Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Abstract Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17-18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' non-coding terminal regions, preserved open reading frames (ORFs) and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in both subgenomes of X. laevis. More recent amplification waves are seen in X. tropicalis (less than 3.2 mya) and X. laevis (around 10 mya) corroborating with transcriptional activity evidence. All DIRS-like families were found in both X. laevis subgenomes, while a few were most represented in the L subgenome. Ngaro-like elements presented less diversity and quantity in X. tropicalis and X. laevis genomes, although potentially active copies were found in both species and this is consistent with a recent amplification wave seen in the evolutionary landscape. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process.

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Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

10.1101/2021.08.05.455354 ◽

2021 ◽

Author(s):

Camilla Borges Gazolla ◽

Adriana Ludwig ◽

Joana Gama Moura ◽

Daniel Pacheco Bruschi

Keyword(s):

Molecular Structure ◽

Xenopus Laevis ◽

Phylogenetic Relationships ◽

Transcriptional Activity ◽

Evolutionary Dynamics ◽

Open Reading Frames ◽

Xenopus Tropicalis ◽

Molecular Signatures ◽

Reading Frames ◽

High Diversity

Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17-18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' non-coding terminal regions, preserved open reading frames (ORFs) and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in the X. laevis. X. tropicalis showed more recent amplification waves estimated around 16 mya and 3.2 mya and corroborate with high diversity-level of families in this species and with transcriptional activity evidence. Ngaro-like elements presented less diversity and quantity in the genomes, although potentially active copies were also found. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in the diploid X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process

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Composite transposable elements in the Xenopus laevis genome.

Molecular and Cellular Biology ◽

10.1128/mcb.9.7.3018 ◽

1989 ◽

Vol 9 (7) ◽

pp. 3018-3027 ◽

Cited By ~ 25

Author(s):

J E Garrett ◽

D S Knutzon ◽

D Carroll

Keyword(s):

Xenopus Laevis ◽

Transposable Elements ◽

Repetitive Sequences ◽

Open Reading Frames ◽

The Other ◽

Inverted Repeats ◽

Terminal Inverted Repeats ◽

Gag Proteins ◽

High Degree ◽

Reading Frames

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.

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Composite transposable elements in the Xenopus laevis genome

Molecular and Cellular Biology ◽

10.1128/mcb.9.7.3018-3027.1989 ◽

1989 ◽

Vol 9 (7) ◽

pp. 3018-3027

Author(s):

J E Garrett ◽

D S Knutzon ◽

D Carroll

Keyword(s):

Xenopus Laevis ◽

Transposable Elements ◽

Repetitive Sequences ◽

Open Reading Frames ◽

The Other ◽

Inverted Repeats ◽

Terminal Inverted Repeats ◽

Gag Proteins ◽

High Degree ◽

Reading Frames

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Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals

10.1101/2020.07.27.223495 ◽

2020 ◽

Cited By ~ 2

Author(s):

Harsha Doddapaneni ◽

Sara Javornik Cregeen ◽

Richard Sucgang ◽

Qingchang Meng ◽

Xiang Qin ◽

...

Keyword(s):

Transcriptional Activity ◽

Oligonucleotide Probe ◽

Threshold Value ◽

Open Reading Frames ◽

Clinical Samples ◽

Viral Loads ◽

Full Length Genome ◽

Probe Set ◽

Reading Frames ◽

Capture Sequencing

AbstractThe newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

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The Insertion Sequences of Anabaena sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames

Journal of Bacteriology ◽

10.1128/jb.00460-10 ◽

2010 ◽

Vol 192 (20) ◽

pp. 5289-5303 ◽

Cited By ~ 7

Author(s):

C. Peter Wolk ◽

Sigal Lechno-Yossef ◽

Karin M. Jäger

Keyword(s):

Transposable Elements ◽

Open Reading Frames ◽

Insertion Sequences ◽

Direct Repeats ◽

Homologous Sequences ◽

Anabaena Sp ◽

Pcc 7120 ◽

Flanking Regions ◽

Adaptive Role ◽

Reading Frames

ABSTRACT Anabaena sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (http://www-is.biotoul.fr/ ) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others—some encoding proteins of predictable function, including protein kinases, and restriction endonucleases—that were interrupted by ISs. Anabaena sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs.

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Novel open reading frames in human accelerated regions and transposable elements reveal new leads to understand schizophrenia and bipolar disorder

Molecular Psychiatry ◽

10.1038/s41380-021-01405-6 ◽

2021 ◽

Author(s):

Chaitanya Erady ◽

Krishna Amin ◽

Temiloluwa O. A. E. Onilogbo ◽

Jakub Tomasik ◽

Rebekah Jukes-Jones ◽

...

Keyword(s):

Bipolar Disorder ◽

Transposable Elements ◽

Drug Targets ◽

Rapid Evolution ◽

Open Reading Frames ◽

Biological Regulation ◽

Genomic Features ◽

Species Specific ◽

Human Accelerated Regions ◽

Reading Frames

AbstractSchizophrenia (SCZ) and bipolar disorder are debilitating neuropsychiatric disorders arising from a combination of environmental and genetic factors. Novel open reading frames (nORFs) are genomic loci that give rise to previously uncharacterized transcripts and protein products. In our previous work, we have shown that nORFs can be biologically regulated and that they may play a role in cancer and rare diseases. More importantly, we have shown that nORFs may emerge in accelerated regions of the genome giving rise to species-specific functions. We hypothesize that nORFs represent a potentially important group of biological factors that may contribute to SCZ and bipolar disorder pathophysiology. Human accelerated regions (HARs) are genomic features showing human-lineage-specific rapid evolution that may be involved in biological regulation and have additionally been found to associate with SCZ genes. Transposable elements (TEs) are another set of genomic features that have been shown to regulate gene expression. As with HARs, their relevance to SCZ has also been suggested. Here, nORFs are investigated in the context of HARs and TEs. This work shows that nORFs whose expression is disrupted in SCZ and bipolar disorder are in close proximity to HARs and TEs and that some of them are significantly associated with SCZ and bipolar disorder genomic hotspots. We also show that nORF encoded proteins can form structures and potentially constitute novel drug targets.

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Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot

Mobile DNA ◽

10.1186/s13100-019-0190-3 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Alicja Macko-Podgórni ◽

Katarzyna Stelmach ◽

Kornelia Kwolek ◽

Dariusz Grzebelus

Keyword(s):

Transposable Elements ◽

Daucus Carota ◽

Inverted Repeat ◽

Insertion Site ◽

Open Reading Frames ◽

Genomic Diversity ◽

Untranslated Regions ◽

Substantial Contribution ◽

Insertion Sites ◽

Reading Frames

Abstract Background Miniature inverted repeat transposable elements (MITEs) are small non-autonomous DNA transposons that are ubiquitous in plant genomes, and are mobilised by their autonomous relatives. Stowaway MITEs are derived from and mobilised by elements from the mariner superfamily. Those elements constitute a significant portion of the carrot genome; however the variation caused by Daucus carota Stowaway MITEs (DcStos), their association with genes and their putative impact on genome evolution has not been comprehensively analysed. Results Fourteen families of Stowaway elements DcStos occupy about 0.5% of the carrot genome. We systematically analysed 31 genomes of wild and cultivated Daucus carota, yielding 18.5 thousand copies of these elements, showing remarkable insertion site polymorphism. DcSto element demography differed based on the origin of the host populations, and corresponded with the four major groups of D. carota, wild European, wild Asian, eastern cultivated and western cultivated. The DcStos elements were associated with genes, and most frequently occurred in 5′ and 3′ untranslated regions (UTRs). Individual families differed in their propensity to reside in particular segments of genes. Most importantly, DcSto copies in the 2 kb regions up- and downstream of genes were more frequently associated with open reading frames encoding transcription factors, suggesting their possible functional impact. More than 1.5% of all DcSto insertion sites in different host genomes contained different copies in exactly the same position, indicating the existence of insertional hotspots. The DcSto7b family was much more polymorphic than the other families in cultivated carrot. A line of evidence pointed at its activity in the course of carrot domestication, and identified Dcmar1 as an active carrot mariner element and a possible source of the transposition machinery for DcSto7b. Conclusion Stowaway MITEs have made a substantial contribution to the structural and functional variability of the carrot genome.

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DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5

Infection and Immunity ◽

10.1128/iai.66.10.4611-4623.1998 ◽

1998 ◽

Vol 66 (10) ◽

pp. 4611-4623 ◽

Cited By ~ 110

Author(s):

Robert D. Perry ◽

Susan C. Straley ◽

Jacqueline D. Fetherston ◽

Debra J. Rose ◽

Jason Gregor ◽

...

Keyword(s):

Transposable Elements ◽

Yersinia Pestis ◽

Yersinia Pseudotuberculosis ◽

Gc Content ◽

Effector Proteins ◽

Open Reading Frames ◽

Is Elements ◽

Virulence Property ◽

Leucine Rich Repeats ◽

Reading Frames

ABSTRACT The low-Ca2+-response (LCR) plasmid pCD1 of the plague agent Yersinia pestis KIM5 was sequenced and analyzed for its genetic structure. pCD1 (70,509 bp) has an IncFIIA-like replicon and a SopABC-like partition region. We have assigned 60 apparently intact open reading frames (ORFs) that are not contained within transposable elements. Of these, 47 are proven or possible members of the LCR, a major virulence property of human-pathogenicYersinia spp., that had been identified previously in one or more of Y. pestis or the enteropathogenic yersiniaeYersinia enterocolitica and Yersinia pseudotuberculosis. Of these 47 LCR-related ORFs, 35 constitute a continuous LCR cluster. The other LCR-related ORFs are interspersed among three intact insertion sequence (IS) elements (IS100and two new IS elements, IS1616 and IS1617) and numerous defective or partial transposable elements. Regional variations in percent GC content and among ORFs encoding effector proteins of the LCR are additional evidence of a complex history for this plasmid. Our analysis suggested the possible addition of a new Syc- and Yop-encoding operon to the LCR-related pCD1 genes and gave no support for the existence of YopL. YadA likely is not expressed, as was the case for Y. pestis EV76, and the gene for the lipoprotein YlpA found in Y. enterocolitica likely is a pseudogene in Y. pestis. The yopM gene is longer than previously thought (by a sequence encoding two leucine-rich repeats), the ORF upstream of ypkA-yopJ is discussed as a potential Syc gene, and a previously undescribed ORF downstream ofyopE was identified as being potentially significant. Eight other ORFs not associated with IS elements were identified and deserve future investigation into their functions.

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Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals

PLoS ONE ◽

10.1371/journal.pone.0244468 ◽

2021 ◽

Vol 16 (8) ◽

pp. e0244468

Author(s):

Harsha Doddapaneni ◽

Sara Javornik Cregeen ◽

Richard Sucgang ◽

Qingchang Meng ◽

Xiang Qin ◽

...

Keyword(s):

Transcriptional Activity ◽

Oligonucleotide Probe ◽

Threshold Value ◽

Open Reading Frames ◽

Clinical Samples ◽

Viral Loads ◽

Full Length Genome ◽

Probe Set ◽

Reading Frames ◽

Capture Sequencing

The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

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Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals

10.1101/2020.12.11.421057 ◽

2020 ◽

Author(s):

harshavardhan doddapaneni ◽

Sara Javornik Cregeen ◽

Richard Sucgang ◽

Qingchang Meng ◽

Xiang Qin ◽

...

Keyword(s):

Transcriptional Activity ◽

Oligonucleotide Probe ◽

Threshold Value ◽

Open Reading Frames ◽

Clinical Samples ◽

Viral Loads ◽

Full Length Genome ◽

Probe Set ◽

Reading Frames ◽

Capture Sequencing

The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

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