scholarly journals Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy

2021 ◽  
Vol 12 ◽  
Author(s):  
Nomar Espinosa Waminal ◽  
Remnyl Joyce Pellerin ◽  
Sang-Ho Kang ◽  
Hyun Hee Kim
Keyword(s):  
Clustering Algorithm ◽  
Tandem Repeats ◽  
Karyotype Evolution ◽  
Chromosomal Rearrangements ◽  
Intergenic Spacer ◽  
Telomeric Repeat ◽  
Chromosomal Mapping ◽  
Chromosomal Distribution ◽  
Copy Numbers

Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant Senna tora dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the S. tora genome and compared the chromosomal distribution of these repeats between S. tora and a closely related euploid, Senna occidentalis. Using a read clustering algorithm, we identified the major S. tora tandem repeats and visualized their chromosomal distribution by fluorescence in situ hybridization. We identified eight independent repeats covering ~85 Mb or ~12% of the S. tora genome. The unit lengths and copy numbers had ranges of 7–5,833 bp and 325–2.89 × 106, respectively. Three short duplicated sequences were found in the 45S rDNA intergenic spacer, one of which was also detected at an extra-NOR locus. The canonical plant telomeric repeat (TTTAGGG)n was also detected as very intense signals in numerous pericentromeric and interstitial loci. StoTR05_180, which showed subtelomeric distribution in Senna occidentalis, was predominantly pericentromeric in S. tora. The unusual chromosomal distribution of tandem repeats in S. tora not only enabled easy identification of individual chromosomes but also revealed the massive chromosomal rearrangements that have likely played important roles in shaping its dysploid karyotype.

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 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.

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

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 860-867 ◽  
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.

Dynamic Changes in the Distribution of a Satellite Homologous to Intergenic 26-18S rDNA Spacer in the Evolution of Nicotiana

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1935-1946
Author(s):  
K Y Lim ◽  
K Skalicka ◽  
B Koukalova ◽  
R A Volkov ◽  
R Matyasek ◽  
...  
Keyword(s):  
18S Rdna ◽  
Intergenic Spacer ◽  
Nucleolar Organizer ◽  
Nucleolar Organizer Regions ◽  
Dynamic Nature ◽  
Dynamic Changes ◽  
Nicotiana Tomentosiformis ◽  
Copy Numbers ◽  
Location Patterns

Abstract An ∼135-bp sequence called the A1/A2 repeat was isolated from the transcribed region of the 26-18S rDNA intergenic spacer (IGS) of Nicotiana tomentosiformis. Fluorescence in situ hybridization (FISH) and Southern blot analysis revealed its occurrence as an independent satellite (termed an A1/A2 satellite) outside of rDNA loci in species of Nicotiana section Tomentosae. The chromosomal location, patterns of genomic dispersion, and copy numbers of its tandemly arranged units varied between the species. In more distantly related Nicotiana species the A1/A2 repeats were found only at the nucleolar organizer regions (NOR). There was a trend toward the elimination of the A1/A2 satellite in N. tabacum (tobacco), an allotetraploid with parents closely related to the diploids N. sylvestris and N. tomentosiformis. This process may have already commenced in an S3 generation of synthetic tobacco. Cytosine residues in the IGS were significantly hypomethylated compared with the A1/A2 satellite. There was no clear separation between the IGS and satellite fractions in sequence analysis of individual clones and we found no evidence for CG suppression. Taken together the data indicate a dynamic nature of the A1/A2 repeats in Nicotiana genomes, with evidence for recurrent integration, copy number expansions, and contractions.

scholarly journals Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat

2018 ◽  
Vol 12 (4) ◽  
pp. 493-513 ◽  
Author(s):  
Ilya Kirov ◽  
Marina Gilyok ◽  
Andrey Knyazev ◽  
Igor Fesenko
Keyword(s):  
Tandem Repeats ◽  
Physcomitrella Patens ◽  
Model Organism ◽  
Intergenic Spacer ◽  
Substantial Part ◽  
The Novel ◽  
Model Plant ◽  
Functional Studies ◽  
Non Coding Rnas

Satellite DNA (satDNA) constitutes a substantial part of eukaryotic genomes. In the last decade, it has been shown that satDNA is not an inert part of the genome and its function extends beyond the nuclear membrane. However, the number of model plant species suitable for studying the novel horizons of satDNA functionality is low. Here, we explored the satellitome of the model “basal” plant, Physcomitrellapatens (Hedwig, 1801) Bruch & Schimper, 1849 (moss), which has a number of advantages for deep functional and evolutionary research. Using a newly developed pyTanFinder pipeline (https://github.com/Kirovez/pyTanFinder) coupled with fluorescence in situ hybridization (FISH), we identified five high copy number tandem repeats (TRs) occupying a long DNA array in the moss genome. The nuclear organization study revealed that two TRs had distinct locations in the moss genome, concentrating in the heterochromatin and knob-rDNA like chromatin bodies. Further genomic, epigenetic and transcriptomic analysis showed that one TR, named PpNATR76, was located in the intergenic spacer (IGS) region and transcribed into long non-coding RNAs (lncRNAs). Several specific features of PpNATR76 lncRNAs make them very similar with the recently discovered human lncRNAs, raising a number of questions for future studies. This work provides new resources for functional studies of satellitome in plants using the model organism P.patens, and describes a list of tandem repeats for further analysis.

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 Unusual de novo Partial Trisomy 17p12p11.2 due to Unbalanced Insertion into 5p13.1 in a Severely Affected Boy

2017 ◽  
Vol 06 (03) ◽  
pp. 165-168 ◽  
Author(s):  
Luis Mendez-Rosado ◽  
Araceli Lantigua ◽  
Juan Galarza ◽  
Ahmed Hamid Al-Rikabi ◽  
Monika Ziegler ◽  
...  
Keyword(s):  
De Novo ◽  
Chromosomal Rearrangements ◽  
Partial Trisomy ◽  
Derivative Chromosome ◽  
Genomic Disorder ◽  
Charcot Marie Tooth Disease ◽  
Dysmorphic Features ◽  
Copy Numbers ◽  
Tooth Disease

AbstractGain of copy numbers can be due to different chromosomal rearrangements such as direct or indirect duplications, translocations, small supernumerary marker chromosomes, or insertions. In a 3-year-old boy with dysmorphic features and developmental delay, chromosome analyses revealed a derivative chromosome 5. Microdissection and reverse fluorescence in situ hybridization identified the in 5p13.1 inserted part as 17p12-p11.2 material. Thus the patient suffered from a rare combination of genomic disorder, that is, Charcot-Marie-Tooth disease type 1A and Potocki-Lupski syndrome. Parental studies indicated that the abnormality was de novo in origin. As the question how this rearrangement arose cannot be answered conclusively, formal genetic counseling is warranted, which includes a discussion regarding the possibility of gonadal mosaicism. In conclusion, this case highlights that chromosome 17p is genetically relatively instable, and thus it can lead to rare chromosomal conditions.

scholarly journals Interstitial Telomeric Repeats Are Rare in Turtles

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 657 ◽  
Author(s):  
Lorenzo Clemente ◽  
Sofia Mazzoleni ◽  
Eleonora Pensabene Bellavia ◽  
Barbora Augstenová ◽  
Markus Auer ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Karyotype Evolution ◽  
Chromosomal Rearrangements ◽  
Telomeric Repeats ◽  
Squamate Reptiles ◽  
Nucleoprotein Complexes ◽  
Interstitial Telomeric Repeats ◽  
Eukaryotic Organisms ◽  
Genomic Regions

Telomeres are nucleoprotein complexes protecting chromosome ends in most eukaryotic organisms. In addition to chromosome ends, telomeric-like motifs can be accumulated in centromeric, pericentromeric and intermediate (i.e., between centromeres and telomeres) positions as so-called interstitial telomeric repeats (ITRs). We mapped the distribution of (TTAGGG)n repeats in the karyotypes of 30 species from nine families of turtles using fluorescence in situ hybridization. All examined species showed the expected terminal topology of telomeric motifs at the edges of chromosomes. We detected ITRs in only five species from three families. Combining our and literature data, we inferred seven independent origins of ITRs among turtles. ITRs occurred in turtles in centromeric positions, often in several chromosomal pairs, in a given species. Their distribution does not correspond directly to interchromosomal rearrangements. Our findings support that centromeres and non-recombining parts of sex chromosomes are very dynamic genomic regions, even in turtles, a group generally thought to be slowly evolving. However, in contrast to squamate reptiles (lizards and snakes), where ITRs were found in more than half of the examined species, and birds, the presence of ITRs is generally rare in turtles, which agrees with the expected low rates of chromosomal rearrangements and rather slow karyotype evolution in this group.

scholarly journals Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dariusz Kadluczka ◽  
Ewa Grzebelus
Keyword(s):  
Wild Species ◽  
Related Species ◽  
Karyotype Evolution ◽  
Chromosomal Distribution ◽  
Closely Related Species ◽  
Chromosomal Structure ◽  
Economic Significance ◽  
Evolutionary Changes ◽  
Outgroup Species

Abstract Background In the course of evolution, chromosomes undergo evolutionary changes; thus, karyotypes may differ considerably among groups of organisms, even within closely related taxa. The genus Daucus seems to be a promising model for exploring the dynamics of karyotype evolution. It comprises some 40 wild species and the cultivated carrot, a crop of great economic significance. However, Daucus species are very diverse morphologically and genetically, and despite extensive research, the taxonomic and phylogenetic relationships between them have still not been fully resolved. Although several molecular cytogenetic studies have been conducted to investigate the chromosomal structure and karyotype evolution of carrot and other Daucus species, detailed karyomorphological research has been limited to carrot and only a few wild species. Therefore, to better understand the karyotype relationships within Daucus, we (1) explored the chromosomal distribution of carrot centromeric repeats (CentDc) in 34 accessions of Daucus and related species by means of fluorescence in situ hybridization (FISH) and (2) performed detailed karyomorphological analysis in 16 of them. Results We determined the genomic organization of CentDc in 26 accessions of Daucus (belonging to both Daucus I and II subclades) and one accession of closely related species. The CentDc repeats were present in the centromeric regions of all chromosomes of 20 accessions (representing 11 taxa). In the other Daucus taxa, the number of chromosome pairs with CentDc signals varied depending on the species, yet their centromeric localization was conserved. In addition, precise chromosome measurements performed in 16 accessions showed the inter- and intraspecific karyological relationships among them. Conclusions The presence of the CentDc repeats in the genomes of taxa belonging to both Daucus subclades and one outgroup species indicated the ancestral status of the repeat. The results of our study provide useful information for further evolutionary, cytotaxonomic, and phylogenetic research on the genus Daucus and may contribute to a better understanding of the dynamic evolution of centromeric satellites in plants.

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