scholarly journals Chromosomal distribution of the retroelements Rex 1, Rex 3 and Rex 6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae)

2019 ◽  
Vol 17 (2) ◽  
Author(s):  
Josiane B. Traldi ◽  
Roberto L. Lui ◽  
Juliana de F. Martinez ◽  
Marcelo R. Vicari ◽  
Viviane Nogaroto ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Physical Mapping ◽  
Genome Organization ◽  
Chromosomal Rearrangements ◽  
Chromosome Mapping ◽  
Chromosomal Evolution ◽  
Chromosomal Distribution ◽  
Chromosome Markers ◽  
Molecular Domestication

ABSTRACT The transposable elements (TE) have been widely applied as physical chromosome markers. However, in Loricariidae there are few physical mapping analyses of these elements. Considering the importance of transposable elements for chromosomal evolution and genome organization, this study conducted the physical chromosome mapping of retroelements (RTEs) Rex1, Rex3 and Rex6 in seven species of the genus Harttia and four species of the genus Hypostomus, aiming to better understand the organization and dynamics of genomes of Loricariidae species. The results showed an intense accumulation of RTEs Rex1, Rex3 and Rex6 and dispersed distribution in heterochromatic and euchromatic regions in the genomes of the species studied here. The presence of retroelements in some chromosomal regions suggests their participation in various chromosomal rearrangements. In addition, the intense accumulation of three retroelements in all species of Harttia and Hypostomus, especially in euchromatic regions, can indicate the participation of these elements in the diversification and evolution of these species through the molecular domestication by genomes of hosts, with these sequences being a co-option for new functions.

scholarly journals Centromere Repeats: Hidden Gems of the Genome

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 223 ◽  
Author(s):  
Gabrielle Hartley ◽  
Rachel O’Neill
Keyword(s):  
Transposable Elements ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Repetitive Sequences ◽  
Chromosomal Evolution ◽  
Satellite Dnas ◽  
Integral Role ◽  
Chromosomal Breakpoints ◽  
Karyotypic Variation ◽  
Species Specific

Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’.

scholarly journals Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna

2021 ◽  
Vol 43 (3) ◽  
pp. 237-249 ◽  
Author(s):  
Thanh Dat Ta ◽  
Nomar Espinosa Waminal ◽  
Thi Hong Nguyen ◽  
Remnyl Joyce Pellerin ◽  
Hyun Hee Kim
Keyword(s):  
Tandem Repeats ◽  
Chromosomal Rearrangements ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Pericentromeric Region ◽  
Its2 Sequence ◽  
Fish Analysis ◽  
Chromosomal Distribution ◽  
Chromosome Dynamics

Abstract Background DNA tandem repeats (TRs) are often abundant and occupy discrete regions in eukaryotic genomes. These TRs often cause or generate chromosomal rearrangements, which, in turn, drive chromosome evolution and speciation. Tracing the chromosomal distribution of TRs could therefore provide insights into the chromosome dynamics and speciation among closely related taxa. The basic chromosome number in the genus Senna is 2n = 28, but dysploid species like Senna tora have also been observed. Objective To understand the dynamics of these TRs and their impact on S. tora dysploidization. Methods We performed a comparative fluorescence in situ hybridization (FISH) analysis among nine closely related Senna species and compared the chromosomal distribution of these repeats from a cytotaxonomic perspective by using the ITS1-5.8S-ITS2 sequence to infer phylogenetic relationships. Results Of the nine S. tora TRs, two did not show any FISH signal whereas seven TRs showed similar and contrasting patterns to other Senna species. StoTR01_86, which was localized in the pericentromeric regions in all S. tora, but not at the nucleolar organizer region (NOR) site, was colocalized at the NOR site in all species except in S. siamea. StoTR02_7_tel was mostly localized at chromosome termini, but some species had an interstitial telomeric repeat in a few chromosomes. StoTR05_180 was distributed in the subtelomeric region in most species and was highly amplified in the pericentromeric region in some species. StoTR06_159 was either absent or colocalized in the NOR site in some species, and StoIGS_463, which was localized at the NOR site in S. tora, was either absent or localized at the subtelomeric or pericentromeric regions in other species. Conclusions These data suggest that TRs play important roles in S. tora dysploidy and suggest the involvement of 45S rDNA intergenic spacers in “carrying” repeats during genome reshuffling.

scholarly journals Transposable Elements and Teleost Migratory Behaviour

2021 ◽  
Vol 22 (2) ◽  
pp. 602
Author(s):  
Elisa Carotti ◽  
Federica Carducci ◽  
Adriana Canapa ◽  
Marco Barucca ◽  
Samuele Greco ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Environmental Changes ◽  
Chromosomal Rearrangements ◽  
Quantitative Difference ◽  
Regulatory Elements ◽  
Phylogenetic Position ◽  
Migratory Behaviour ◽  
Relative Contribution ◽  
Migratory Routes ◽  
Eukaryotic Genomes

Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.

scholarly journals Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis

2021 ◽  
Vol 22 (4) ◽  
pp. 1614
Author(s):  
María Esther Rodríguez ◽  
Ismael Cross ◽  
Alberto Arias-Pérez ◽  
Silvia Portela-Bens ◽  
Manuel Alejandro Merlo ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Fish Species ◽  
Gasterosteus Aculeatus ◽  
Sparus Aurata ◽  
Chromosomal Rearrangements ◽  
Scophthalmus Maximus ◽  
Cynoglossus Semilaevis ◽  
Solea Senegalensis ◽  
Reference Species ◽  
Artificial Chromosomes

Cytogenomics, the integration of cytogenetic and genomic data, has been used here to reconstruct the evolution of chromosomes 2 and 4 of Solea senegalensis. S. senegalensis is a flat fish with a karyotype comprising 2n = 42 chromosomes: 6 metacentric + 4 submetacentric + 8 subtelocentric + 24 telocentric. The Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (FISH-BAC) technique was applied to locate BACs in these chromosomes (11 and 10 BACs in chromosomes 2 and 4, respectively) and to generate integrated maps. Synteny analysis, taking eight reference fish species (Cynoglossus semilaevis, Scophthalmus maximus, Sparus aurata, Gasterosteus aculeatus, Xiphophorus maculatus, Oryzias latipes, Danio rerio, and Lepisosteus oculatus) for comparison, showed that the BACs of these two chromosomes of S. senegalensis were mainly distributed in two principal chromosomes in the reference species. Transposable Elements (TE) analysis showed significant differences between the two chromosomes, in terms of number of loci per Mb and coverage, and the class of TE (I or II) present. Analysis of TE divergence in chromosomes 2 and 4 compared to their syntenic regions in four reference fish species (C. semilaevis, S. maximus, O. latipes, and D. rerio) revealed differences in their age of activity compared with those species but less notable differences between the two chromosomes. Differences were also observed in peaks of divergence and coverage of TE families for all reference species even in those close to S. senegalensis, like S. maximus and C. semilaevis. Considered together, chromosomes 2 and 4 have evolved by Robertsonian fusions, pericentric inversions, and other chromosomal rearrangements mediated by TEs.

scholarly journals Chromosomal Evolution in the Lizard Genus Varanus (Reptilia)

1975 ◽  
Vol 28 (1) ◽  
pp. 89 ◽  
Author(s):  
Max Kinga ◽  
Dennis King
Keyword(s):  
Chromosome Number ◽  
Pericentric Inversion ◽  
Sex Chromosome ◽  
Chromosomal Rearrangements ◽  
Chromosomal Evolution ◽  
Size Groups ◽  
Sex Chromosome System

The karyotypes have been determined of 16 of the 32 species of the genus Varanus, including animals from Africa, Israel, Malaya and Australia. A constant chromosome number of 2n = 40 was observed. The karyotype is divided into eight pairs of large chromosomes and 12 pairs of microchromosomes. A series of chromosomal rearrangements have become established in both size groups of the karyotype and are restricted to centromere shifts, probably caused by pericentric inversion. Species could be placed in one of six distinct karyotype groups which are differentiated by these rearrangements and whose grouping does not always correspond with the current taxonomy. An unusual sex chromosome system of the ZZjZW type was present in a number of the species examined.

Chromosome Mapping of H1 and H4 Histones in Parodontidae (Actinopterygii: Characiformes): Dispersed and/or Co-Opted Transposable Elements?

2019 ◽  
Vol 158 (2) ◽  
pp. 106-113 ◽  
Author(s):  
Josiane B. Traldi ◽  
Kaline Ziemniczak ◽  
Juliana de Fátima Martinez ◽  
Daniel R. Blanco ◽  
Roberto L. Lui ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Chromosome Mapping ◽  
Endogenous Retrovirus ◽  
Histone Gene ◽  
Chromosome Rearrangements ◽  
Paralogous Sequence ◽  
Reading Frame ◽  
Evolutionary Changes ◽  
The Family ◽  
Autosomal Pair

The karyotypes of the family Parodontidae consist of 2n = 54 chromosomes. The main chromosomal evolutionary changes of its species are attributed to chromosome rearrangements in repetitive DNA regions in their genomes. Physical mapping of the H1 and H4 histones was performed in 7 Parodontidae species to analyze the chromosome rearrangements involved in karyotype diversification in the group. In parallel, the observation of a partial sequence of an endogenous retrovirus (ERV) retrotransposon in the H1 histone sequence was evaluated to verify molecular co-option of the transposable elements (TEs) and to assess paralogous sequence dispersion in the karyotypes. Six of the studied species had an interstitial histone gene cluster in the short arm of the autosomal pair 13. Besides this interstitial cluster, in Apareiodon davisi, a probable further site was detected in the terminal region of the long arm in the same chromosome pair. The H1/H4 clusters in Parodon cf. pongoensis were located in the smallest chromosomes (pair 20). In addition, scattered H1 signals were observed on the chromosomes in all species. The H1 sequence showed an ERV in the open reading frame (ORF), and the scattered H1 signals on the chromosomes were attributed to the ERV's location. The H4 sequence had no similarity to the TEs and displayed no dispersed signals. Furthermore, the degeneration of the inner ERV in the H1 sequence (which overlapped a stretch of the H1 ORF) was discussed regarding the likelihood of molecular co-option of this retroelement in histone gene function in Parodontidae.

scholarly journals Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 259 ◽  
Author(s):  
Karolina Susek ◽  
Wojciech Bielski ◽  
Katarzyna B. Czyż ◽  
Robert Hasterok ◽  
Scott A. Jackson ◽  
...  
Keyword(s):  
Karyotype Evolution ◽  
Chromosomal Rearrangements ◽  
Chromosome Mapping ◽  
Artificial Chromosome ◽  
Basic Chromosome Number ◽  
Plant Genome ◽  
Old World ◽  
Whole Genome Duplications ◽  
Genome Duplications

Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins.

scholarly journals Molecular Characterization and Chromosomal Distribution ofGalileo,KeplerandNewton, Three Foldback Transposable Elements of theDrosophila buzzatiiSpecies Complex

Genetics ◽  
2005 ◽  
Vol 169 (4) ◽  
pp. 2047-2059 ◽  
Author(s):  
Ferran Casals ◽  
Mario Cáceres ◽  
Maura Helena Manfrin ◽  
Josefa González ◽  
Alfredo Ruiz
Keyword(s):  
Transposable Elements ◽  
Molecular Characterization ◽  
Chromosomal Distribution

Extraordinary and extensive karyotypic variation: A 48-fold range in chromosome number in the gall-inducing scale insect Apiomorpha (Hemiptera: Coccoidea: Eriococcidae)

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 255-263 ◽  
Author(s):  
Lyn G Cook
Keyword(s):  
Chromosome Number ◽  
Chromosomal Rearrangements ◽  
Chromosomal Polymorphism ◽  
Chromosomal Evolution ◽  
Scale Insect ◽  
Closely Related Species ◽  
Host Genus ◽  
Species Complexes ◽  
Species Groups ◽  
Karyotypic Variation

Chromosome number reflects strong constraints on karyotype evolution, unescaped by the majority of animal taxa. Although there is commonly chromosomal polymorphism among closely related taxa, very large differences in chromosome number are rare. This study reports one of the most extensive chromosomal ranges yet reported for an animal genus. Apiomorpha Rübsaamen (Hemiptera: Coccoidea: Eriococcidae), an endemic Australian gall-inducing scale insect genus, exhibits an extraordinary 48-fold variation in chromosome number with diploid numbers ranging from 4 to about 192. Diploid complements of all other eriococcids examined to date range only from 6 to 28. Closely related species of Apiomorpha usually have very different karyotypes, to the extent that the variation within some species- groups is as great as that across the entire genus. There is extensive chromosomal variation among populations within 17 of the morphologically defined species of Apiomorpha indicating the existence of cryptic species-complexes. The extent and pattern of karyotypic variation suggests rapid chromosomal evolution via fissions and (or) fusions. It is hypothesized that chromosomal rearrangements in Apiomorpha species may be associated with these insects' tracking the radiation of their speciose host genus, Eucalyptus. Key words: Apiomorpha, cytogenetics, chromosomal evolution, holocentric.

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