scholarly journals Genome-wide characterization of satellite DNA arrays in a complex plant genome using nanopore reads

2019 ◽  
Author(s):  
Tihana Vondrak ◽  
Laura Ávila Robledillo ◽  
Petr Novák ◽  
Andrea Koblížková ◽  
Pavel Neumann ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats ◽  
Length Distribution ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Satellite Repeat ◽  
Major Satellite ◽  
Satellite Repeats ◽  
Genome Wide

AbstractBackgroundAmplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities.ResultsWe have developed a computational workflow for similarity-based detection and downstream analysis of satellite repeats in individual nanopore reads that led to genome-wide characterization of their properties. Using the satellite DNA-rich legume plantLathyrus sativusas a model, we demonstrated this approach by analyzing eleven major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73x genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of theL. sativuschromosomes, which suggests that these genome regions are favorable for satellite DNA accumulation.ConclusionsThe presented approach proved to be efficient in revealing differences in long-range organization of satellite repeats that can be used to investigate their origin and evolution in the genome.

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.

Fluorescent in situ hybridization and characterization of the SalI family of satellite repeats in the Haliotis L. species (abalone) of the Northeast Pacific

Genome ◽  
2008 ◽  
Vol 51 (8) ◽  
pp. 570-579 ◽  
Author(s):  
Norma Karina Hernández-Ibarra ◽  
Andrew R. Leitch ◽  
Pedro Cruz ◽  
Ana M. Ibarra
Keyword(s):  
Tandem Repeats ◽  
Sequence Divergence ◽  
Satellite Repeat ◽  
Northeast Pacific ◽  
Satellite Repeats ◽  
In The Wild ◽  
High Sequence Conservation ◽  
Heterochromatin Silencing

The SalI satellite repeat previously identified in Haliotis L. (abalone) was thought to be present in H. rufescens and absent in H. fulgens . However, we show here that SalI is also found in H. fulgens and is not useful for screening hybrid individuals bred in aquaculture or occurring naturally in the wild. SalI is a family of predominantly subtelomeric tandemly repeated sequences, and sequenced clones revealed clustering to species and little intraspecific variation. Analysis of SalI sequence divergence between Haliotis species of the Northeast Pacific revealed that evolutionary distances correlate well with bathymetric and latitudinal species distributions. Analysis of the structure of the tandem repeats revealed two regions of high sequence conservation that may contain conserved transcription factor binding sites, a surprise for an apparently “non-coding” tandem repeat. We speculate that these regions might be involved in heterochromatin silencing, perhaps mediated via transcriptional activity and RNA interference. The repeats show substantial differences in their chromosomal distributions, even between individuals of the same species, indicating a dynamic organization of repeats, perhaps mediated via sequence homogenization.

scholarly journals Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Oluchi Aroh ◽  
Kenneth M. Halanych
Keyword(s):  
Deep Sea ◽  
Long Terminal Repeat Retrotransposons ◽  
Marine Organisms ◽  
Model Systems ◽  
Ltr Retrotransposons ◽  
Genome Wide ◽  
Lamellibrachia Luymesi ◽  
Vestimentiferan Tubeworm ◽  
Retrotransposon Activity

Abstract Background Long Terminal Repeat retrotransposons (LTR retrotransposons) are mobile genetic elements composed of a few genes between terminal repeats and, in some cases, can comprise over half of a genome’s content. Available data on LTR retrotransposons have facilitated comparative studies and provided insight on genome evolution. However, data are biased to model systems and marine organisms, including annelids, have been underrepresented in transposable elements studies. Here, we focus on genome of Lamellibrachia luymesi, a vestimentiferan tubeworm from deep-sea hydrocarbon seeps, to gain knowledge of LTR retrotransposons in a deep-sea annelid. Results We characterized LTR retrotransposons present in the genome of L. luymesi using bioinformatic approaches and found that intact LTR retrotransposons makes up about 0.1% of L. luymesi genome. Previous characterization of the genome has shown that this tubeworm hosts several known LTR-retrotransposons. Here we describe and classify LTR retrotransposons in L. luymesi as within the Gypsy, Copia and Bel-pao superfamilies. Although, many elements fell within already recognized families (e.g., Mag, CSRN1), others formed clades distinct from previously recognized families within these superfamilies. However, approximately 19% (41) of recovered elements could not be classified. Gypsy elements were the most abundant while only 2 Copia and 2 Bel-pao elements were present. In addition, analysis of insertion times indicated that several LTR-retrotransposons were recently transposed into the genome of L. luymesi, these elements had identical LTR’s raising possibility of recent or ongoing retrotransposon activity. Conclusions Our analysis contributes to knowledge on diversity of LTR-retrotransposons in marine settings and also serves as an important step to assist our understanding of the potential role of retroelements in marine organisms. We find that many LTR retrotransposons, which have been inserted in the last few million years, are similar to those found in terrestrial model species. However, several new groups of LTR retrotransposons were discovered suggesting that the representation of LTR retrotransposons may be different in marine settings. Further study would improve understanding of the diversity of retrotransposons across animal groups and environments.

Isolation and characterization of tandem repeats in nematode genomes.

2021 ◽  
pp. 240-249
Author(s):  
Philippe Castagnone-Sereno
Keyword(s):  
Case Studies ◽  
Genetic Markers ◽  
Satellite Dna ◽  
Entomopathogenic Nematodes ◽  
Tandem Repeats ◽  
Genomic Resources ◽  
Isolation And Characterization ◽  
Nematode Genomes ◽  
Plant Parasitic

Abstract This chapter provides an overview of the practical methodologies that can be used to identify and characterize the tandem repeats that are most frequently used as genetic markers in nematodes (including plant-parasitic and entomopathogenic nematodes), namely satellite DNA and microsatellites. The objective is not to provide turnkey protocols, but rather to return to the main principles that govern these protocols. Case studies on nematodes will serve to illustrate the point. In that respect, two well-defined situations are to be considered, depending on whether genomic resources for the species under investigation are available or not.

scholarly journals Genome-Wide Characterization of Lectin Receptor Kinases in Saccharum spontaneum L. and Their Responses to Stagonospora tainanensis Infection

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 322
Author(s):  
Zhoutao Wang ◽  
Hui Ren ◽  
Fu Xu ◽  
Guilong Lu ◽  
Wei Cheng ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Saccharum Spontaneum ◽  
Unequal Distribution ◽  
Lectin Receptor ◽  
Gene Sets ◽  
Genome Wide ◽  
Receptor Kinases ◽  
Plant Pathogen Interaction ◽  
Basic Reference

Sugarcane is an important sugar and bioenergy ethanol crop, and the hyperploidy has led to stagnant progress in sugarcane genome decipherment, which also hindered the genome-wide analyses of versatile lectin receptor kinases (LecRKs). The published genome of Saccharum spontaneum, one of the two sugarcane ancestor species, enables us to study the characterization of LecRKs and their responses to sugarcane leaf blight (SLB) triggered by Stagonospora tainanensis. A total of 429 allelic and non-allelic LecRKs, which were classified into evolved independently three types according to signal domains and phylogeny, were identified based on the genome. Regarding those closely related LecRKs in the phylogenetic tree, their motifs and exon architectures of representative L- and G-types were similar or identical. LecRKs showed an unequal distribution on chromosomes and more G-type tandem repeats may come from the gene expansion. Comparing the differentially expressed LecRKs (DELs) in response to SLB in sugarcane hybrid and ancestor species S. spontaneum, we found that the DEL number in the shared gene sets was highly variable among each sugarcane accession, which indicated that the expression dynamics of LecRKs in response to SLB were quite different between hybrids and particularly between sugarcane hybrid and S. spontaneum. In addition, C-type LecRKs may participate in metabolic processes of plant–pathogen interaction, mainly including pathogenicity and plant resistance, indicating their putative roles in sugarcane responses to SLB infection. The present study provides a basic reference and global insight into the further study and utilization of LecRKs in plants.

scholarly journals Evolutionary adaptability linked to length variation in short genic tandem repeats

2018 ◽  
Author(s):  
William B Reinar ◽  
Jonfinn B Knutsen ◽  
Sissel Jentoft ◽  
Ole K Tørresen ◽  
Melinka A Butenko ◽  
...  
Keyword(s):  
Protein Function ◽  
Tandem Repeats ◽  
Phenotypic Traits ◽  
Length Variation ◽  
Interaction Sites ◽  
Genome Wide ◽  
Mutational Hotspots ◽  
Intergenic Regions ◽  
Gene Expression Levels

AbstractThere is increasing evidence that short tandem repeats (STRs) – mutational hotspots present in genes and in intergenic regions throughout most genomes – may influence gene and protein function and consequently affect the phenotype of an organism. However, the overall importance of STRs and their standing genetic variation within a population, e.g. if and how they facilitate evolutionary change and local adaptation, is still debated. Through genome-wide characterization of STRs in over a thousand wild Arabidopsis thaliana accessions we demonstrate that STRs display significant variation in length across the species’ geographical distribution. We find that length variants are correlated with environmental conditions, key adaptive phenotypic traits as well as gene expression levels. Further, we show that coding STRs are overrepresented in putative protein interaction sites. Taken together, our results suggest that these hypervariable loci play a major role in facilitating adaptation in plants, and due to the ubiquitous presence of STRs throughout the tree of life, similar roles in other organisms are likely.

scholarly journals Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 527
Author(s):  
Nusrat Sultana ◽  
Gerhard Menzel ◽  
Tony Heitkam ◽  
Kenji K. Kojima ◽  
Weidong Bao ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Sequence Similarity ◽  
Diploid Species ◽  
Vaccinium Corymbosum ◽  
Satellite Repeat ◽  
Comprehensive Overview ◽  
Vaccinium Uliginosum ◽  
Satellite Repeats ◽  
The Impact

Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well as the tetraploid species Vaccinium corymbosum and Vaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid V. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in Vaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.

scholarly journals Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats

2019 ◽  
Vol 101 (2) ◽  
pp. 484-500 ◽  
Author(s):  
Tihana Vondrak ◽  
Laura Ávila Robledillo ◽  
Petr Novák ◽  
Andrea Koblížková ◽  
Pavel Neumann ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats

scholarly journals Distinct Regulation of the Expression of Satellite DNAs in the Beetle Tribolium castaneum

2020 ◽  
Vol 22 (1) ◽  
pp. 296
Author(s):  
Antonio Sermek ◽  
Isidoro Feliciello ◽  
Đurđica Ugarković
Keyword(s):  
Heat Stress ◽  
Tribolium Castaneum ◽  
Satellite Dna ◽  
Centromeric Heterochromatin ◽  
Satellite Dnas ◽  
Major Satellite ◽  
Satellite Repeats ◽  
Satellite Rnas ◽  
H3k9me3 Level ◽  
A Minor

In the flour beetle, Tribolium castaneum (peri)centromeric heterochromatin is mainly composed of a major satellite DNA TCAST1 interspersed with minor satellites. With the exception of heterochromatin, clustered satellite repeats are found dispersed within euchromatin. In order to uncover a possible satellite DNA function within the beetle genome, we analysed the expression of the major TCAST1 and a minor TCAST2 satellite during the development and upon heat stress. The results reveal that TCAST1 transcription was strongly induced at specific embryonic stages and upon heat stress, while TCAST2 transcription is stable during both processes. TCAST1 transcripts are processed preferentially into piRNAs during embryogenesis and into siRNAs during later development, contrary to TCAST2 transcripts, which are processed exclusively into piRNAs. In addition, increased TCAST1 expression upon heat stress is accompanied by the enrichment of the silent histone mark H3K9me3 on the major satellite, while the H3K9me3 level at TCAST2 remains unchanged. The transcription of the two satellites is proposed to be affected by the chromatin state: heterochromatin and euchromatin, which are assumed to be the prevalent sources of TCAST1 and TCAST2 transcripts, respectively. In addition, distinct regulation of the expression might be related to diverse roles that major and minor satellite RNAs play during the development and stress response.

scholarly journals Epigenetic features improve TALE target prediction

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Annett Erkes ◽  
Stefanie Mücke ◽  
Maik Reschke ◽  
Jens Boch ◽  
Jan Grau
Keyword(s):  
Host Plant ◽  
Tandem Repeats ◽  
Target Prediction ◽  
Ground Truth ◽  
Chromatin Accessibility ◽  
Plant Genome ◽  
Host Cells ◽  
Transcription Activator ◽  
Genome Wide ◽  
Plant Genes

Abstract Background The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box. Results To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets. Conclusions Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs.

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