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 Chromosomal Mapping of Repetitive DNAs in Characidium (Teleostei, Characiformes): Genomic Organization and Diversification of ZW Sex Chromosomes

2015 ◽  
Vol 146 (2) ◽  
pp. 136-143 ◽  
Author(s):  
Priscilla C. Scacchetti ◽  
Ricardo Utsunomia ◽  
José C. Pansonato-Alves ◽  
Marcelo R. Vicari ◽  
Roberto F. Artoni ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Dna Sequences ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
5S Rdna ◽  
Chromosome Mapping ◽  
Chromosomal Mapping ◽  
Specific Probe ◽  
W Chromosome ◽  
Sex Chromosome System

The speciose neotropical genus Characidium has proven to be a good model for cytogenetic exploration. Representatives of this genus often have a conserved diploid chromosome number; some species exhibit a highly differentiated ZZ/ZW sex chromosome system, while others do not show any sex-related chromosome heteromorphism. In this study, chromosome painting using a W-specific probe and comparative chromosome mapping of repetitive sequences, including ribosomal clusters and 4 microsatellite motifs - (CA)15, (GA)15, (CG)15, and (TTA)10 -, were performed in 6 Characidium species, 5 of which possessed a heteromorphic ZW sex chromosome system. The W-specific probe showed hybridization signals on the W chromosome of all analyzed species, indicating homology among the W chromosomes. Remarkably, a single major rDNA-bearing chromosome pair was found in all species. The 18S rDNA localized to the sex chromosomes in C. lanei, C. timbuiense and C. pterostictum, while the major rDNA localized to one autosome pair in C. vidali and C. gomesi. In contrast, the number of 5S rDNA-bearing chromosomes varied. Notably, minor ribosomal clusters were identified in the W chromosome of C. vidali. Microsatellites were widely distributed across almost all chromosomes of the karyotypes, with a greater accumulation in the subtelomeric regions. However, clear differences in the abundance of each motif were detected in each species. In addition, the Z and W chromosomes showed the differential accumulation of distinct motifs. Our results revealed variability in the distribution of repetitive DNA sequences and their possible association with sex chromosome diversification in Characidium species.

Heteromorphic Sex Chromosomes and Their DNA Content in Fish: An Insight through Satellite DNA Accumulation in Megaleporinus elongatus

2020 ◽  
Vol 160 (1) ◽  
pp. 38-46 ◽  
Author(s):  
Carolina Crepaldi ◽  
Patricia P. Parise-Maltempi
Keyword(s):  
Sex Chromosomes ◽  
Dna Content ◽  
Satellite Dna ◽  
Sex Chromosome ◽  
Neotropical Fish ◽  
High Throughput Analysis ◽  
Multiple Sex Chromosomes ◽  
Heteromorphic Sex Chromosomes ◽  
Sex Chromosome System ◽  
Graph Based Clustering

The repetitive DNA content of fish sex chromosomes provides valuable insights into specificities and patterns of their genetic sex determination systems. In this study, we revealed the genomic satellite DNA (satDNA) content of Megaleporinuselongatus, a Neotropical fish species with Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosomes, through high-throughput analysis and graph-based clustering, isolating 68 satDNA families. By physically mapping these sequences in female metaphases, we discovered 15 of the most abundant satDNAs clustered in its chromosomes, 9 of which were found exclusively in the highly heterochromatic W1. This heteromorphic sex chromosome showed the highest amount of satDNA accumulations in this species. The second most abundant family, MelSat02-26, shared FISH signals with the NOR-bearing pair in similar patterns and is linked to the multiple sex chromosome system. Our results demonstrate the diverse satDNA content in M. elongatus, especially in its heteromorphic sex chromosome. Additionally, we highlighted the different accumulation patterns and distribution of these sequences across species by physically mapping these satDNAs in other Anostomidae, Megaleporinusmacrocephalus and Leporinusfriderici (a species without differentiated sex chromosomes).

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.

scholarly journals Repetitive Sequence and Sex Chromosome Evolution in Vertebrates

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Tariq Ezaz ◽  
Janine E. Deakin
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Repetitive Sequence ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Sex Chromosome Evolution ◽  
Genomic Changes ◽  
Heteromorphic Sex Chromosomes ◽  
Simple Repetitive Sequences

Sex chromosomes are the most dynamic entity in any genome having unique morphology, gene content, and evolution. They have evolved multiple times and independently throughout vertebrate evolution. One of the major genomic changes that pertain to sex chromosomes involves the amplification of common repeats. It is hypothesized that such amplification of repeats facilitates the suppression of recombination, leading to the evolution of heteromorphic sex chromosomes through genetic degradation of Y or W chromosomes. Although contrasting evidence is available, it is clear that amplification of simple repetitive sequences played a major role in the evolution of Y and W chromosomes in vertebrates. In this review, we present a brief overview of the repetitive DNA classes that accumulated during sex chromosome evolution, mainly focusing on vertebrates, and discuss their possible role and potential function in this process.

A subtelomeric satellite DNA family isolated from the genome of the dioecious plant Silene latifolia

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 442-446 ◽  
Author(s):  
M A Garrido-Ramos ◽  
R de la Herrán ◽  
M Ruiz Rejón ◽  
C Ruiz Rejón
Keyword(s):  
Sex Chromosomes ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Consensus Sequence ◽  
Repetitive Sequences ◽  
Restriction Enzymes ◽  
Repeat Sequence ◽  
Silene Latifolia ◽  
Telomere Repeat ◽  
Significant Length

In an ongoing effort to trace the evolution of the sex chromosomes of Silene latifolia, we have searched for the existence of repetitive sequences specific to these chromosomes in the genome of this species by direct isolation from low-melting agarose gels of satellite DNA bands generated by digestion with restriction enzymes. Five monomeric units belonging to a highly repetitive family isolated from Silene latifolia, the SacI family, have been cloned and characterized. The consensus sequence of the repetitive units is 313 bp in length (however, high variability exists for monomer length variants) and 52.9% in AT. Repeating units are tandemly arranged at the subtelomeric regions of the chromosomes in this species. The sequence does not possess direct or inverted sequences of significant length, but short direct repeats are scattered throughout the monomer sequence. Several short sequence motives resemble degenerate monomers of the telomere repeat sequence of plants (TTTAGGG), confirming a tight association between this subtelomeric satellite DNA and the telomere repeats. Our approach in this work confirms that SacI satellite DNA sequences are among the most abundant in the genome of S. latifolia and, on the other hand, that satellite DNA sequences specific of sex chromosomes are absent in this species. This agrees with a sex determination system less cytogenetically diverged from a bisexual state than the system present in other plant species, such as R. acetosa, or at least a lesser degree of differentiation between the sex chromosomes of S. latifolia and the autosomes.Key words: satellite DNA, sex chromosomes, Silene latifolia, subtelomeric sequences.

scholarly journals Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes

2021 ◽  
Author(s):  
D Prentout ◽  
N Stajner ◽  
A Cerenak ◽  
T Tricou ◽  
C Brochier-Armanet ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Cannabis Sativa ◽  
Sex Chromosome ◽  
Probabilistic Method ◽  
List Type ◽  
Recombination Suppression ◽  
Sex Chromosome System ◽  
The Common ◽  
Well Differentiated ◽  
First Time

SummaryWe recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants. Based on our estimate of its age, we predicted that it should be shared by its sister genus Humulus, which is known to also possess XY sex chromosomes.Here, we used transcriptome sequencing of a F1 family of Humulus lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector.We identified 265 sex-linked genes in H. lupulus, located on the chromosome that is also the C. sativa sex chromosome pair. Using phylogenies of sex-linked genes, we show that a region of these chromosomes had already stopped recombining in the common ancestor of the two species. Furthermore, as in C. sativa, Y gene expression was reduced in correlation to the position on the X chromosome, and strongly Y degenerated genes showed dosage compensation.Here we report, for the first time in the Angiosperms, a sex chromosome system that is shared by two different genera. Recombination suppression started at least 21-25 My ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes, leading to a strongly degenerated Y.

scholarly journals Genome-Wide Analysis of Transposable Elements and Satellite DNAs in Spinacia Species to Shed Light on Their Roles in Sex Chromosome Evolution

2021 ◽  
Vol 11 ◽  
Author(s):  
Ning Li ◽  
Xiaoyue Li ◽  
Jian Zhou ◽  
Li’ang Yu ◽  
Shufen Li ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Chromosome 1 ◽  
Sex Chromosome Evolution ◽  
Satellite Dnas ◽  
Heteromorphic Sex Chromosomes

Sex chromosome evolution has mostly been studied in species with heteromorphic sex chromosomes. The Spinacia genus serves as an ideal model for investigating evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. Among evolutionary factors, repetitive sequences play multiple roles in sex chromosome evolution while their forces have not been fully explored in Spinacia species. Here, we identified major repetitive sequence classes in male and female genomes of Spinacia species and their ancestral relative sugar beet to elucidate the evolutionary processes of sex chromosome evolution using next-generation sequencing (NGS) data. Comparative analysis revealed that the repeat elements of Spinacia species are considerably higher than of sugar beet, especially the Ty3/Gypsy and Ty1/Copia retrotransposons. The long terminal repeat retroelements (LTR) Angela, Athila, and Ogre may be accounted for the higher proportion of repeats in the spinach genome. Comparison of the repeats proportion between female and male genomes of three Spinacia species indicated the different representation in Spinacia tetrandra samples but not in the S. oleracea or S. turkestanica samples. From these results, we speculated that emergence of repetitive DNA sequences may correlate the formation of sex chromosome and the transition from homomorphic sex chromosomes to heteromorphic sex chromosomes as heteromorphic sex chromosomes exclusively existed in Spinacia tetrandra. Three novel sugar beet-specific satellites were identified and confirmed by fluorescence in situ hybridization (FISH); six out of eight new spinach-specific satellites were mapped to the short arm of sex chromosomes. A total of 141 copies of SolSat01-171-s were found in the sex determination region (SDR). Thus, the accumulation of satellite DNA on the short arm of chromosome 1 may be involved in the sex chromosome evolution in Spinacia species. Our study provides a fundamental resource for understanding repeat sequences in Spinacia species and their roles in sex chromosome evolution.

scholarly journals Novel repetitive sequences decipher the evolution and phylogeny in Carthamus L

2019 ◽  
Author(s):  
Shweta Mehrotra ◽  
Vinod Goyal
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Carthamus Tinctorius ◽  
Phylogeny Reconstruction ◽  
Reconstruction Method ◽  
Crop Species ◽  
Isolation And Characterization ◽  
Eukaryotic Genomes

Abstract Repetitive sequences are ubiquitous features of eukaryotic genomes, which contribute up to 70-80% of the nuclear genomic DNA. They are known to impact genome evolution and organization and play important role in genome remodelling. The widespread distribution and sufficient conservation of repeats reinforce the value of repetitive DNA sequences as markers of evolutionary processes. The repetitive DNA-based phylogeny reconstruction method is consistent in resolving expected phylogenetic and evolutionary relationships. In the present study, we address the isolation and characterization of four novel repetitive sequences (pCtHaeIII-I, pCtHaeIII-II, pCtHaeIII-III and pCtTaqI-I) from Carthamus tinctorius. Detailed phylogenetic analysis of 18 taxa belonging to 7 species of Carthamus has also been done with pCtHaeIII-I, and pCtHaeIII-II which clearly indicated concerted evolution while delineating phylogenetic relationships among the 18 taxa studied. The above understanding can assist in the marker assisted genetic improvement/ enhancement programmes in this crop species.

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.

scholarly journals Evolution of a Multiple Sex-Chromosome System by Three-Sequential Translocations among Potential Sex-Chromosomes in the Taiwanese Frog Odorrana swinhoana

Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 661
Author(s):  
Ikuo Miura ◽  
Foyez Shams ◽  
Si-Min Lin ◽  
Marcelo de Bello Cioffi ◽  
Thomas Liehr ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Rare Case ◽  
Sex Chromosome ◽  
Sex Chromosome System ◽  
Brown Frog ◽  
Male Specific

Translocation between sex-chromosomes and autosomes generates multiple sex-chromosome systems. It happens unexpectedly, and therefore, the evolutionary meaning is not clear. The current study shows a multiple sex chromosome system comprising three different chromosome pairs in a Taiwanese brown frog (Odorrana swinhoana). The male-specific three translocations created a system of six sex-chromosomes, ♂X1Y1X2Y2X3Y3 -♀X1X1X2X2X3X3. It is unique in that the translocations occurred among three out of the six members of potential sex-determining chromosomes, which are known to be involved in sex-chromosome turnover in frogs, and the two out of three include orthologs of the sex-determining genes in mammals, birds and fishes. This rare case suggests sex-specific, nonrandom translocations and thus provides a new viewpoint for the evolutionary meaning of the multiple sex chromosome system.

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