Isolation and characterization of novel Ty1-copia-like retrotransposons from lily.

Abstract:

:Species of the genus Lilium are well known for their large genomes. Although expansion of noncoding repeated DNA is believed to account for this genome size, retroelement del Ty3-gypsy is the only one described so far in the genus Lilium. We isolated Ty1-copia elements from Lilium longiflorum and named them LIREs (lily retrotransposons). The long terminal repeats, primer binding site, and polypurine tract sequences are highly similar among the LIRE elements, indicating that they are in the same lineage. Although the protein-coding regions were highly decayed, the sequence motifs of the integrase, reverse transcriptase, and RNase H domains were identifiable as belonging to the order of Ty1-copia elements. Phylogenetic analysis and primer binding site sequences revealed that these elements belonged to the Ale lineage among the six lineages of plant Ty1-copia elements. Base substitutions in the long terminal repeats estimated that the integration times of the LIRE Ty1-copia elements were between 0.7 and 5.5 mya. In situ hybridization showed that the LIRE elements were present in all the chromosomes of L. longiflorum and L. lancifolium, but absent in centromeres, telomeres, and 45S rRNA sites in both species. The LIRE elements were present very abundantly in species of the genus Lilium, but absent in other genera of the family Liliaceae, implying that the LIRE elements might have contributed to the expansion of the genome in the genus Lilium.

journal_name

Genome

journal_title

Genome

authors

Lee SI,Park KC,Son JH,Hwang YJ,Lim KB,Song YS,Kim JH,Kim NS

doi

10.1139/gen-2013-0088

subject

Has Abstract

pub_date

2013-09-01 00:00:00

pages

495-503

issue

9

eissn

0831-2796

issn

1480-3321

journal_volume

56

pub_type

杂志文章

相关文献

GENOME文献大全
  • Phenetic relationships among different races of Striga gesnerioides (Willd.) Vatke from West Africa.

    abstract::Striga gesnerioides is a root hemiparasite that primarily parasitizes dicotyledonous species, including cowpea (Vigna unguiculata L.) and other legumes. Based on the differential resistance response of various cultivars, landraces, and breeding lines, it has been proposed that several distinct races of cowpea-parasiti...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g06-086

    authors: Botanga CJ,Timko MP

    更新日期:2006-11-01 00:00:00

  • An improved genetic linkage map for cowpea (Vigna unguiculata L.) combining AFLP, RFLP, RAPD, biochemical markers, and biological resistance traits.

    abstract::An improved genetic linkage map has been constructed for cowpea (Vigna unguiculata L. Walp.) based on the segregation of various molecular markers and biological resistance traits in a population of 94 recombinant inbred lines (RILs) derived from the cross between 'IT84S-2049' and '524B'. A set of 242 molecular marker...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g01-102

    authors: Ouédraogo JT,Gowda BS,Jean M,Close TJ,Ehlers JD,Hall AE,Gillaspie AG,Roberts PA,Ismail AM,Bruening G,Gepts P,Timko MP,Belzile FJ

    更新日期:2002-02-01 00:00:00

  • Authentication of Ginkgo biloba herbal dietary supplements using DNA barcoding.

    abstract::Ginkgo biloba L. (known as ginkgo or maidenhair tree) is a phylogenetically isolated, charismatic, gymnosperm tree. Herbal dietary supplements, prepared from G. biloba leaves, are consumed to boost cognitive capacity via improved blood perfusion and mitochondrial function. A novel DNA mini-barcode assay was designed a...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2014-0130

    authors: Little DP

    更新日期:2014-09-01 00:00:00

  • The first mitochondrial genome for the wasp superfamily Platygastroidea: the egg parasitoid Trissolcus basalis.

    abstract::The nearly complete mitochondrial (mt) genome of an egg parasitoid, Trissolcus basalis (Wollaston), was sequenced using both 454 and Illumina next-generation sequencing technologies. A portion of the noncoding region remained unsequenced, possibly owing to the presence of repeats. The sequenced portion of the genome i...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g2012-005

    authors: Mao M,Valerio A,Austin AD,Dowton M,Johnson NF

    更新日期:2012-03-01 00:00:00

  • Development of a selection index to improve market value of cultured Atlantic salmon (Salmo salar).

    abstract::Genetic parameters were estimated on growth and development traits using analyses of variance and covariance of 42 full-sib families from a select line, 39 full-sib families from a control line of the same strain, and 37 full-sib families from another unselected strain. The traits included percent 1+ smolts, percent s...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g92-046

    authors: O'Flynn FM,Friars GW,Bailey JK,Terhune JM

    更新日期:1992-04-01 00:00:00

  • Identification of ISSR markers associated with productivity traits in silkworm, Bombyx moni L.

    abstract::Bombyx mori L., commonly recognised around the world as the mulberry silkworm, is characterized by a wide variability in yield and developmental traits, which have been proven through conventional genetic analysis to be of polygenic nature. A large number of morpho-biochemical traits and RFLP and RAPD markers are mapp...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g03-024

    authors: Chatterjee SN,Mohandas TP

    更新日期:2003-06-01 00:00:00

  • Genetic analysis and mapping of a thermosensitive genic male sterility gene, tms6(t), in rice (Oryza sativa L.).

    abstract::Thermosensitive genic male-sterile (TGMS) rice is widely used in hybrid rice production. Because of its specific temperature requirement, it can be used only in a narrow rice-growing zone in Asia. A newly discovered TGMS line, G20S, has an opposite phenotype compared with normal TGMS lines. G20S is completely sterile ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g09-092

    authors: Liu X,Li X,Zhang X,Wang S

    更新日期:2010-02-01 00:00:00

  • Development of genetic research in the USSR.

    abstract::Two periods of the development of genetic research in the USSR with reference to its current trends of plant and animal genetics, cytogenetics, and molecular genetics are reviewed. A short list of priority areas is established: the maintenance and use of unique gene pools of plants and animals; the domestication of an...

    journal_title:Genome

    pub_type: 历史文章,杂志文章

    doi:10.1139/g89-160

    authors: Shumny VK

    更新日期:1989-01-01 00:00:00

  • Genetic relationship among cultivated and wild grapevine accessions from Tunisia.

    abstract::We have used nuclear and chloroplast molecular markers to genotype cultivated and wild accessions of Vitis vinifera L. from Tunisia and assess their genetic relationships. Fifty-five distinct genotypes were identified among 80 cultivated accessions, including 18 genotypic groups containing between 2 and 5 accessions p...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g04-072

    authors: Snoussi H,Slimane MH,Ruiz-García L,Martínez-Zapater JM,Arroyo-García R

    更新日期:2004-12-01 00:00:00

  • Variation among the dispersed (GATA)n sequences in Drosophila melanogaster.

    abstract::Five nonallelic copies of the dispersed (GATA)n repeated sequence of Drosophila melanogaster (referred to as GATA elements) have been sequenced and analysed. The GATA elements range in size from 111 to 444 bp, consisting predominantly of tandemly repeated GATAs, interspersed with variants of the subunit. The types and...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g90-113

    authors: Simpson PR

    更新日期:1990-10-01 00:00:00

  • Changes of cytosine methylation induced by wide hybridization and allopolyploidy in Cucumis.

    abstract::We previously demonstrated that allopolyploidization could induce phenotypic variations and genome changes in a newly synthesized allotetraploid in Cucumis. To explore the molecular involvement of epigenetic phenomena, we investigated cytosine methylation in Cucumis by using methylation-sensitive amplified polymorphis...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G08-063

    authors: Chen L,Chen J

    更新日期:2008-10-01 00:00:00

  • Phylogenetic analysis of Carthamus species based on the nucleotide sequence of the nuclear SACPD gene and chloroplast trnL-trnF IGS region.

    abstract::To clarify the phylogenetic relationships of Carthamus species, we performed sequence analysis of the nuclear stearoyl acyl carrier protein desaturase (SACPD) gene and the chloroplast intergenic spacer region between leucine and phenylalanine tRNA genes (trnL-trnF IGS) in 13 taxa of Carthamus. The previous division of...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G08-059

    authors: Sasanuma T,Sehgal D,Sasakuma T,Raina SN

    更新日期:2008-09-01 00:00:00

  • Chromosome segregation from cell hybrids. III. Segregation is independent of spindle constitution.

    abstract::Hamster beta-tubulin (detected as a mutant subunit that confers Colcemid resistance) is either not expressed or is underexpressed in Chinese hamster-mouse somatic cell hybrids. This selectivity of tubulin expression suggests that a uniparental mouse spindle might preferentially engage mouse chromosomes and lead to los...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g87-090

    authors: Zelesco PA,Graves JA

    更新日期:1987-08-01 00:00:00

  • A comparative study of the structure of the rDNA intergenic spacer of Lens culinaris Medik., and other legume species.

    abstract::As part of a project on lentil molecular genetics, the sequence of the 18S-25S ribosomal RNA gene intergenic spacer (IGS) of Lens culinaris Medik. was determined. DNA was cloned after polymerase chain reaction (PCR) amplification. The spacer of 2939 bp was composed of nonrepetitive sequences and four tandem arrays of ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g00-022

    authors: Fernández M,Polanco C,Ruiz ML,Pérez de la Vega M

    更新日期:2000-08-01 00:00:00

  • Molecular differentiation of two sibling species of the black fly Simulium vittatum (Diptera: Simuliidae) based on random amplified polymorphic DNA.

    abstract::Larvae of the black fly morphospecies Simulium vittatum from Colorado, Montana, Nebraska, and New Hampshire were cytologically identified as either the IS-7 or the IIIL-1 cytospecies. DNA was PCR amplified from cytotyped larvae using eight 10-mer primers, labeled with 33P, and run on polyacrylamide gels. The entire da...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g03-144

    authors: Duncan GA,Adler PH,Pruess KP,Powers TO

    更新日期:2004-04-01 00:00:00

  • The Bo1-specific PCR marker AWW5L7 is predictive of boron tolerance status in a range of exotic durum and bread wheats.

    abstract::High soil boron (B) constitutes a major soil problem in many parts of the world, particularly in low-rainfall areas and land under irrigation. Low accumulation of B in the shoot or grain of cereal crops is correlated with the maintenance of biomass production and grain yield under high B conditions, suggesting that th...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G08-084

    authors: Schnurbusch T,Langridge P,Sutton T

    更新日期:2008-12-01 00:00:00

  • Endonuclease banding reveals that atrazine-induced aneuploidy resembles spontaneous chromosome loss in Crassostrea gigas.

    abstract::Aneuploidy has previously been observed in the Pacific oyster, Crassostrea gigas, and shown to be negatively correlated with growth. Moreover, a significant impact of atrazine exposure has been described in C. gigas, and persistence of that effect has been observed between generations. Evidence of differential chromos...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g04-087

    authors: Bouilly K,Leitão A,Chaves R,Guedes-Pinto H,Boudry P,Lapègue S

    更新日期:2005-02-01 00:00:00

  • Microsatellites in the silkworm, Bombyx mori: abundance, polymorphism, and strain characterization.

    abstract::We have isolated and characterized microsatellites (simple sequence repeat (SSR) loci) from the silkworm genome. The screening of a partial genomic library by the conventional hybridization method led to the isolation of 28 microsatellites harbouring clones. The abundance of (CA)n repeats in the silkworm genome was ak...

    journal_title:Genome

    pub_type: 杂志文章

    doi:

    authors: Reddy KD,Abraham EG,Nagaraju J

    更新日期:1999-12-01 00:00:00

  • User Centric Genomics Infrastructure: trends and technologies.

    abstract::Genomics is both data and compute intensive discipline. The success of genomics depends on adequate informatics infrastructure that can address growing data demands and enable a diverse range of resource-intensive computational activities. Designing a suitable Infrastructure is a challenging task, and its success larg...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2020-0096

    authors: Krishna R,Elisseev V

    更新日期:2020-11-20 00:00:00

  • Relationship between bruchid resistance and seed mass in mungbean based on QTL analysis.

    abstract::Bruchids (Coleoptera: Bruchidae) can cause serious damage to mungbean and several other leguminous crops and there is a strong association between small seed size and bruchid resistance. In investigating the feasibility of breeding large-seeded cultivars with high levels of bruchid resistance, we studied the relations...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G09-031

    authors: Mei L,Cheng XZ,Wang SH,Wang LX,Liu CY,Sun L,Xu N,Humphry ME,Lambrides CJ,Li HB,Liu CJ

    更新日期:2009-07-01 00:00:00

  • SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus.

    abstract::Oilseed rape (Brassica napus) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G10-079

    authors: Durstewitz G,Polley A,Plieske J,Luerssen H,Graner EM,Wieseke R,Ganal MW

    更新日期:2010-11-01 00:00:00

  • Darwin's legacy: why biology is not physics, or why evolution has not become a common sense.

    abstract::Cosmology and evolution together have enabled us to look deep into the past and comprehend evolution-from the big bang to the cosmos, from molecules to humans. Here, I compare the nature of theories in biology and physics and ask why physical theories get accepted by the public without necessarily comprehending them b...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g11-046

    authors: Singh RS

    更新日期:2011-10-01 00:00:00

  • Fast-GBS v2.0: an analysis toolkit for genotyping-by-sequencing data.

    abstract::Genotyping-by-sequencing (GBS) is a rapid, flexible, low-cost, and robust genotyping method that simultaneously discovers variants and calls genotypes within a broad range of samples. These characteristics make GBS an excellent tool for many applications and research questions from conservation biology to functional g...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2020-0077

    authors: Torkamaneh D,Laroche J,Belzile F

    更新日期:2020-11-01 00:00:00

  • Clonal variation in the parthenogenetic rock lizard Lacerta armeniaca.

    abstract::Genetic diversity at 35 allozyme loci was surveyed in seven populations of Lacerta armeniaca. Fixed heterozygotes were present at 16 loci, with homozygotes at 17 loci. Variation occurred at two loci, one in each of two populations, indicating one widespread clone, one restricted clone, and one apparently restricted cl...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g95-141

    authors: Macculloch RD,Murphy RW,Kupriyanova LA,Darevsky IS,Danielyan FD

    更新日期:1995-12-01 00:00:00

  • Cryptic biodiversity and phylogenetic relationships revealed by DNA barcoding of Oriental black flies in the subgenus Gomphostilbia (Diptera: Simuliidae).

    abstract::Understanding the medical, economic, and ecological importance of black flies relies on correct identification of species. However, traditional taxonomy of black flies is impeded by a high degree of morphological uniformity, especially the presence of cryptic biodiversity, historically recognized by details of chromos...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G10-100

    authors: Pramual P,Wongpakam K,Adler PH

    更新日期:2011-01-01 00:00:00

  • An AFLP marker tightly linked to apomixis reveals hemizygosity in a portion of the apomixis-controlling locus in Paspalum simplex.

    abstract::A mapping population of Paspalum simplex segregating for apomixis (asexual reproduction through seeds) was screened with AFLPs to find apomixis-linked markers. Four AFLPs linked to apomixis in coupling phase were found. Three of them did not show recombinants among the 87 individuals of the mapping population, whereas...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g02-014

    authors: Labombarda P,Busti A,Caceres ME,Pupilli F,Arcioni S

    更新日期:2002-06-01 00:00:00

  • A study of homologous chromosomes using a morphometric approach.

    abstract::A previous study of 100 karyotyped metaphase cells has demonstrated the utility of a graphic arts tool in deriving chromosome measurements for relative length determination. In the present study we utilize this same approach to address the question: "What are the average differences in relative lengths between apparen...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g93-132

    authors: Mark HF,Wyandt HE,Pan T,Mark R Jr,Paramenter M,Campbell W,Mark Y

    更新日期:1993-10-01 00:00:00

  • Genomic diversity and multiple origins of tetraploid (2n = 78, 80) Glycine tomentella.

    abstract::Among 15 wild perennial species of the genus Glycine Willd. subgenus Glycine, G. tomentella is exceptional. It is composed of four cytotypes (2n = 38, 40, 78, 80), is diverse in morphological features, and covers a wide geographical area. The objectives of this study were to uncover the genomic diversity in 78- and 80...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g94-063

    authors: Kollipara KP,Singh RJ,Hymowitz T

    更新日期:1994-06-01 00:00:00

  • Post-glacial recolonization of insular Newfoundland across the Strait of Belle Isle gave rise to an endemic subspecies of woodland caribou, Rangifer tarandus terranovae (Bangs, 1896): evidence from mtDNA haplotypes.

    abstract::Post-glacial origins of woodland caribou (Rangifer tarandus subsp.) on the island of Newfoundland and their relationship to mainland populations have been uncertain. Sequence analysis of 2223 bp of the mitochondrial DNA control region and cytochrome b gene from 233 Newfoundland caribou identified 32 haplotypes in four...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2017-0199

    authors: Wilkerson CD,Mahoney SP,Carr SM

    更新日期:2018-08-01 00:00:00

  • A major suppressor of cell death, slm1, modifies the expression of the maize (Zea mays L.) lesion mimic mutation les23.

    abstract::Disease lesion mimics provide an excellent biological system to study the genetic basis of cell death in plants. Many lesion mimics show variation in phenotype expression in different genetic backgrounds. Our goal was to identify quantitative trait loci (QTL) modifying lesion mimic expression thereby identifying genet...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g04-046

    authors: Penning BW,Johal GS,McMullen MD

    更新日期:2004-10-01 00:00:00