Cloning and characterization of dispersed repetitive DNA derived from microdissected sex chromosomes of Rumex acetosa

Genome ◽  
2006 ◽  
Vol 49 (2) ◽  
pp. 114-121 ◽  
Author(s):  
Beatrice Mariotti ◽  
Rafael Navajas-Pérez ◽  
Rafael Lozano ◽  
John S Parker ◽  
Roberto de la Herrán ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Sex Chromosome ◽  
Rumex Acetosa ◽  
Dioecious Species ◽  
Rumex Crispus ◽  
Origin And Evolution ◽  
Y Chromosomes ◽  
Plant Sex Chromosomes

Rumex acetosa is characterized by a multiple chromosome system (2n = 12 + XX for females, and 2n = 12 + XY1Y2 for males), in which sex is determined by the ratio between the number of X chromosomes and autosome sets. For a better understanding of the molecular structure and evolution of plant sex chromosomes, we have generated a sex chromosome specific library of R. acetosa by microdissection. The screening of this library has allowed us to identify 5 repetitive DNA families that have been characterized in detail. One of these families, DOP-20, has shown no homology with other sequences in databases. Nevertheless, the putative proteins encoded by the other 4 families, DOP-8, DOP-47, DOP-60, and DOP-61, show homology with proteins from different plant retroelements, including poly proteins from Ty3-gypsy- and Ty1-copia-like long terminal repeat (LTR) retroelements, and reverse transcriptase from non-LTR retro elements. Results indicate that sequences from these 5 families are dispersed throughout the genome of both males and females, but no appreciable accumulation or differentiation of these types of sequences have been found in the Y chromosomes. These repetitive DNA sequences are more conserved in the genome of other dioecious species such as Rumex papillaris, Rumex intermedius, Rumex thyrsoides, Rumex hastatulus, and Rumex suffruticosus, than in the polygamous, gynodioecious, or hermaphrodite species Rumex induratus, Rumex lunaria, Rumex con glom er atus, Rumex crispus, and Rumex bucephalo phorus, which supports a single origin of dioecious species in this genus. The implication of these transposable elements in the origin and evolution of the heteromorphic sex chromosomes of R. acetosa is discussed.Key words: Rumex acetosa, sex chromosomes, microdissection, evolution, retroelements.

Laser isolation of plant sex chromosomes: studies on the DNA composition of the X and Y sex chromosomes of Silene latifolia

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 705-715 ◽  
Author(s):  
Charles P. Scutt ◽  
Yasuko Kamisugi ◽  
Philip M. Gilmartin ◽  
Fukumi Sakai
Keyword(s):  
In Situ Hybridization ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Sex Chromosome ◽  
Silene Latifolia ◽  
Dioecious Species ◽  
Mitotic Metaphase Chromosome ◽  
Degenerate Oligonucleotide ◽  
Plant Sex Chromosomes

X and Y sex chromosomes from the dioecious plant Silene latifolia (white campion) were isolated from mitotic metaphase chromosome preparations on polyester membranes. Autosomes were ablated using an argon ion laser microbeam and isolated sex chromosomes were then recovered on excised fragments of polyester membrane. Sex chromosome associated DNA sequences were amplified using the degenerate oligonucleotide primed polymerase chain reaction (DOP–PCR) and pools of DOP–PCR products were used to investigate the genomic organization of the S. latifolia sex chromosomes. The chromosomal locations of cloned sex chromosome repeat sequences were analysed by fluorescence in situ hybridization and data complementary to laser ablation studies were obtained by genomic in situ hybridization. In combination, these studies demonstrate that the X and Y sex chromosomes of S. latifolia are of very similar DNA composition and also that they share a significant repetitive DNA content with the autosomes. The evolution of sex chromosomes in Silene is discussed and compared with that in another dioecious species, Rumex acetosa.Key words: FISH, GISH, laser-microdissection, sex chromosome, Silene latifolia.

scholarly journals Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa

2020 ◽  
Vol 127 (1) ◽  
pp. 33-47
Author(s):  
Wojciech Jesionek ◽  
Markéta Bodláková ◽  
Zdeněk Kubát ◽  
Radim Čegan ◽  
Boris Vyskot ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Tandem Repeats ◽  
Sex Chromosome ◽  
Rumex Acetosa ◽  
Dioecious Species ◽  
Y Chromosomes

Abstract Background and Aims Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes. Methods We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons. Key Results We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes. Conclusions The X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage.

scholarly journals Chromosomal Spreading of Microsatellites and (TTAGGG)n Sequences in the Characidium zebra and C. gomesi Genomes (Characiformes: Crenuchidae)

2016 ◽  
Vol 149 (3) ◽  
pp. 182-190 ◽  
Author(s):  
Marcela B. Pucci ◽  
Patricia Barbosa ◽  
Viviane Nogaroto ◽  
Mara C. Almeida ◽  
Roberto F. Artoni ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Additional Data ◽  
Sex Chromosome ◽  
Binding Motif ◽  
W Chromosome ◽  
Repeat Sequences ◽  
Heteromorphic Sex Chromosomes

Sex chromosome evolution involves the accumulation of repeat sequences such as multigenic families, noncoding repetitive DNA (satellite, minisatellite, and microsatellite), and mobile elements such as transposons and retrotransposons. Most species of Characidium exhibit heteromorphic ZZ/ZW sex chromosomes; the W is characterized by an intense accumulation of repetitive DNA including dispersed satellite DNA sequences and transposable elements. The aim of this study was to analyze the distribution pattern of 18 different tandem repeats, including (GATA)n and (TTAGGG)n, in the genomes of C. zebra and C. gomesi, especially in the C. gomesi W chromosome. In the C. gomesi W chromosome, weak signals were seen for (CAA)10, (CAC)10, (CAT)10, (CGG)10, (GAC)10, and (CA)15 probes. (GA)15 and (TA)15 hybridized to the autosomes but not to the W chromosome. The (GATA)n probe hybridized to the short arms of the W chromosome as well as the (CG)15 probe. The (GATA)n repeat is known to be a protein-binding motif. GATA-binding proteins are necessary for the decondensation of heterochromatic regions that hold coding genes, especially in some heteromorphic sex chromosomes that may keep genes related to oocyte development. The (TAA)10 repeat is accumulated in the entire W chromosome, and this microsatellite accumulation is probably involved in the sex chromosome differentiation process and crossover suppression in C. gomesi. These additional data on the W chromosome DNA composition help to explain the evolution of sex chromosomes in Characidium.

LTR retrotransposons in the dioecious plant Silene latifolia

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 745-751 ◽  
Author(s):  
Sachihiro Matsunaga ◽  
Fumi Yagisawa ◽  
Maki Yamamoto ◽  
Wakana Uchida ◽  
Shunsuke Nakao ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Evolutionary Dynamics ◽  
Sex Chromosome ◽  
Silene Latifolia ◽  
Ltr Retrotransposons ◽  
Dioecious Plant ◽  
Dioecious Species ◽  
Y Chromosomes ◽  
Genus Silene ◽  
Silene Species

Conserved domains of two types of LTR retrotransposons, Ty1–copia- and Ty3–gypsy-like retrotransposons, were isolated from the dioecious plant Silene latifolia, whose sex is determined by X and Y chromosomes. Southern hybridization analyses using these retrotransposons as probes resulted in identical patterns from male and female genomes. Fluorescence in situ hybridization indicated that these retrotransposons do not accumulate specifically in the sex chromosomes. These results suggest that recombination between the sex chromosomes of S. latifolia has not been severely reduced. Conserved reverse transcriptase regions of Ty1–copia-like retrotransposons were isolated from 13 different Silene species and classified into two major families. Their categorization suggests that parallel divergence of the Ty1–copia-like retrotransposons occurred during the differentiation of Silene species. Most functional retrotransposons from three dioecious species, S. latifolia, S. dioica, and S. diclinis, fell into two clusters. The evolutionary dynamics of retrotransposons implies that, in the genus Silene, dioecious species evolved recently from gynodioecious species.Key words: retrotransposon, dioecious plant, sex chromosome.

Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing

2020 ◽  
Vol 160 (3) ◽  
pp. 141-147 ◽  
Author(s):  
Marcelo J. da Silva ◽  
Raquel Fogarin Destro ◽  
Thiago Gazoni ◽  
Hideki Narimatsu ◽  
Paulo S. Pereira dos Santos ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Centromere Function ◽  
Sex Chromosome System ◽  
First Time ◽  
Eukaryotic Genomes

Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.

scholarly journals Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lingzhan Xue ◽  
Yu Gao ◽  
Meiying Wu ◽  
Tian Tian ◽  
Haiping Fan ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Chromosome Pair ◽  
Sex Chromosome ◽  
Structural Variations ◽  
Recombination Suppression ◽  
Chromosome Differentiation ◽  
Y Chromosomes ◽  
Recent Origin ◽  
Mastacembelus Armatus

Abstract Background The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged. Results Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. Conclusions Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.

scholarly journals Differences in recombination frequencies during female and male meioses of the sex chromosomes of the medaka, Oryzias latipes

2001 ◽  
Vol 78 (1) ◽  
pp. 23-30 ◽  
Author(s):  
MARIKO KONDO ◽  
ERIKO NAGAO ◽  
HIROSHI MITANI ◽  
AKIHIRO SHIMA
Keyword(s):  
Genetic Map ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Oryzias Latipes ◽  
Male Recombination ◽  
Male And Female ◽  
Y Chromosomes ◽  
Genetic Length ◽  
Expressed Sequence ◽  
Group 1

In the medaka, Oryzias latipes, sex is determined chromosomally. The sex chromosomes differ from those of mammals in that the X and Y chromosomes are highly homologous. Using backcross panels for linkage analysis, we mapped 21 sequence tagged site (STS) markers on the sex chromosomes (linkage group 1). The genetic map of the sex chromosome was established using male and female meioses. The genetic length of the sex chromosome was shorter in male than in female meioses. The region where male recombination is suppressed is the region close to the sex-determining gene y, while female recombination was suppressed in both the telomeric regions. The restriction in recombination does not occur uniformly on the sex chromosome, as the genetic map distances of the markers are not proportional in male and female recombination. Thus, this observation seems to support the hypothesis that the heterogeneous sex chromosomes were derived from suppression of recombination between autosomal chromosomes. In two of the markers, Yc-2 and Casp6, which were expressed sequence-tagged (EST) sites, polymorphisms of both X and Y chromosomes were detected. The alleles of the X and Y chromosomes were also detected in O. curvinotus, a species related to the medaka. These markers could be used for genotyping the sex chromosomes in the medaka and other species, and could be used in other studies on sex chromosomes.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

Polymorphism and differentiation of rainbow trout Y chromosomes

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1105-1113 ◽  
Author(s):  
Alicia Felip ◽  
Atushi Fujiwara ◽  
William P Young ◽  
Paul A Wheeler ◽  
Marc Noakes ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Morphological Differentiation ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Y Chromosomes ◽  
Cytogenetic Analyses ◽  
Clonal Lines ◽  
Sex Locus

Most fish species show little morphological differentiation in the sex chromosomes. We have coupled molecular and cytogenetic analyses to characterize the male-determining region of the rainbow trout (Oncorhynchus mykiss) Y chromosome. Four genetically diverse male clonal lines of this species were used for genetic and physical mapping of regions in the vicinity of the sex locus. Five markers were genetically mapped to the Y chromosome in these male lines, indicating that the sex locus was located on the same linkage group in each of the lines. We also confirmed the presence of a Y chromosome morphological polymorphism among these lines, with the Y chromosomes from two of the lines having the more common heteromorphic Y chromosome and two of the lines having Y chromosomes morphologically similar to the X chromosome. The fluorescence in situ hybridization (FISH) pattern of two probes linked to sex suggested that the sex locus is physically located on the long arm of the Y chromosome. Fishes appear to be an excellent group of organisms for studying sex chromosome evolution and differentiation in vertebrates because they show considerable variability in the mechanisms and (or) patterns involved in sex determination.Key words: sex chromosomes, sex markers, cytogenetics, rainbow trout, fish.

Molecular Cytogenetic Analysis of Karyotype and Y Chromosome Conservation in Species of the Genus Talpa (Insectivora)

2020 ◽  
Vol 160 (5) ◽  
pp. 264-271
Author(s):  
Juana Gutierrez ◽  
Gael Aleix-Mata ◽  
Juan A. Marchal ◽  
María Arroyo ◽  
Riccardo Castiglia ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Y Chromosome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Chromosome Painting ◽  
Chromosomal Mapping ◽  
Repeated Dna ◽  
Molecular Cytogenetic ◽  
Y Chromosomes ◽  
Cytogenetic Analyses

The Talpidae family has a highly stable karyotype. Most of the chromosome studies in this mammal group, however, employed classical cytogenetic techniques. Molecular cytogenetic analyses are still scarce and, for example, no repeated DNA sequences have been described to date. In this work, we used sequence analysis, chromosomal mapping of a LINE1 retroelement sequence, as well as chromosome painting with a whole Y chromosome probe of T. occidentalis to compare the karyotypes of 3 species of the genus Talpa (T. occidentalis, T. romana, and T. aquitania). Our results demonstrate that in Talpa genomes LINE1 sequences are widely distributed on all chromosomes but are enriched in pericentromeric C-band-positive regions. In addition, these LINE1 accumulate on the Y chromosomes of the 3 Talpa species regardless of their euchromatic or heterochromatic condition. Chromosome painting shows that the Y chromosomes in these 3 species are highly conserved. Interestingly, they share sequences with heterochromatic blocks on chromosome pairs 14 and 16 and, to a lesser degree, with the pericentromeric regions of other autosomes. Together, our analyses demonstrate that the repetitive DNA content of chromosomes from Talpa species is highly conserved.

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