scholarly journals The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA

2021 ◽  
Vol 11 ◽  
Author(s):  
Ljudevit Luka Boštjančić ◽  
Lena Bonassin ◽  
Lucija Anušić ◽  
Leona Lovrenčić ◽  
Višnja Besendorfer ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Satellite Dna ◽  
Chromosomal Evolution ◽  
Repetitive Elements ◽  
Centromeric Heterochromatin ◽  
Dna Repeats ◽  
Satellite Repeats ◽  
Interstitial Telomeric Repeats ◽  
Low Coverage ◽  
First Time

Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/Gypsy retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in P. leptodactylus. The genome of P. leptodactylus is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some P. leptodactylus chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in P. leptodactylus. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the P. leptodactylus genome.

scholarly journals Correction to: low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Vanessa Carvalho Cayres Pamponét ◽  
Margarete Magalhães Souza ◽  
Gonçalo Santos Silva ◽  
Fabienne Micheli ◽  
Cláusio Antônio Ferreira de Melo ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Repetitive Dna ◽  
Satellite Dna ◽  
Dna Analysis ◽  
Passiflora Edulis ◽  
Passiflora Edulis Sims ◽  
Low Coverage

Satellite DNA in Plants: More than Just Rubbish

2015 ◽  
Vol 146 (2) ◽  
pp. 153-170 ◽  
Author(s):  
Manuel A. Garrido-Ramos
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Dna Repeats ◽  
Satellite Dnas ◽  
Factors Affecting ◽  
Functional Roles ◽  
Tandem Repeat Sequences ◽  
Satellite Repeats ◽  
History Of ◽  
Main Components

For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

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

BMC Biology ◽  
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.

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

2020 ◽  
Vol 160 (3) ◽  
pp. 141-147 ◽  
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.

scholarly journals Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin

2020 ◽  
Vol 12 (11) ◽  
pp. 2125-2138
Author(s):  
Isidoro Feliciello ◽  
Željka Pezer ◽  
Dušan Kordiš ◽  
Branka Bruvo Mađarić ◽  
Đurđica Ugarković
Keyword(s):  
Satellite Dna ◽  
Evolutionary History ◽  
Genomic Sequence ◽  
Sequence Divergence ◽  
Dna Repeats ◽  
Alpha Satellite ◽  
Alpha Satellite Dna ◽  
Satellite Repeats ◽  
Number Variation ◽  
History Of

Abstract Major human alpha satellite DNA repeats are preferentially assembled within (peri)centromeric regions but are also dispersed within euchromatin in the form of clustered or short single repeat arrays. To study the evolutionary history of single euchromatic human alpha satellite repeats (ARs), we analyzed their orthologous loci across the primate genomes. The continuous insertion of euchromatic ARs throughout the evolutionary history of primates starting with the ancestors of Simiformes (45–60 Ma) and continuing up to the ancestors of Homo is revealed. Once inserted, the euchromatic ARs were stably transmitted to the descendant species, some exhibiting copy number variation, whereas their sequence divergence followed the species phylogeny. Many euchromatic ARs have sequence characteristics of (peri)centromeric alpha repeats suggesting heterochromatin as a source of dispersed euchromatic ARs. The majority of euchromatic ARs are inserted in the vicinity of other repetitive elements such as L1, Alu, and ERV or are embedded within them. Irrespective of the insertion context, each AR insertion seems to be unique and once inserted, ARs do not seem to be subsequently spread to new genomic locations. In spite of association with (retro)transposable elements, there is no indication that such elements play a role in ARs proliferation. The presence of short duplications at most of ARs insertion sites suggests site-directed recombination between homologous motifs in ARs and in the target genomic sequence, probably mediated by extrachromosomal circular DNA, as a mechanism of spreading within euchromatin.

scholarly journals Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species

2021 ◽  
Vol 22 (11) ◽  
pp. 6052
Author(s):  
Eugenia E. Montiel ◽  
Francisco Panzera ◽  
Teresa Palomeque ◽  
Pedro Lorite ◽  
Sebastián Pita
Keyword(s):  
Chagas Disease ◽  
Satellite Dna ◽  
Rhodnius Prolixus ◽  
Triatoma Infestans ◽  
Repeated Dna ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Disease Vector ◽  
Low Coverage ◽  
First Time

The triatomine Rhodnius prolixus is the main vector of Chagas disease in countries such as Colombia and Venezuela, and the first kissing bug whose genome has been sequenced and assembled. In the repetitive genome fraction (repeatome) of this species, the transposable elements represented 19% of R. prolixus genome, being mostly DNA transposon (Class II elements). However, scarce information has been published regarding another important repeated DNA fraction, the satellite DNA (satDNA), or satellitome. Here, we offer, for the first time, extended data about satellite DNA families in the R. prolixus genome using bioinformatics pipeline based on low-coverage sequencing data. The satellitome of R. prolixus represents 8% of the total genome and it is composed by 39 satDNA families, including four satDNA families that are shared with Triatoma infestans, as well as telomeric (TTAGG)n and (GATA)n repeats, also present in the T. infestans genome. Only three of them exceed 1% of the genome. Chromosomal hybridization with these satDNA probes showed dispersed signals over the euchromatin of all chromosomes, both in autosomes and sex chromosomes. Moreover, clustering analysis revealed that most abundant satDNA families configured several superclusters, indicating that R. prolixus satellitome is complex and that the four most abundant satDNA families are composed by different subfamilies. Additionally, transcription of satDNA families was analyzed in different tissues, showing that 33 out of 39 satDNA families are transcribed in four different patterns of expression across samples.

scholarly journals Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1707
Author(s):  
Syed Farhan Ahmad ◽  
Worapong Singchat ◽  
Thitipong Panthum ◽  
Kornsorn Srikulnath
Keyword(s):  
Repetitive Dna ◽  
Repetitive Elements ◽  
Model Systems ◽  
Satellite Repeats ◽  
Evolutionary Features ◽  
Dna Elements ◽  
Genomic Repeats ◽  
The Impact ◽  
Repetitive Dna Elements

The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.

scholarly journals The B Chromosomes of Prochilodus lineatus (Teleostei, Characiformes) Are Highly Enriched in Satellite DNAs

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1527
Author(s):  
José Henrique Forte Stornioli ◽  
Caio Augusto Gomes Goes ◽  
Rodrigo Milan Calegari ◽  
Rodrigo Zeni dos Santos ◽  
Leonardo Moura Giglio ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Fish Species ◽  
Satellite Dna ◽  
B Chromosomes ◽  
Entire Population ◽  
Satellite Dnas ◽  
Prochilodus Lineatus ◽  
Supernumerary Chromosomes ◽  
Morphological Variants ◽  
First Time

B or supernumerary chromosomes are dispensable elements that are widely present in numerous eukaryotes. Due to their non-recombining nature, there is an evident tendency for repetitive DNA accumulation in these elements. Thus, satellite DNA plays an important role in the evolution and diversification of B chromosomes and can provide clues regarding their origin. The characiform Prochilodus lineatus was one of the first discovered fish species bearing B chromosomes, with all populations analyzed so far showing one to nine micro-B chromosomes and exhibiting at least three morphological variants (Ba, Bsm, and Bm). To date, a single satellite DNA is known to be located on the B chromosomes of this species, but no information regarding the differentiation of the proposed B-types is available. Here, we characterized the satellitome of P. lineatus and mapped 35 satellite DNAs against the chromosomes of P. lineatus, of which six were equally located on all B-types and this indicates a similar genomic content. In addition, we describe, for the first time, an entire population without B chromosomes.

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