Cloning and characterization of repetitive sequences and development of SCAR markers specific for the P genome of Agropyron cristatum

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

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Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

International Journal of Molecular Sciences ◽

10.3390/ijms22094707 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4707

Author(s):

Mariana Lopes ◽

Sandra Louzada ◽

Margarida Gama-Carvalho ◽

Raquel Chaves

Keyword(s):

Human Genome ◽

Satellite Dna ◽

Repetitive Sequences ◽

Nucleotide Composition ◽

Genomic Component ◽

Genomic Studies ◽

Human Genomic ◽

Definition Of ◽

High Degree

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.

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Development and Characterization of Wheat-Agropyron cristatum Introgression Lines Induced by Gametocidal Genes and Wheat ph1b Mutant

Agronomy ◽

10.3390/agronomy11020277 ◽

2021 ◽

Vol 11 (2) ◽

pp. 277

Author(s):

Alejandro Copete-Parada ◽

Carmen Palomino ◽

Adoración Cabrera

Keyword(s):

Genetic Resources ◽

Agropyron Cristatum ◽

Homologous Gene ◽

Aegilops Cylindrica ◽

Induction Frequency ◽

Structural Aberrations ◽

Translocation Lines ◽

New Germplasm

The P genome of Agropyron cristatum Gaertn. contains many desirable genes that can be utilized as genetic resources to improve wheat. In this research, we used both the gametocidal chromosome 2Cc and the pairing homologous gene (Ph1b) mutant to induce structural aberrations and translocations between wheat and the 4P, 5P, and 6P genome chromosomes. By using the two approaches, a total of 19 wheat-A. cristatum translocations have been identified, in which 13 were induced by the Triticum aestivum cv. Chinese Spring (CS) ph1b mutant (CS ph1b) and six were induced by gametocidal chromosome 2Cc from Aegilops cylindrica Host. The wheat-4P, -5P and -6P A. cristatum translocations were characterized by in situ hybridization and by a set of conserved orthologous set (COS) molecular markers. The aberrations included centromeric translocations, terminal translocations, dicentric translocations, and deletions. The average induction frequency of chromosome structural aberrations was 10.9% using gametocidal 2Cc chromosome and 8.8% using ph1b mutant. The highest frequency obtained was for chromosome 4P using both approaches. All the wheat-A. cristatum translocation lines obtained were valuable for identifying A. cristatum chromosome 4P, 5P, and 6P related genes. In addition, these lines provided genetic resources and new germplasm accessions for the genetic improvement of wheat.

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Chromosome Mapping of Repetitive Sequences inRachycentron canadum(Perciformes: Rachycentridae): Implications for Karyotypic Evolution and Perspectives for Biotechnological Uses

Journal of Biomedicine and Biotechnology ◽

10.1155/2011/218231 ◽

2011 ◽

Vol 2011 ◽

pp. 1-8 ◽

Cited By ~ 10

Author(s):

Uedson Pereira Jacobina ◽

Marcelo de Bello Cioffi ◽

Luiz Gustavo Rodrigues Souza ◽

Leonardo Luiz Calado ◽

Manoel Tavares ◽

...

Keyword(s):

Repetitive Sequences ◽

Chromosome Mapping ◽

Karyotypic Evolution ◽

Dapi Staining ◽

Telomeric Sequences ◽

Replication Banding ◽

The Family ◽

Early Replication

The cobia,Rachycentron canadum, a species of marine fish, has been increasingly used in aquaculture worldwide. It is the only member of the family Rachycentridae (Perciformes) showing wide geographic distribution and phylogenetic patterns still not fully understood. In this study, the species was cytogenetically analyzed by different methodologies, including Ag-NOR and chromomycin A3(CMA3)/DAPI staining, C-banding, early replication banding (RGB), andin situfluorescent hybridization with probes for 18S and 5S ribosomal genes and for telomeric sequences (TTAGGG)n. The results obtained allow a detailed chromosomal characterization of the Atlantic population. The chromosome diversification found in the karyotype of the cobia is apparently related to pericentric inversions, the main mechanism associated to the karyotypic evolution of Perciformes. The differential heterochromatin replication patterns found were in part associated to functional genes. Despite maintaining conservative chromosomal characteristics in relation to the basal pattern established for Perciformes, some chromosome pairs in the analyzed population exhibit markers that may be important for cytotaxonomic, population, and biodiversity studies as well as for monitoring the species in question.

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Families of repeated DNA in the oomycete Phytophthora infestans and their distribution within the genus

Genome ◽

10.1139/g98-060 ◽

1998 ◽

Vol 41 (4) ◽

pp. 605-615 ◽

Cited By ~ 20

Author(s):

Howard S Judelson ◽

Thomas A Randall

Keyword(s):

Reverse Transcriptase ◽

Phytophthora Infestans ◽

Repetitive Sequences ◽

Nuclear Genome ◽

Repeated Sequences ◽

Close Relative ◽

Repeat Elements ◽

Copy Numbers ◽

Taxonomic Groups

The abundance, genomic organization, species distribution, and structure of 33 distinct families of repetitive DNA in Phytophthora are described. The families were identified by screening a library of Phytophthora infestans DNA for repetitive sequences. These were subsequently characterized within 26 species distributed within each of the six taxonomic groups traditionally defined within the genus. Some repeat elements were specific to P. infestans and its close relative, Phytophthora mirabilis, while other repeated sequences were present in most species. The distribution of the DNA families did not conform to the traditional taxonomic groups used for the genus. Characterization of the repeated sequences in P. infestans indicated that they included both dispersed and tandemly repeated elements, with copy numbers ranging from 70 to 8400 per haploid genome. In total, these repeats were estimated to represent 51% of the nuclear genome of P. infestans. Reverse transcriptase motifs were detected in seven of the repeat families that were widely distributed throughout the genus.Key words: chromosome structure, genome evolution, speciation, reverse transcriptase, transposable element.

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Evolutionary characterization of a Y chromosomal sequence conserved in the genus Mus

Genetics Research ◽

10.1017/s001667230002752x ◽

1988 ◽

Vol 52 (2) ◽

pp. 145-150 ◽

Cited By ~ 5

Author(s):

Yutaka Nishioka

Keyword(s):

Related Species ◽

Rattus Norvegicus ◽

Phylogenetic Relationships ◽

Repetitive Sequence ◽

Repetitive Sequences ◽

Closely Related Species ◽

Specific Hybridization ◽

Male Specific ◽

Chromosomal Sequence

SummaryThe extent of accumulation of mouse Y chromosomal repetitive sequences generally correlates with the known phylogenetic relationships in the genus Mus. However, we describe here a M. musculus Y chromosomal repetitive sequence, designated as ACClfl, whose accumulation patterns among eight Mus species do not correspond to their phylogenetic relationships. Although male-specific hybridization bands were present in all the species examined, significant accumulation (> 200 copies) in the Y chromosomes was found in M. minutoides (subgenus Nannomys), M. pahari (subgenus Coelomys) and M. saxicola (subgenus Pyromys) as well as in the three closely related species M. hortulanus, M. musculus and M. spretus that belong to the subgenus Mus. Unexpectedly, the Y chromosomes of M. caroli and M. cookii (both subgenus Mus) had considerably reduced amounts of ACClfl-related sequences. Furthermore, in rats (Rattus norvegicus) the major accumulation sites appear to be autosomal. These observations suggest that caution must be taken in the interpretation of data obtained with repetitive sequences that have evolved quickly.

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Characterization of the genome of the mealybug Planococcus lilacinus, a model organism for studying whole-chromosome imprinting and inactivation

Genetics Research ◽

10.1017/s0016672302005566 ◽

2002 ◽

Vol 79 (2) ◽

pp. 111-118 ◽

Cited By ~ 6

Author(s):

K. NAGA MOHAN ◽

PARAMITA RAY ◽

H. SHARAT CHANDRA

Keyword(s):

Drosophila Melanogaster ◽

Repetitive Sequences ◽

Gc Content ◽

Model Organism ◽

Fruit Fly ◽

Single Copy ◽

Coding Sequences ◽

Repeat Sequences ◽

Chromosome Imprinting

The co-occurrence of three chromosome-wide phenomena – imprinting, facultative heterochromatization and diffuse centromere – in the mealybug Planococcus lilacinus makes investigation of the genomics of this species an attractive prospect. In order to estimate the complexity of the genome of this species, 300 random stretches of its DNA, constituting ∼0·1% of the genome, were sequenced. Coding sequences appear to constitute ∼53·5%, repeat sequences ∼44·5% and non-coding single-copy sequences ∼2% of the genome. The proportion of repetitive sequences in the mealybug is higher than that in the fruit fly Drosophila melanogaster (∼30%). The mealybug genome (∼220 Mb) is about 1·3 times the size of the fly genome (∼165 Mb) and its GC content (∼35%) less than that of the fly genome (∼40%). The relative abundance of various dinucleotides, as analysed by the method of Gentles and Karlin, shows that the dinucleotide signatures of the two species are moderately similar and that in the mealybug there is neither over-representation nor under-representation of any dinucleotide.

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