scholarly journals Comparative genomic mapping reveals mechanisms of chromosome diversification in Rhipidomys species (Rodentia, Thomasomyini) and syntenic relationship between species of Sigmodontinae

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258474
Author(s):  
Vergiana dos Santos Paixão ◽  
Pablo Suárez ◽  
Willam Oliveira da Silva ◽  
Lena Geise ◽  
Malcolm Andrew Ferguson-Smith ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Chromosomal Rearrangements ◽  
Chromosomal Evolution ◽  
Wide Distribution ◽  
Comparative Genomic ◽  
Syntenic Block ◽  
Syntenic Relationship ◽  
Pericentric Inversions ◽  
High Level

Rhipidomys (Sigmodontinae, Thomasomyini) has 25 recognized species, with a wide distribution ranging from eastern Panama to northern Argentina. Cytogenetic data has been described for 13 species with 12 of them having 2n = 44 with a high level of autosomal fundamental number (FN) variation, ranging from 46 to 80, assigned to pericentric inversions. The species are grouped in groups with low FN (46–52) and high FN (72–80). In this work the karyotypes of Rhipidomys emiliae (2n = 44, FN = 50) and Rhipidomys mastacalis (2n = 44, FN = 74), were studied by classical cytogenetics and by fluorescence in situ hybridization using telomeric and whole chromosome probes (chromosome painting) of Hylaeamys megacephalus (HME). Chromosome painting revealed homology between 36 segments of REM and 37 of RMA. We tested the hypothesis that pericentric inversions are the predominant chromosomal rearrangements responsible for karyotypic divergence between these species, as proposed in literature. Our results show that the genomic diversification between the karyotypes of the two species resulted from translocations, centromeric repositioning and pericentric inversions. The chromosomal evolution in Rhipidomys was associated with karyotypical orthoselection. The HME probes revealed that seven syntenic probably ancestral blocks for Sigmodontinae are present in Rhipidomys. An additional syntenic block described here is suggested as part of the subfamily ancestral karyotype. We also define five synapomorphies that can be used as chromosomal signatures for Rhipidomys.

scholarly journals Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Melquizedec Luiz Silva Pinheiro ◽  
Cleusa Yoshiko Nagamachi ◽  
Talita Fernanda Augusto Ribas ◽  
Cristovam Guerreiro Diniz ◽  
Patricia Caroline Mary O´Brien ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Diploid Number ◽  
Chromosomal Evolution ◽  
Long Distance ◽  
Chromosomal Painting ◽  
Cytogenetic Studies ◽  
Burhinus Oedicnemus ◽  
Clear Idea ◽  
First Time

Abstract Background The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting. Results The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype (a common feature among Scolopaci), suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence in situ hybridization using Burhinus oedicnemus whole chromosome probes confirmed the fissions in pairs 1, 2, 3, 4 and 6 of macrochromosomes. Conclusion Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of how chromosomal evolution occurred in this suborder.

scholarly journals Generation of a whole chromosome painting probe from monochromosomal hybrid cells by the alu-polymerase chain reaction

2007 ◽  
Vol 59 (2) ◽  
pp. 89-95 ◽  
Author(s):  
Danijela Drakulic ◽  
Gordana Nikcevic ◽  
Vesna Djordjevic ◽  
Milena Stevanovic
Keyword(s):  
Chromosome Painting ◽  
Fluorescent In Situ Hybridization ◽  
Chromosomal Rearrangements ◽  
Painting Probe ◽  
Complex Chromosomal Rearrangements ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Complex Chromosome ◽  
Whole Chromosome Painting

Fluorescent in situ hybridization (FISH) has become a widespread technique applicable in basic science and diagnostics. Chromosome painting represents a special application of FISH that has found increasing use in identification of complex chromosome rearrangements. Here we present a version of the Alu-PCR method modified to generate a whole chromosome painting probe (WCP) for human chromosome 19 using monochromosomal cell hybrids. In setting up conditions for this method, we established a cheap and fast approach to generation of WCPs for other human chromosomes that could be particularly useful for unambiguous identification of complex chromosomal rearrangements associated with cancer. .

scholarly journals Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes)

2020 ◽  
Author(s):  
Melquizedec Luiz Silva Pinheiro ◽  
Cleusa Yoshiko Nagamachi ◽  
Talita Fernanda Augusto Ribas ◽  
Cristovam Guerreiro Diniz ◽  
Patricia Caroline Mary O´Brien ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Diploid Number ◽  
Chromosomal Evolution ◽  
Long Distance ◽  
Chromosomal Painting ◽  
Cytogenetic Studies ◽  
Burhinus Oedicnemus ◽  
Clear Idea ◽  
First Time

Abstract Background: The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting. Results: The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype, suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence In Situ Hybridization using Burhinus oedicnemus whole chromosome probes confirmed these fissions in all pairs of macrochromosomes. Conclusion: Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of ​​how chromosomal evolution occurred in this suborder.

Clinical and Cytogenomic Characterization of De Novo 11p14.3-p15.5 Duplication Associated with 18q23 Deletion in an Egyptian Female Infant

2020 ◽  
Author(s):  
Hanan H. Afifi ◽  
Ghada Y. El-Kamah ◽  
Alaa K. Kamel ◽  
Sally G. Abd Allah ◽  
Sayda Hammad ◽  
...  
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Ductus Arteriosus ◽  
Chromosomal Rearrangements ◽  
Clinical Manifestations ◽  
Brain Magnetic Resonance Imaging ◽  
Comparative Genomic ◽  
Septal Hypertrophy

AbstractPaternal microduplication of 11p14.3-p15.5 causes the clinical manifestations of Beckwith–Wiedemann syndrome (BWS), while microdeletion of 18q23-ter is clinically characterized by short stature, congenital malformations, and developmental delay. We describe a 15-month-old girl presenting with protruding tongue, dysmorphic facial features, moderate developmental delay, umbilical hernia, hypotonia, mild-to-moderate pulmonary hypertension, small patent ductus arteriosus, and mild ventricular septal hypertrophy. Brain magnetic resonance imaging showed mild atrophic changes. Chromosomal analysis revealed 46, XX, add(18)(q23). Fluorescence in situ hybridization using subtelomere 18q and whole chromosome painting 18 showed subtelomere deletion in 18q, and the add segment was not derived from chromosome 18. Microarray-based comparative genomic hybridization detected a 22 Mb duplication of chromosome 11p15.5p14.3 and a 3.7 Mb deletion of chromosome 18q23. The phenotype of the chromosomal rearrangements is probably resulted from a combination of dosage-sensitive genes. Our patient had clinical manifestations of both 18q deletion and BWS.

scholarly journals Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species

Agronomy ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 60 ◽  
Author(s):  
Tao Lang ◽  
Guangrong Li ◽  
Zhihui Yu ◽  
Jiwei Ma ◽  
Qiheng Chen ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats ◽  
Chromosomal Rearrangements ◽  
Wide Distribution ◽  
Fish Analysis ◽  
Satellite Repeats ◽  
Genome Wide ◽  
Rapid Sequence ◽  
Group 5

A large proportion of the genomes of grasses is comprised of tandem repeats (TRs), which include satellite DNA. A mini-satellite DNA sequence with a length of 44 bp, named Ta-3A1, was found to be highly accumulated in wheat genome, as revealed by a comprehensive sequence analysis. The physical distribution of Ta-3A1 in chromosomes 3A, 5A, 5B, 5D, and 7A of wheat was confirmed by nondenaturing fluorescence in situ hybridization (ND-FISH) after labeling the oligonucleotide probe. The analysis of monomer variants indicated that rapid sequence amplification of Ta-3A1 occurred first on chromosomes of linkage group 5, then groups 3 and 7. Comparative ND-FISH analysis suggested that rapid changes occurred in copy number and chromosomal locations of Ta-3A1 among the different species in the tribe Triticeae, which may have been associated with chromosomal rearrangements during speciation and polyploidization. The labeling and subsequent use of Ta-3A1 by ND-FISH may assist in the precise identification and documentation of novel wheat germplasm engineered by chromosome manipulation.

scholarly journals Comparative Genomic In Situ Hybridization and the Possible Role of Retroelements in the Karyotypic Evolution of Three Akodontini Species

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Naiara Pereira Araújo ◽  
Gustavo Campos Silva Kuhn ◽  
Flávia Nunes Vieira ◽  
Thaís Queiroz Morcatty ◽  
Adriano Pereira Paglia ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Molecular Cytogenetics ◽  
Endogenous Retrovirus ◽  
Comparative Genomic ◽  
South American ◽  
Telomeric Sequences ◽  
Pericentric Inversions ◽  
Robertsonian Rearrangements ◽  
Genomic Dnas

South American Akodontini rodents are characterized by a large number of chromosome rearrangements. Among them, the genus Akodon has been extensively analyzed with classical and molecular cytogenetics, which allowed the identification of a large number of intra- and interspecific chromosomal variation due to Robertsonian rearrangements, pericentric inversions, and heterochromatin additions/deletions. In order to shed some light on the cause of these rearrangements, we comparatively analyzed the karyotypes of three Akodontini species, Akodon cursor (2n = 14, FN = 19), A. montensis (2n = 24, FN = 42), and Necromys lasiurus (2n = 34, FN = 34), after GTG- and CBG-banding. The karyotypes differed by Robertsonian rearrangements, pericentric inversions, centromere repositioning, and heterochromatin variation. Genome comparisons were performed through interspecific fluorescent in situ hybridization (FISH) with total genomic DNAs of each species as probes (GISH). Our results revealed considerable conservation of the euchromatic portions among the three karyotypes suggesting that they mostly differ in their heterochromatic regions. FISH was also performed to assess the distribution of telomeric sequences, long and short interspersed repetitive elements (LINE-1 and B1 SINE) and of the endogenous retrovirus mysTR in the genomes of the three species. The results led us to infer that transposable elements have played an important role in the enormous chromosome variation found in Akodontini.

Recurrent involvement of the REL and BCL11Aloci in classical Hodgkin lymphoma

Blood ◽  
2002 ◽  
Vol 99 (4) ◽  
pp. 1474-1477 ◽  
Author(s):  
José I. Martı́n-Subero ◽  
Stefan Gesk ◽  
Lana Harder ◽  
Takashi Sonoki ◽  
Philip W. Tucker ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Hodgkin Lymphoma ◽  
Copy Number ◽  
Chromosome Region ◽  
Comparative Genomic ◽  
Classical Hodgkin Lymphoma ◽  
Interphase Cytogenetics ◽  
High Level ◽  
Minimal Region

Comparative genomic hybridization studies have shown gains in chromosome region 2p as the most common imbalance in classical Hodgkin lymphoma (cHL). The minimal region of gain contained 2 candidate oncogenes, REL and BCL11A. This study examined the involvement of REL and BCL11A loci in 44 primary cases of cHL by combined immunophenotyping and interphase cytogenetics (FICTION). A median 2p13 copy number above the tetraploid range was detected in 24 (55%) cases. Adjustment for centromere 2 copy number indicated gains of 2p13 in 11 of 31 cHLs (35%) with 8 (26%) high-level amplifications. One cHL displayed selective amplification of the REL locus not affectingBCL11A; another case studied by FICTION and a cHL with cytogenetic 2p change investigated by fluorescence in situ hybridization showed signal patterns suggesting breakpoints in the region spanned by the REL probe. These data indicate thatREL rather than BCL11A may be the target of the 2p13 alterations in cHL.

Chromosomal Evolution in the Diplodactylinae (Gekkonidae, Reptilia) .1. Evolutionary Relationships and Patterns of Change

1987 ◽  
Vol 35 (5) ◽  
pp. 507 ◽  
Author(s):  
M King
Keyword(s):  
Pericentric Inversion ◽  
Chromosomal Rearrangements ◽  
Chromosomal Evolution ◽  
Species Group ◽  
Individual Species ◽  
Ancestral Karyotype ◽  
Chromosome Fusion ◽  
Gross Chromosomal Rearrangements ◽  
Extant Species ◽  
Pericentric Inversions

A chromosomal analysis of 47 species of diplodactyline gekkos indicates that these are a monophyletic assemblage derived from a 2n = 38 acrocentric ancestral karyotype. Four major clades are present, the first possessing the ancestral karyotype. The remainder are defined by the possession of a series of shared derived chromosomal rearrangements, or by the type of chromosome change. The first of these derived clades includes the subgenus Strophurus, which has five fixed, presumed pericentric inversion differences. The second includes members of the D. vittatus species group. Here, a number of chromosome fusions have been established which appear to have been associated with speciation. The third derived clade is distinguished by 19 fixed, presumed pericentric inversions, and includes the genera, Oedura, Rhacodactylus, Bavayia, Pseudothecadactylus, Carphodactylus and Hoplodactylus. It is argued that the 2n=38 acrocentric karyotype common to many of the species is the ancestral karyomorph, and the modifications of this format have been achieved by both chromosome fusion and pericentric inversion. The decision that this is the ancestral karyomorph was based on its dominance in extant species; the fact that similar karyotypes are present in other gekkonid subfamilies (effective out-groups), that 2n =38 all acrocentric ancestral karyotypes are also found in some other lizard families, and that such a diversity of rearrangements was established, provide arguments against any other viable ancestral format. Two discrete modes of chromosomal repatterning are found in the Diplodactylinae: the fixation of presumptive multiple pericentric inversions, producing a karyomorph which characterises large groups of species; and the fixation of fusion or presumptive inversion differences which distinguish individual species or chromosome races. The latter appear to have been associated with speciation. It is clear that in certain groups, such as the Strophurus species group (the members of which all share a derived karyomorph defined by the presence of five inverted chromosomes), speciation has proceeded without gross chromosomal rearrangements.

Sign in / Sign up

Export Citation Format

Share Document