scholarly journals Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan Filée ◽  
Sarah Farhat ◽  
Dominique Higuet ◽  
Laure Teysset ◽  
Dominique Marie ◽  
...  
Keyword(s):  
Transposable Elements ◽  
High Throughput Sequencing ◽  
Comparative Genomic ◽  
Ltr Retrotransposon ◽  
Genomic Evolution ◽  
Genome Wide ◽  
Genomic Analyses ◽  
Different Types ◽  
Evolutionary Success ◽  
Low Coverage

Abstract Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades.

scholarly journals Discovery and comparative genomic analysis of elk circovirus (ElkCV), a novel circovirus species and the first reported from a cervid host

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mathew Fisher ◽  
Thomas M. R. Harrison ◽  
Michelle Nebroski ◽  
Peter Kruczkiewicz ◽  
Jamie L. Rothenburger ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Analysis ◽  
Rocky Mountain ◽  
International Committee ◽  
Comparative Genomic Analysis ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Stem Loop ◽  
Genome Wide ◽  
Replication Region

Abstract The complete genome sequence of a novel circovirus (elk circovirus (ElkCV) Banff/2019) was determined via high throughput sequencing of liver tissue from a euthanized Rocky Mountain elk (Cervus canadensis nelsoni) from Alberta, Canada. The genome is circular and 1,787 nucleotides long, with two major ORFs encoding predicted proteins. Comparative genomic analysis to 4,164 publicly available complete and near complete circovirus genomes showed that ElkCV shares approximately 65% pairwise genome-wide nucleotide identity with the most closely related circovirus species, porcine circoviruses (PCV) 1 and 2 and bat-associated circovirus (BatACV) 11. ElkCV features a stem-loop within the origin of replication region characteristic of circoviruses. However, it differs from those found in PCV1, PCV2 and BatACV11 since it has a longer stem and contains hexamer repeats that overlap the stem in opposing orientations. Interestingly, stem-loop structures of similar length featuring repeats in a similar position and orientation are also seen in some avian circoviruses. Based on the demarcation threshold established by the International Committee on Taxonomy of Viruses (ICTV) for members of Circoviridae (80% pairwise genome-wide nucleotide identity), ElkCV represents a novel species and is the first complete circovirus genome reported from a cervid host.

scholarly journals Considerations and complications of mapping small RNA libraries to transposable elements

2016 ◽  
Author(s):  
Alexandros Bousios ◽  
Brandon S. Gaut ◽  
Nikos Darzentas
Keyword(s):  
Transposable Elements ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Careful Consideration ◽  
Rna Seq ◽  
Critical Feature ◽  
Different Types ◽  
The Relationship ◽  
Epigenetic Research ◽  
Shed Light

ABSTRACTThe advent of high-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. Often coupled with the availability of fully sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), and especially when such genomes are large as is often the case in plants. Here, to shed light on the challenges of mapping sRNAs to TEs, we focus on the 2,300Mb maize genome, of which >85% is derived from TEs. We compare various methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiple mapping sRNAs, and the selection among different types of sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and explore and contrast their effect on low copy regions (exons) and other popular HTS data (RNA-seq). Finally, based on our analysis, we share a series of take-home messages to help guide TE epigenetic studies specifically, but our conclusions may also apply to any work that involves mapping and analysis of HTS data.

scholarly journals Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans

2020 ◽  
Vol 22 (6) ◽  
pp. 760-771
Author(s):  
Masa-aki Yoshida ◽  
Junichi Imoto ◽  
Yuri Kawai ◽  
Satomi Funahashi ◽  
Ryuhei Minei ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Luciferase Activity ◽  
Draft Genome ◽  
3D Models ◽  
Comparative Genomic ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Different Types ◽  
Transcriptome Variation ◽  
Lineage Specific Genes

AbstractWatasenia scintillans, a sparkling enope squid, has bioluminescence organs to illuminate its body with its own luciferase activity. To clarify the molecular mechanism underlying its scintillation, we analysed high-throughput sequencing data acquired previously and obtained draft genome sequences accomplished with comparative genomic data among the cephalopods. The genome mapped by transcriptome data showed that (1) RNA editing contributed to transcriptome variation of lineage specific genes, such as W. scintillans luciferase, and (2) two types of luciferase enzymes were characterized with reasonable 3D models docked to a luciferin molecule. We report two different types of luciferase in one organism and possibly related to variety of colour types in the W. scintillans fluorescent organs.

scholarly journals Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 850 ◽  
Author(s):  
Krzysztof Romaniuk ◽  
Michal Styczynski ◽  
Przemyslaw Decewicz ◽  
Oliwia Buraczewska ◽  
Witold Uhrynowski ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Horizontal Transfer ◽  
Comparative Genomic ◽  
Narrow Host Range ◽  
Antarctic Soils ◽  
Pseudomonas Spp ◽  
Genomic Analyses ◽  
Genes Encoding ◽  
Pilin Protein ◽  
Functional Analyses

Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp.

scholarly journals Silencing of transposable elements may not be a major driver of regulatory evolution in primate induced pluripotent stem cells

2017 ◽  
Author(s):  
Michelle C. Ward ◽  
Siming Zhao ◽  
Kaixuan Luo ◽  
Bryan J. Pavlovic ◽  
Mohammad M. Karimi ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transposable Elements ◽  
Induced Pluripotent Stem Cells ◽  
Pluripotent Stem Cells ◽  
High Throughput Sequencing ◽  
Wide Distribution ◽  
Genome Wide ◽  
Repressive Histone Modification ◽  
Induced Pluripotent ◽  
Line Elements

AbstractTransposable elements (TEs) comprise a substantial proportion of primate genomes. The regulatory potential of TEs can result in deleterious effects, especially during development. It has been suggested that, in pluripotent stem cells, TEs are targeted for silencing by KRAB-ZNF proteins, which recruit the TRIM28-SETDB1 complex, to deposit the repressive histone modification H3K9me3. TEs, in turn, can acquire mutations that allow them to evade detection by the host, and hence KRAB-ZNF proteins need to rapidly evolve to counteract them. To investigate the short-term evolution of TE silencing, we profiled the genome-wide distribution of H3K9me3 in induced pluripotent stem cells from ten human and seven chimpanzee individuals. We performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) for H3K9me3, as well as total RNA sequencing. We focused specifically on cross-species H3K9me3 ChIP-seq data that mapped to four million orthologous TEs. We found that, depending on the TE class, 10-60% of elements are marked by H3K9me3, with SVA, LTR and LINE elements marked most frequently. We found little evidence of inter-species differences in TE silencing, with as many as 80% of orthologous, putatively silenced, TEs marked at similar levels in humans and chimpanzees. Our data suggest limited species-specificity of TE silencing across six million years of primate evolution. Interestingly, the minority of TEs enriched for H3K9me3 in one species are not more likely to be associated with gene expression divergence of nearby orthologous genes. We conclude that orthologous TEs may not play a major role in driving gene regulatory divergence between humans and chimpanzees.

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