Molecular Composition of Heterochromatin and Its Contribution to Chromosome Variation in the Microtus thomasi/Microtus atticus Species Complex

The voles of the Microtus thomasi/M. atticus species complex demonstrate a remarkable variability in diploid chromosomal number (2n = 38–44 chromosomes) and sex chromosome morphology. In the current study, we examined by in situ hybridization the topology of four satellite DNA motifs (Msat-160, Mth-Alu900, Mth-Alu2.2, TTAGGG telomeric sequences) and two transposons (LINE, SINE) on the karyotypes of nine chromosome races (i.e., populations with unique cytogenetic traits) of Microtus thomasi, and two chromosomal races of M. atticus. According to the topology of the repetitive DNA motifs, we were able to identify six types of biarmed chromosomes formed from either Robertsonian or/and tandem fusions. In addition, we identified 14 X chromosome variants and 12 Y chromosome variants, and we were able to reconstruct their evolutionary relations, caused mainly by distinct mechanisms of amplification of repetitive DNA elements, including the telomeric sequences. Our study used the model of the Microtus thomasi/M. atticus species complex to explore how repetitive centromeric content can alter from chromosomal rearrangements and can shape the morphology of sex chromosomes, resulting in extensive inter-species cytogenetic variability.

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Genome Organization and Evolution of the AVR-Pita Avirulence Gene Family in the Magnaporthe grisea Species Complex

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-21-5-0658 ◽

2008 ◽

Vol 21 (5) ◽

pp. 658-670 ◽

Cited By ~ 72

Author(s):

Chang Hyun Khang ◽

Sook-Young Park ◽

Yong-Hwan Lee ◽

Barbara Valent ◽

Seogchan Kang

Keyword(s):

Gene Family ◽

Repetitive Dna ◽

Species Complex ◽

Magnaporthe Grisea ◽

Fungal Species ◽

Avirulence Gene ◽

Genomic Context ◽

Dna Elements ◽

Avr Gene ◽

Repetitive Dna Elements

The avirulence (AVR) gene AVR-Pita in Magnaporthe oryzae prevents the fungus from infecting rice cultivars containing the resistance gene Pi-ta. A survey of isolates of the M. grisea species complex from diverse hosts showed that AVR-Pita is a member of a gene family, which led us to rename it to AVR-Pita1. Avirulence function, distribution, and genomic context of two other members, named AVR-Pita2 and AVR-Pita3, were characterized. AVR-Pita2, but not AVR-Pita3, was functional as an AVR gene corresponding to Pi-ta. The AVR-Pita1 and AVR-Pita2 genes were present in isolates of both M. oryzae and M. grisea, whereas the AVR-Pita3 gene was present only in isolates of M. oryzae. Orthologues of members of the AVR-Pita family could not be found in any fungal species sequenced to date, suggesting that the gene family may be unique to the M. grisea species complex. The genomic context of its members was analyzed in eight strains. The AVR-Pita1 and AVR-Pita2 genes in some isolates appeared to be located near telomeres and flanked by diverse repetitive DNA elements, suggesting that frequent deletion or amplification of these genes within the M. grisea species complex might have resulted from recombination mediated by repetitive DNA elements.

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Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

BMC Biology ◽

10.1186/s12915-020-00925-x ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Octavio M. Palacios-Gimenez ◽

Julia Koelman ◽

Marc Palmada-Flores ◽

Tessa M. Bradford ◽

Karl K. Jones ◽

...

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

Repetitive Dna ◽

Dna Sequences ◽

Satellite Dna ◽

Species Complex ◽

Repetitive Dna Sequences ◽

Dna Repeats ◽

Large Genome ◽

Chromosomal Races

Abstract Background Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution. Results We obtained linked-read genome assemblies of 2.73–3.27 Gb from estimated genome sizes of 4.26–5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314–463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. Conclusion This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.

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Too much too many: comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

10.1101/2020.08.22.247130 ◽

2020 ◽

Author(s):

Octavio M. Palacios-Gimenez ◽

Julia Koelman ◽

Marc Palmada Flores ◽

Tessa M. Bradford ◽

Karl K. Jones ◽

...

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

Repetitive Dna ◽

Dna Sequences ◽

Satellite Dna ◽

Species Complex ◽

Rapid Evolution ◽

Dna Repeats ◽

Large Genome ◽

Chromosomal Races

BackgroundThe repeatome, the collection of repetitive DNA sequences represented by transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), is found in high proportion in organisms across the tree of life. Grasshoppers have large genomes (average 9 Gb), containing large amounts of repetitive DNA which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of the repeatome and its contribution to genome evolution, in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex.ResultsWe obtained linked-read genome assemblies of 2.73-3.27 Gb from estimated genome sizes of 4.26-5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far (the largest being two locust grasshoppers). Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs constituting 66 to 75 % per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314-463 Mb per assembly), indicating that their large genome size is likely due to similar rates of TE accumulation across the four races. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a repertoire of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex.ConclusionIn-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Although the TE and satDNA repertoires were rather similar between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.

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Comparative cytogenetics among Leporinus friderici and Leporellus vittatus populations (Characiformes, Anostomidae): focus on repetitive DNA elements

Comparative Cytogenetics ◽

10.3897/compcytogen.v13i2.33764 ◽

2019 ◽

Vol 13 (2) ◽

pp. 105-120 ◽

Cited By ~ 3

Author(s):

Thais Aparecida Dulz ◽

Carla Andrea Lorscheider ◽

Viviane Demetrio Nascimento ◽

Rafael Bueno Noleto ◽

Orlando Moreira-Filho ◽

...

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Chromosomal Rearrangements ◽

5S Rdna ◽

Neotropical Fish ◽

Comparative Cytogenetics ◽

Fish Family ◽

Telomere Sequence ◽

Dna Elements ◽

Chromosomal Changes

Anostomidae are a neotropical fish family rich in number of species. Cytogenetically, they show a conserved karyotype with 2n = 54 chromosomes, although they present intraspecific/interspecific variations in the number and chromosomal location of repetitive DNA sequences. The aim of the present study was to perform a comparative description of the karyotypes of two populations of Leporinusfriderici Bloch, 1794 and three populations of Leporellusvittatus Valenciennes, 1850. We used conventional cytogenetic techniques allied to fluorescence in situ hybridization, using 18S ribosomal DNA (rDNA) and 5S rDNA, a general telomere sequence for vertebrates (TTAGGG)n and retrotransposon (RTE) Rex1 probes. The anostomids in all studied populations presented 2n = 54 chromosomes, with a chromosome formula of 32m + 22sm for L.friderici and 28m + 26sm for L.vittatus. Variations in the number and location of the 5S and 18S rDNA chromosomal sites were observed between L.friderici and L.vittatus populations and species. Accumulation of Rex1 was observed in the terminal region of most chromosomes in all populations, and telomere sequences were located just on all ends of the 54 chromosomes in all populations. The intraspecific and intergeneric chromosomal changes occurred in karyotype differentiation, indicating that minor chromosomal rearrangements had present in anostomid species diversification.

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DNA methylation in satellite repeats disorders

Essays in Biochemistry ◽

10.1042/ebc20190028 ◽

2019 ◽

Vol 63 (6) ◽

pp. 757-771 ◽

Cited By ~ 4

Author(s):

Claire Francastel ◽

Frédérique Magdinier

Keyword(s):

Dna Methylation ◽

Human Genome ◽

Repetitive Dna ◽

Dna Sequences ◽

Satellite Repeats ◽

Tremendous Progress ◽

Genes Encoding ◽

Dna Elements ◽

Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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Chromosomal Analysis in Crotophaga ani (Aves, Cuculiformes) Reveals Extensive Genomic Reorganization and an Unusual Z-Autosome Robertsonian Translocation

Cells ◽

10.3390/cells10010004 ◽

2020 ◽

Vol 10 (1) ◽

pp. 4

Author(s):

Rafael Kretschmer ◽

Ricardo José Gunski ◽

Analía del Valle Garnero ◽

Thales Renato Ochotorena de Freitas ◽

Gustavo Akira Toma ◽

...

Keyword(s):

Robertsonian Translocation ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Rare Event ◽

Chromosome Morphology ◽

Z Chromosome ◽

Molecular Cytogenetic ◽

Intrachromosomal Rearrangements ◽

Genomic Reorganization

Although cytogenetics studies in cuckoos (Aves, Cuculiformes) have demonstrated an interesting karyotype variation, such as variations in the chromosome morphology and diploid number, their chromosome organization and evolution, and relation with other birds are poorly understood. Hence, we combined conventional and molecular cytogenetic approaches to investigate chromosome homologies between chicken and the smooth-billed ani (Crotophaga ani). Our results demonstrate extensive chromosome reorganization in C. ani, with interchromosomal rearrangements involving macro and microchromosomes. Intrachromosomal rearrangements were observed in some macrochromosomes, including the Z chromosome. The most evolutionary notable finding was a Robertsonian translocation between the microchromosome 17 and the Z chromosome, a rare event in birds. Additionally, the simple short repeats (SSRs) tested here were preferentially accumulated in the microchromosomes and in the Z and W chromosomes, showing no relationship with the constitutive heterochromatin regions, except in the W chromosome. Taken together, our results suggest that the avian sex chromosome is more complex than previously postulated and revealed the role of microchromosomes in the avian sex chromosome evolution, especially cuckoos.

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A repetitive DNA element, associated with telomeric sequences in Drosophila melanogaster, contains open reading frames

Chromosoma ◽

10.1007/bf00352288 ◽

1992 ◽

Vol 102 (1) ◽

pp. 32-40 ◽

Cited By ~ 26

Author(s):

Olga N. Danilevskaya ◽

Dmitri A. Petrov ◽

Maria N. Pavlova ◽

Akihiko Koga ◽

Elena V. Kurenova ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Repetitive Dna ◽

Open Reading Frames ◽

Telomeric Sequences ◽

Reading Frames

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Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽

10.1093/genetics/162.3.1435 ◽

2002 ◽

Vol 162 (3) ◽

pp. 1435-1444 ◽

Cited By ~ 1

Author(s):

Robert M Stupar ◽

Junqi Song ◽

Ahmet L Tek ◽

Zhukuan Cheng ◽

Fenggao Dong ◽

...

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Tandem Repeats ◽

Intergenic Spacer ◽

Pericentromeric Heterochromatin ◽

Dna Repeats ◽

Solanum Bulbocastanum ◽

Origin And Evolution ◽

Potato Genome ◽

Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

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