochromatic regions. In most eukaryotes, ribosomal genes, as well as centromeres and telomeres or subtelomeres, are associated with abundant tandem arrays of repetitive sequences and typically represent...


    pub_type: 杂志文章


    authors: Zhang D,Yang Q,Ding Y,Cao X,Xue Y,Cheng Z

    更新日期:2008-08-01 00:00:00

  • Detection of three rare frameshift mutations in the cystic fibrosis gene in an African-American (CF444delA), an Italian (CF2522insC), and a Soviet (CF3821delT).

    abstract::We have identified three new frameshift mutations in the CFTR gene in patients with cystic fibrosis (CF). The first one involves the deletion of an adenine nucleotide in exon 4 in an African-American patient (CF444delA), the second involves the insertion of a cytosine nucleotide in exon 13 in an Italian patient (CF252...


    pub_type: 杂志文章


    authors: White MB,Krueger LJ,Holsclaw DS Jr,Gerrard BC,Stewart C,Quittell L,Dolganov G,Baranov V,Ivaschenko T,Kapronov NI

    更新日期:1991-05-01 00:00:00

  • An explanation for the phenotypic differences between patients bearing partial deletions of the DMD locus.

    abstract::Deletions giving rise to Duchenne muscular dystrophy (DMD) and the less severe Becker muscular dystrophy (BMD) occur in the same large gene on the short arm of the human X chromosome. We present a molecular mechanism to explain the clinical difference in severity between DMD and BMD patients who bear partial deletions...


    pub_type: 杂志文章


    authors: Monaco AP,Bertelson CJ,Liechti-Gallati S,Moser H,Kunkel LM

    更新日期:1988-01-01 00:00:00

  • Genomic organization, alternative splicing, and expression patterns of the DSCR1 (Down syndrome candidate region 1) gene.

    abstract::Down syndrome is a major cause of mental retardation and congenital heart defects and is due to the presence of three copies of human chromosome 21 in the affected individual. We have identified a gene, DSCR1 (HGMW-approved symbol), from the region 21q22.1-q22.2, which is highly expressed in human fetal brain and adul...


    pub_type: 杂志文章


    authors: Fuentes JJ,Pritchard MA,Estivill X

    更新日期:1997-09-15 00:00:00

  • Construction, database integration, and application of an Oenothera EST library.

    abstract::Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmenta...


    pub_type: 杂志文章


    authors: Mrácek J,Greiner S,Cho WK,Rauwolf U,Braun M,Umate P,Altstätter J,Stoppel R,Mlcochová L,Silber MV,Volz SM,White S,Selmeier R,Rudd S,Herrmann RG,Meurer J

    更新日期:2006-09-01 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

  • Comparative sequence analysis of the Gdf6 locus reveals a duplicon-mediated chromosomal rearrangement in rodents and rapidly diverging coding and regulatory sequences.

    abstract::Duplicated segments of genomic DNA can catalyze both gene evolution and chromosome evolution. Here we describe a rodent-specific duplication involving the Uqcrb gene, a cis-regulatory element for the Gdf6 gene, and a chromosomal rearrangement. Comparisons of Gdf6 sequences from several placental mammals and platypus r...


    pub_type: 杂志文章


    authors: Mortlock DP,Portnoy ME,Chandler RL,NISC Comparative Sequencing Program.,Green ED

    更新日期:2004-11-01 00:00:00

  • The proximity of DNA sequences in interphase cell nuclei is correlated to genomic distance and permits ordering of cosmids spanning 250 kilobase pairs.

    abstract::The physical distance between DNA sequences in interphase nuclei was determined using eight cosmids containing fragments of the Chinese hamster genome that span 273 kb surrounding the dihydrofolate reductase (DHFR) gene. The distance between these sequences at the molecular level has been determined previously by rest...


    pub_type: 杂志文章


    authors: Trask B,Pinkel D,van den Engh G

    更新日期:1989-11-01 00:00:00

  • The study of variation in the human genome.

    abstract::Regions of the genome showing high evolutionary stability are often conserved as a result of functional constraints. Conversely, more variable regions are likely to represent DNA with no functional or structural importance. However, as in the case of immunologically important regions, sequence divergence does not alwa...


    pub_type: 杂志文章


    authors: Bowcock A,Cavalli-Sforza L

    更新日期:1991-10-01 00:00:00

  • Localization of three novel hybrid breakpoints and refinement of 18 marker assignments in the human 3cen-p21.1 region.

    abstract::Using the human/hamster cell line UCTP2A-3, we have generated and isolated three hybrids, each containing a novel human chromosome 3p break. All chromosome 3 materials distal to the breaks were lost. Two of the breakpoints were produced using aphidicolin induction; the third breakpoint occurred spontaneously. The aphi...


    pub_type: 杂志文章


    authors: Wang ND,Testa JR,Smith DI

    更新日期:1992-12-01 00:00:00

  • RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds.

    abstract::The rice genome annotation has been greatly improved in recent years, largely due to the availability of full length cDNA sequences derived from many tissues. Among those yet to be studied is the aleurone layer, which produces hydrolases for mobilization of seed storage reserves during seed germination and post germin...


    pub_type: 杂志文章


    authors: Watanabe KA,Ringler P,Gu L,Shen QJ

    更新日期:2014-01-01 00:00:00

  • XY sex reversal associated with a nonsense mutation in SRY.

    abstract::Sex determination in humans is mediated through the expression of a testis-determining gene on the Y chromosome. In humans, a candidate gene for the testis-determining factor (TDF) that encodes a protein with a putative DNA-binding motif and has been isolated is termed SRY. Here we describe an XY sex-reversed female w...


    pub_type: 杂志文章


    authors: McElreavey KD,Vilain E,Boucekkine C,Vidaud M,Jaubert F,Richaud F,Fellous M

    更新日期:1992-07-01 00:00:00