Evolution of genome structure in the Drosophila simulans species complex

ABSTRACTThe rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 years ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster due to structural divergence—twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, while the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.

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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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Long-Term Rasamsonia argillacea Complex Species Colonization Revealed by PCR Amplification of Repetitive DNA Sequences in Cystic Fibrosis Patients

Journal of Clinical Microbiology ◽

10.1128/jcm.01462-16 ◽

2016 ◽

Vol 54 (11) ◽

pp. 2804-2812 ◽

Cited By ~ 10

Author(s):

Abdelmounaim Mouhajir ◽

Olivier Matray ◽

Sandrine Giraud ◽

Laurent Mély ◽

Christophe Marguet ◽

...

Keyword(s):

Cystic Fibrosis ◽

Repetitive Dna ◽

Dna Sequences ◽

Species Complex ◽

Pcr Amplification ◽

Patient Specific ◽

Molecular Evidence ◽

Repetitive Dna Sequences ◽

Complex Species ◽

Content Type

The aim of this work was to document molecular epidemiology of Rasamsonia argillacea species complex isolates from cystic fibrosis (CF) patients. In this work, 116 isolates belonging to this species complex and collected from 26 CF patients and one patient with chronic granulomatous disease were characterized using PCR amplification assays of repetitive DNA sequences and electrophoretic separation of amplicons (rep-PCR). Data revealed a clustering consistent with molecular species identification. A single species was recovered from most patients. Rasamsonia aegroticola was the most common species, followed by R. argillacea sensu stricto and R. piperina , while R. eburnea was not identified. Of 29 genotypes, 7 were shared by distinct patients while 22 were patient specific. In each clinical sample, most isolates exhibited an identical genotype. Genotyping of isolates recovered from sequential samples from the same patient confirmed the capability of R. aegroticola and R. argillacea isolates to chronically colonize the airways. A unique genotype was recovered from two siblings during a 6-month period. In the other cases, a largely dominant genotype was detected. Present results which support the use of rep-PCR for both identification and genotyping for the R. argillacea species complex provide the first molecular evidence of chronic airway colonization by these fungi in CF patients.

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Organization and Chromosomal Distribution of Histone Genes and Transposable Rex Elements in the Genome of Astyanax bockmanni (Teleostei, Characiformes)

Cytogenetic and Genome Research ◽

10.1159/000441613 ◽

2015 ◽

Vol 146 (4) ◽

pp. 311-318 ◽

Cited By ~ 7

Author(s):

Sandro N. Daniel ◽

Manolo Penitente ◽

Duílio M.Z.A. Silva ◽

Diogo T. Hashimoto ◽

Daniela C. Ferreira ◽

...

Keyword(s):

Transposable Elements ◽

Dna Sequences ◽

Repetitive Sequences ◽

B Chromosome ◽

Gene Probe ◽

Histone Genes ◽

Chromosomal Distribution ◽

Evolutionary Mechanisms ◽

Small Sites ◽

Eukaryotic Organisms

An important feature of eukaryotic organisms is the number of different repetitive DNA sequences in their genome, a feature not observed in prokaryotes. These sequences are considered to be important components for understanding evolutionary mechanisms and the karyotypic differentiation processes. Thus, we aimed to physically map the histone genes and transposable elements of the Rex family in 6 fish populations of Astyanax bockmanni. FISH results using a histone H1 gene probe showed fluorescent clusters in 2 chromosome pairs in all 6 samples analyzed. In contrast, FISH with a histone H3 probe showed conspicuous blocks in 4 chromosomes in 5 of the 6 populations analyzed. The sixth population revealed 7 chromosomes marked with this probe. Probes for the transposable elements Rex1 and Rex6 showed small sites dispersed on most chromosomes of the 6 populations, and the Rex3 element is located in a big block concentrated in only 1 acrocentric chromosome of 2 populations. As for the other populations, a Rex3 probe showed large blocks in more than 1 chromosome. Fish from Alambari and Campo Novo Stream have Rex3 elements dispersed along most of the chromosomes. Additionally, the conspicuous signals of Rex1, Rex3, and Rex6 were identified in the acrocentric B microchromosome of A. bockmanni found only in individuals of the Alambari River. Thus, we believe that different mechanisms drive the spread of repetitive sequences among the populations analyzed, which appear to be organized differently in the genome of A. bockmanni. The presence of transposable elements in the B chromosome also suggests that these sequences could play a role in the origin and maintenance of the supernumerary element in the genome of this species.

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Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing

Cytogenetic and Genome Research ◽

10.1159/000506531 ◽

2020 ◽

Vol 160 (3) ◽

pp. 141-147 ◽

Cited By ~ 1

Author(s):

Marcelo J. da Silva ◽

Raquel Fogarin Destro ◽

Thiago Gazoni ◽

Hideki Narimatsu ◽

Paulo S. Pereira dos Santos ◽

...

Keyword(s):

Repetitive Dna ◽

Sex Chromosomes ◽

Dna Sequences ◽

Satellite Dna ◽

Sex Chromosome ◽

Repetitive Sequences ◽

Centromere Function ◽

Sex Chromosome System ◽

First Time ◽

Eukaryotic Genomes

Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.

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A subtelomeric satellite DNA family isolated from the genome of the dioecious plant Silene latifolia

Genome ◽

10.1139/g98-156 ◽

1999 ◽

Vol 42 (3) ◽

pp. 442-446 ◽

Cited By ~ 12

Author(s):

M A Garrido-Ramos ◽

R de la Herrán ◽

M Ruiz Rejón ◽

C Ruiz Rejón

Keyword(s):

Sex Chromosomes ◽

Dna Sequences ◽

Satellite Dna ◽

Consensus Sequence ◽

Repetitive Sequences ◽

Restriction Enzymes ◽

Repeat Sequence ◽

Silene Latifolia ◽

Telomere Repeat ◽

Significant Length

In an ongoing effort to trace the evolution of the sex chromosomes of Silene latifolia, we have searched for the existence of repetitive sequences specific to these chromosomes in the genome of this species by direct isolation from low-melting agarose gels of satellite DNA bands generated by digestion with restriction enzymes. Five monomeric units belonging to a highly repetitive family isolated from Silene latifolia, the SacI family, have been cloned and characterized. The consensus sequence of the repetitive units is 313 bp in length (however, high variability exists for monomer length variants) and 52.9% in AT. Repeating units are tandemly arranged at the subtelomeric regions of the chromosomes in this species. The sequence does not possess direct or inverted sequences of significant length, but short direct repeats are scattered throughout the monomer sequence. Several short sequence motives resemble degenerate monomers of the telomere repeat sequence of plants (TTTAGGG), confirming a tight association between this subtelomeric satellite DNA and the telomere repeats. Our approach in this work confirms that SacI satellite DNA sequences are among the most abundant in the genome of S. latifolia and, on the other hand, that satellite DNA sequences specific of sex chromosomes are absent in this species. This agrees with a sex determination system less cytogenetically diverged from a bisexual state than the system present in other plant species, such as R. acetosa, or at least a lesser degree of differentiation between the sex chromosomes of S. latifolia and the autosomes.Key words: satellite DNA, sex chromosomes, Silene latifolia, subtelomeric sequences.

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Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species

Genes ◽

10.3390/genes11020170 ◽

2020 ◽

Vol 11 (2) ◽

pp. 170 ◽

Cited By ~ 1

Author(s):

Marcelo R. J. Castro ◽

Clément Goubert ◽

Fernando A. Monteiro ◽

Cristina Vieira ◽

Claudia M. A. Carareto

Keyword(s):

New Species ◽

Genetic Variability ◽

Transposable Elements ◽

Species Complex ◽

De Novo ◽

Repetitive Sequences ◽

Sudden Expansion ◽

Additional Species ◽

Original Genome ◽

Evolutionary Trajectories

Transposable elements (TEs) are widely distributed repetitive sequences in the genomes across the tree of life, and represent an important source of genetic variability. Their distribution among genomes is specific to each lineage. A phenomenon associated with this feature is the sudden expansion of one or several TE families, called bursts of transposition. We previously proposed that bursts of the Mariner family (DNA transposons) contributed to the speciation of Rhodnius prolixus Stål, 1859. This hypothesis motivated us to study two additional species of the R. prolixus complex: Rhodnius montenegrensis da Rosa et al., 2012 and Rhodnius marabaensis Souza et al., 2016, together with a new, de novo annotation of the R. prolixus repeatome using unassembled short reads. Our analysis reveals that the total amount of TEs present in Rhodnius genomes (19% to 23.5%) is three to four times higher than that expected based on the original quantifications performed for the original genome description of R. prolixus. We confirm here that the repeatome of the three species is dominated by Class II elements of the superfamily Tc1-Mariner, as well as members of the LINE order (Class I). In addition to R. prolixus, we also identified a recent burst of transposition of the Mariner family in R. montenegrensis and R. marabaensis, suggesting that this phenomenon may not be exclusive to R. prolixus. Rather, we hypothesize that whilst the expansion of Mariner elements may have contributed to the diversification of the R. prolixus-R. robustus species complex, the distinct ecological characteristics of these new species did not drive the general evolutionary trajectories of these TEs.

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Satellite DNA induces unstable expression of the adjacent herpes simplex virus tk gene cotransfected in mouse cells.

Molecular and Cellular Biology ◽

10.1128/mcb.8.3.1336 ◽

1988 ◽

Vol 8 (3) ◽

pp. 1336-1344 ◽

Cited By ~ 5

Author(s):

D Talarico ◽

A F Peverali ◽

E Ginelli ◽

R Meneveri ◽

C Mondello ◽

...

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Dna Sequences ◽

Satellite Dna ◽

Repetitive Sequences ◽

Metaphase Chromosomes ◽

Highly Repetitive Dna ◽

Cellular Dna ◽

Mouse Satellite Dna ◽

Simplex Virus

To study the influence of clustered highly repetitive DNA sequences on the expression of adjacent genes, LTK- cells were cotransfected with the herpes simplex virus thymidine kinase (tk) gene and mouse satellite DNA. TK+ transformants containing a few copies of the tk genes flanked by satellite DNA were isolated. In situ hybridization on the metaphase chromosomes indicated that in each cell line the TK sequences resided at a single chromosomal site and that integration occurred preferentially into regions of the cellular DNA rich in highly repetitive sequences. The prominent feature of these cell lines was their phenotypic instability. Suppression and reexpression of the tk gene occurred at high frequency (greater than 3%) and did not correlate with any significant change in the organization of foreign DNA or with the presence of selective agents. These results indicate that satellite DNA, the major component of constitutive heterochromatin, may influence the expression of adjacent genes by affecting the chromatin structure.

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Transposable elements in individual genotypes of Drosophila simulans

10.1101/781419 ◽

2019 ◽

Author(s):

Sarah Signor

Keyword(s):

Transposable Elements ◽

Transposable Element ◽

Dna Sequences ◽

Copy Number ◽

Natural Populations ◽

Population Level ◽

Drosophila Simulans ◽

Mobile Dna ◽

Open Question ◽

Number Of Individuals

AbstractTransposable elements are mobile DNA sequences that are able to copy themselves within a host’s genome. Within insects they often make up a substantial proportion of the genome. While they are the subject of intense research, often times when copy number is estimated it is estimated only at the population level, or in a limited number of individuals within a population. However, an important aspect of transposable element spread is the variance between individuals in activity. Do transposable elements accumulate at different rates in different genetic backgrounds? Using two populations of Drosophila simulans from California and Africa I estimated transposable element copy number in individual genotypes. Some active transposable elements seem to be a property of the species, while others of the populations. I find that in addition to population level differences in transposable element load certain genotypes accumulate transposable elements at a much higher rate than others. Most likely active transposable elements are fairly rare, and were inherited only by specific genotypes that were used to create the inbred lines. Whether or not this reflects dynamics in natural populations, where transposable elements may accumulate in specific genotypes and maintain themselves in the population rather than being active at low levels population wide, is an open question.

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Evolutionary diversification of satellite DNA sequences from Leymus (Poaceae: Triticeae)

Genome ◽

10.1139/g09-013 ◽

2009 ◽

Vol 52 (4) ◽

pp. 381-390 ◽

Cited By ~ 8

Author(s):

K. Anamthawat-Jónsson ◽

T. Wenke ◽

Æ. Th. Thórsson ◽

S. Sveinsson ◽

F. Zakrzewski ◽

...

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Cytosine Methylation ◽

Repetitive Sequences ◽

Grass Species ◽

Evolutionary Diversification ◽

Plasmid Library ◽

Genomic Relationships ◽

Leymus Racemosus ◽

Leymus Triticoides

The genus Leymus (lymegrass) comprises about 30 polyploid, perennial, temperate grass species in the tribe Triticeae (family Poaceae). Previous studies indicated a large diversity in the Leymus genome, and therefore, the aim of this study was to isolate new repetitive DNA sequences that can be used for differentiating Leymus species and elucidating their genomic relationships. A C0t-1 DNA plasmid library was generated from genomic DNA of American tetraploid species Leymus triticoides . A family of highly repetitive satellite DNA sequences, designated Lt1, was obtained from this library. The Lt1 family consisted of 380 bp SacI repeating units arranging in tandem arrays. A 120 bp MspI subfamily was discovered within this family, indicating that cytosine methylation may have played an important role in the evolution of satellite sequences. The Lt1 satellite was localized in the subtelomeric heterochromatic blocks of L. triticoides chromosomes, which are present on all chromosomes and often on both arms. The Lt1 sequences are abundant in L. triticoides but absent in its closely related species Leymus racemosus . Significant homology was found between the Lt1 family and numerous repetitive sequences from Poaceae species, indicating that the Lt1 is an ancient family of tandemly repeated sequences in grasses.

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