Large-scale comparative analysis of cytogenetic markers across Lepidoptera

AbstractFluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. In contrast, the hybridization pattern of histone H3 genes was well conserved, reflecting the stable organisation of lepidopteran genomes. Unlike 5S rDNA and U1 and U2 snRNA genes which we failed to detect, except for 5S rDNA in a few representatives of early diverging lepidopteran lineages. To explain the negative FISH results, we used quantitative PCR and Southern hybridization to estimate the copy number and organization of the studied genes in selected species. The results suggested that their detection was hampered by long spacers between the genes and/or their scattered distribution. Our results question homology of 5S rDNA and U1 and U2 snRNA loci in comparative studies. We recommend the use of histone H3 in studies of karyotype evolution.

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The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S–5.8S–26S rDNA and a C genome specific DNA sequence in the genus Avena

Genome ◽

10.1139/g96-068 ◽

1996 ◽

Vol 39 (3) ◽

pp. 535-542 ◽

Cited By ~ 63

Author(s):

Concha Linares ◽

Juan González ◽

Esther Ferrer ◽

Araceli Fominaya

Keyword(s):

In Situ Hybridization ◽

Dna Sequence ◽

Diploid Species ◽

5S Rdna ◽

Rdna Genes ◽

26S Rdna ◽

A Genome ◽

Rdna Loci ◽

C Genome

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S–5.8S–26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A–C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C–A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S–5.8S–26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

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Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat

Genome ◽

10.1139/g04-044 ◽

2004 ◽

Vol 47 (5) ◽

pp. 860-867 ◽

Cited By ~ 46

Author(s):

E A Salina ◽

O M Numerova ◽

H Ozkan ◽

M Feldman

Keyword(s):

In Situ Hybridization ◽

Copy Number ◽

First Generation ◽

Tandem Repeats ◽

Southern Hybridization ◽

Homoeologous Pairing ◽

Genomic Changes ◽

Intergenomic Recombination ◽

Copy Numbers

The genomic content of the subtelomeric repeated sequences Spelt1 and Spelt52 was studied by dot, Southern, and in situ hybridization in 11 newly synthesized amphiploids of Aegilops and Triticum, and data were compared with the parental plants. Spelt1 had reduced copy numbers in the first generation of three synthetic amphiploids, but two others did not change; Spelt52 was amplified in nine amphiploids and did not change in two. In the second allopolyploid generation, Spelt1 copy number did not change, whereas there was amplification of Spelt52 in some allopolyploids and decreases in others. Neither allopolyploidy level nor the direction of the cross affected the patterns of change in the newly synthesized amphiploids. Changes did not result from intergenomic recombination because similar alterations were noticed in allopolyploids with and without Ph1, a gene that suppresses homoeologous pairing. No differences in Spelt1 and Spelt52 tandem organization were found by Southern hybridization. The significance of these data are discussed in relation to the establishment of newly formed allopolyploids.Key words: Aegilops, genomic changes, polyploidy, subtelomeric tandem repeats, Triticum, wheat.

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Heterochromatin patterns and ribosomal DNA loci distribution in diploid and polyploid Crotalaria species (Leguminosae, Papilionoideae), and inferences on karyotype evolution

Genome ◽

10.1139/g11-034 ◽

2011 ◽

Vol 54 (9) ◽

pp. 718-726 ◽

Cited By ~ 9

Author(s):

Mateus Mondin ◽

Margarida L.R. Aguiar-Perecin

Keyword(s):

Dna Sequence ◽

Ribosomal Dna ◽

Karyotype Evolution ◽

5S Rdna ◽

Rdna Locus ◽

Variable Number ◽

Chromosome 1 ◽

Distamycin A ◽

Rdna Sites

Most Crotalaria species display a symmetric karyotype with 2n = 16, but 2n = 14 is found in Chrysocalycinae subsection Incanae and 2n = 32 in American species of the section Calycinae. Seven species of the sections Chrysocalycinae, Calycinae, and Crotalaria were analyzed for the identification of heterochromatin types with GC- and AT-specific fluorochromes and chromosomal location of ribosomal DNA loci using fluorescent in situ hybridization (FISH). A major 45S rDNA locus was observed on chromosome 1 in all the species, and a variable number of minor ones were revealed. Only one 5S rDNA locus was observed in the species investigated. Chromomycin A3 (CMA) revealed CMA+ bands colocalized with most rDNA loci, small bands unrelated to ribosomal DNA on two chromosome pairs in Crotalaria incana, and CMA+ centromeric bands that were quenched by distamycin A were detected in species of Calycinae and Crotalaria sections. DAPI+ bands were detected in C. incana. The results support the species relationships based on flower specialization and were useful for providing insight into mechanisms of karyotype evolution. The heterochromatin types revealed by fluorochromes suggest the occurrence of rearrangements in repetitive DNA families in these heterochromatic blocks during species diversification. This DNA sequence turnover and the variability in number/position of rDNA sites could be interpreted as resulting from unequal crossing over and (or) transposition events. The occurrence of only one 5S rDNA locus and the smaller chromosome size in the polyploids suggest that DNA sequence losses took place following polyploidization events.

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LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci

10.1101/2021.06.18.449059 ◽

2021 ◽

Author(s):

Luca Comai ◽

Kirk R Amundson ◽

Benny Ordonez ◽

Xin Zhao ◽

Guilherme Tomaz Braz ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Copy Number ◽

Fluorescent In Situ Hybridization ◽

Large Scale ◽

Chromosomal Translocations ◽

Chromosome 1 ◽

Structural Variations ◽

Painting Probes ◽

Two Populations

Large scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1Mb bin, we tested linkage disequilibrium with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a non-reciprocal translocation between chromosome 7 and 8 resulted in a 5-3 copy number change affecting several Mb at the respective chromosome tips. In cv. Alca Tarma the terminal arm of chromosome 4 translocated to the tip of chromosome 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, but we identified pericentromeric LD suggesting the effect of repeats. This method should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.

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Cytogenetic Analysis of Panaqolus tankei Cramer & Sousa, 2016 (Siluriformes, Loricariidae), an Ornamental Fish Endemic to Xingu River, Brazil

Cytogenetic and Genome Research ◽

10.1159/000514061 ◽

2021 ◽

pp. 1-8

Author(s):

Alex M.V. Ferreira ◽

Patrik F. Viana ◽

Jansen Zuanon ◽

Tariq Ezaz ◽

Marcelo B. Cioffi ◽

...

Keyword(s):

18S Rdna ◽

Diploid Number ◽

5S Rdna ◽

Sister Group ◽

Nucleolus Organizer ◽

Comparative Genomic ◽

Nucleolus Organizer Regions ◽

Chromosomal Changes ◽

The Impact

Despite conservation of the diploid number, a huge diversity in karyotype formulae is found in the Ancistrini tribe (Loricariidae, Hypostominae). However, the lack of cytogenetic data for many groups impairs a comprehensive understanding of the chromosomal relationships and the impact of chromosomal changes on their evolutionary history. Here, we present for the first time the karyotype of Panaqolus tankei Cramer & Sousa, 2016. We focused on the chromosomal characterization, using conventional and molecular cytogenetic techniques to unravel the evolutionary trends of this tribe. P. tankei, as most species of its sister group Pterygoplichthini, also possessess a conserved diploid number of 52 chromosomes. We observed heterochromatin regions in the centromeres of many chromosomes; pairs 5 and 6 presented interstitial heterochromatin regions, whereas pairs 23 and 24 showed extensive heterochromatin regions in their q arms. In situ localization of 18S rDNA showed hybridization signals correlating with the nucleolus organizer regions, which are located in the q arms of pair 5. However, the 5S rDNA was detected in the centromeric and terminal regions of the q arms of pair 8. (TTAGGG)n hybridized only in the terminal regions of all chromosomes. Microsatellite in situ localization showed divergent patterns, (GA)15 repeated sequences were restricted to the terminal regions of some chromosomes, whereas (AC)15 and (GT)15 showed a scattered hybridization pattern throughout the genome. Intraspecific comparative genomic hybridization was performed on the chromosomes of P. tankei to verify the existence of sex-specific regions. The results revealed only a limited number of overlapping hybridization signals, coinciding with the heterochromatin in centromeric regions without any sex-specific signals in both males and females. Our study provides a karyotype description of P. tankei, highlighting extensive differences in the karyotype formula, the heterochromatin regions, and sites of 5S and 18S rDNA, as compared with data available for the genus.

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LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci

Genetics ◽

10.1093/genetics/iyab137 ◽

2021 ◽

Author(s):

Luca Comai ◽

Kirk Amundson ◽

Benny Ordonez ◽

Xin Zhao ◽

Guilherme Tomaz Braz ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Copy Number ◽

Fluorescent In Situ Hybridization ◽

Large Scale ◽

Chromosomal Translocations ◽

Chromosome 1 ◽

Structural Variations ◽

Painting Probes ◽

Two Populations

Abstract Large scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1Mb bin, we tested independence, effectively an apparent linkage disequilibrium (LD), with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a non-reciprocal translocation between chromosome 7 and 8 resulted in a 5-3 copy number change affecting several Mb at the respective chromosome tips. In cv. “Alca Tarma”, the terminal arm of chromosome 4 translocated to the tip of chromosome 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, while apparent LD between pericentromeric regions suggested the effect of repeats. This method, LD-CNV, should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.

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Physical Mapping of the 5S and 18S rDNA in Ten Species ofHypostomusLacépède 1803 (Siluriformes: Loricariidae): Evolutionary Tendencies in the Genus

The Scientific World JOURNAL ◽

10.1155/2014/943825 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8 ◽

Cited By ~ 17

Author(s):

Vanessa Bueno ◽

Paulo César Venere ◽

Jocicléia Thums Konerat ◽

Cláudio Henrique Zawadzki ◽

Marcelo Ricardo Vicari ◽

...

Keyword(s):

18S Rdna ◽

Chromosome Pair ◽

5S Rdna ◽

Pericentromeric Region ◽

Telomeric Region ◽

Diverse Group ◽

Rdna Genes ◽

Rdna Sites ◽

Metacentric Pair

Hypostomusis a diverse group with unclear aspects regarding its biology, including the mechanisms that led to chromosome diversification within the group. Fluorescencein situhybridization (FISH) with 5S and 18S rDNA probes was performed on ten Hypostomini species.Hypostomus faveolus,H. cochliodon,H. albopunctatus,H.aff.paulinus,andH. topavaehad only one chromosome pair with 18S rDNA sites, whileH. ancistroides,H. commersoni,H. hermanni,H. regani,andH. strigaticepshad multiple 18S rDNA sites. Regarding the 5S rDNA genes,H. ancistroides,H. regani,H. albopunctatus,H.aff.paulinus,andH. topavaehad 5S rDNA sites on only one chromosome pair andH. faveolus,H. cochliodon,H. commersoni,H. hermanni,andH. strigaticepshad multiple 5S rDNA sites. Most species had 18S rDNA sites in the telomeric region of the chromosomes. All species butH. cochliodonhad 5S rDNA in the centromeric/pericentromeric region of one metacentric pair. Obtained results are discussed based on existent phylogenies for the genus, with comments on possible dispersion mechanisms to justify the variability of the rDNA sites inHypostomus.

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Chromosome analysis in Saccodon wagneri (Characiformes) and insights into the karyotype evolution of Parodontidae

Neotropical Ichthyology ◽

10.1590/1982-0224-2020-0103 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Mauro Nirchio ◽

Maria Cecilia Masache ◽

Fabilene Gomes Paim ◽

Marcelo de Bello Cioffi ◽

Orlando Moreira Filho ◽

...

Keyword(s):

Sex Chromosomes ◽

5S Rdna ◽

Chromosome Analysis ◽

Valid Species ◽

Z Chromosome ◽

Rdna Genes ◽

Heteromorphic Sex Chromosomes ◽

Karyotype Structure ◽

Interstitial Telomeric Sites

ABSTRACT Parodontidae is a relatively small group of Neotropical characiform fishes consisting of three genera (Apareiodon, Parodon, and Saccodon) with 32 valid species. A vast cytogenetic literature is available on Apareiodon and Parodon, but to date, there is no cytogenetic data about Saccodon, a genus that contains only three species with a trans-Andean distribution. In the present study the karyotype of S. wagneri was described, based on both conventional (Giemsa staining, Ag-NOR, C-bands) and molecular (repetitive DNA mapping by fluorescent in situ hybridization) methods. A diploid chromosome number of 2n = 54 was observed in both sexes, and the presence of heteromorphic sex chromosomes of the ZZ/ZW type was detected. The W chromosome has a terminal heterochromatin band that occupies approximately half of the long arm, being this band approximately half the size of the Z chromosome. The FISH assay showed a synteny of the 18S-rDNA and 5S-rDNA genes in the chromosome pair 14, and the absence of interstitial telomeric sites. Our data reinforce the hypothesis of a conservative karyotype structure in Parodontidae and suggest an ancient origin of the sex chromosomes in the fishes of this family.

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