scholarly journals Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2681
Author(s):  
Ilya Kirov ◽  
Pavel Merkulov ◽  
Maxim Dudnikov ◽  
Ekaterina Polkhovskaya ◽  
Roman A. Komakhin ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Assembly ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Gag Protein ◽  
Reading Frame ◽  
Retrotransposon Family ◽  
Long Read ◽  
Low Coverage ◽  
Arabidopsis Thaliana Genome

Long-read data is a great tool to discover new active transposable elements (TEs). However, no ready-to-use tools were available to gather this information from low coverage ONT datasets. Here, we developed a novel pipeline, nanotei, that allows detection of TE-contained structural variants, including individual TE transpositions. We exploited this pipeline to identify TE insertion in the Arabidopsis thaliana genome. Using nanotei, we identified tens of TE copies, including ones for the well-characterized ONSEN retrotransposon family that were hidden in genome assembly gaps. The results demonstrate that some TEs are inaccessible for analysis with the current A. thaliana (TAIR10.1) genome assembly. We further explored the mobilome of the ddm1 mutant with elevated TE activity. Nanotei captured all TEs previously known to be active in ddm1 and also identified transposition of non-autonomous TEs. Of them, one non-autonomous TE derived from (AT5TE33540) belongs to TR-GAG retrotransposons with a single open reading frame (ORF) encoding the GAG protein. These results provide the first direct evidence that TR-GAGs and other non-autonomous LTR retrotransposons can transpose in the plant genome, albeit in the absence of most of the encoded proteins. In summary, nanotei is a useful tool to detect active TEs and their insertions in plant genomes using low-coverage data from Nanopore genome sequencing.

scholarly journals Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower (Helianthus annuus L.)

2020 ◽  
Vol 21 (23) ◽  
pp. 9331 ◽  
Author(s):  
Ilya Kirov ◽  
Murad Omarov ◽  
Pavel Merkulov ◽  
Maxim Dudnikov ◽  
Sofya Gvaramiya ◽  
...  
Keyword(s):  
Helianthus Annuus ◽  
Defense Mechanisms ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Reading Frame ◽  
Transposition Activity ◽  
Helianthus Annuus L ◽  
Genome Defense ◽  
Hidden Layer ◽  
Sunflower Genome

LTR retrotransposons (RTEs) play a crucial role in plant genome evolution and adaptation. Although RTEs are generally silenced in somatic plant tissues under non-stressed conditions, some expressed RTEs (exRTEs) escape genome defense mechanisms. As our understanding of exRTE organization in plants is rudimentary, we systematically surveyed the genomic and transcriptomic organization and mobilome (transposition) activity of sunflower (Helianthus annuus L.) exRTEs. We identified 44 transcribed RTEs in the sunflower genome and demonstrated their distinct genomic features: more recent insertion time, longer open reading frame (ORF) length, and smaller distance to neighboring genes. We showed that GAG-encoding ORFs are present at significantly higher frequencies in exRTEs, compared with non-expressed RTEs. Most exRTEs exhibit variation in copy number among sunflower cultivars and one exRTE Gagarin produces extrachromosomal circular DNA in seedling, demonstrating recent and ongoing transposition activity. Nanopore direct RNA sequencing of full-length RTE RNA revealed complex patterns of alternative splicing in RTE RNAs, resulting in isoforms that carry ORFs for distinct RTE proteins. Together, our study demonstrates that tens of expressed sunflower RTEs with specific genomic organization shape the hidden layer of the transcriptome, pointing to the evolution of specific strategies that circumvent existing genome defense mechanisms.

scholarly journals De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

2015 ◽  
Vol 8 (3) ◽  
pp. 489-492 ◽  
Author(s):  
Ting Xie ◽  
Jue-Fei Zheng ◽  
Sheng Liu ◽  
Cheng Peng ◽  
Yong-Ming Zhou ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Assembly ◽  
De Novo ◽  
Plant Genome ◽  
Chromatin Interactions

scholarly journals High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

2017 ◽  
Author(s):  
Todd P. Michael ◽  
Florian Jupe ◽  
Felix Bemm ◽  
S. Timothy Motley ◽  
Justin P. Sandoval ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Large Scale ◽  
Cost Effective ◽  
New Era ◽  
Genome Maps ◽  
Oxford Nanopore ◽  
Long Read ◽  
Genome Assemblies ◽  
Typical Consumer ◽  
Arabidopsis Thaliana Genome

AbstractWhile many evolutionary questions can be answered by short read re-sequencing, presence/absence polymorphisms of genes and/or transposons have been largely ignored in large-scale intraspecific evolutionary studies. To enable the rigorous analysis of such variants, multiple high quality and contiguous genome assemblies are essential. Similarly, while genome assemblies based on short reads have made genomics accessible for non-reference species, these assemblies have limitations due to low contiguity. Long-read sequencers and long-read technologies have ushered in a new era of genome sequencing where the lengths of reads exceed those of most repeats. However, because these technologies are not only costly, but also time and compute intensive, it has been unclear how scalable they are. Here we demonstrate a fast and cost effective reference assembly for an Arabidopsis thaliana accession using the USB-sized Oxford Nanopore MinION sequencer and typical consumer computing hardware (4 Cores, 16Gb RAM). We assemble the accession KBS-Mac-74 into 62 contigs with an N50 length of 12.3 Mb covering 100% (119 Mb) of the non-repetitive genome. We demonstrate that the polished KBS-Mac-74 assembly is highly contiguous with BioNano optical genome maps, and of high per-base quality against a likewise polished Pacific Biosciences long-read assembly. The approach we implemented took a total of four days at a cost of less than 1,000 USD for sequencing consumables including instrument depreciation.

scholarly journals High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Todd P. Michael ◽  
Florian Jupe ◽  
Felix Bemm ◽  
S. Timothy Motley ◽  
Justin P. Sandoval ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Assembly ◽  
Flow Cell ◽  
Arabidopsis Thaliana Genome

scholarly journals LazyB: fast and cheap genome assembly

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Thomas Gatter ◽  
Sarah von Löhneysen ◽  
Jörg Fallmann ◽  
Polina Drozdova ◽  
Tom Hartmann ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Hybrid Methods ◽  
Computational Effort ◽  
Sequencing Data ◽  
Long Reads ◽  
Hybrid Genome ◽  
Long Read ◽  
Low Coverage ◽  
Genome Assembler ◽  
Large Genomes

Abstract Background Advances in genome sequencing over the last years have lead to a fundamental paradigm shift in the field. With steadily decreasing sequencing costs, genome projects are no longer limited by the cost of raw sequencing data, but rather by computational problems associated with genome assembly. There is an urgent demand for more efficient and and more accurate methods is particular with regard to the highly complex and often very large genomes of animals and plants. Most recently, “hybrid” methods that integrate short and long read data have been devised to address this need. Results is such a hybrid genome assembler. It has been designed specificially with an emphasis on utilizing low-coverage short and long reads. starts from a bipartite overlap graph between long reads and restrictively filtered short-read unitigs. This graph is translated into a long-read overlap graph G. Instead of the more conventional approach of removing tips, bubbles, and other local features, stepwisely extracts subgraphs whose global properties approach a disjoint union of paths. First, a consistently oriented subgraph is extracted, which in a second step is reduced to a directed acyclic graph. In the next step, properties of proper interval graphs are used to extract contigs as maximum weight paths. These path are translated into genomic sequences only in the final step. A prototype implementation of , entirely written in python, not only yields significantly more accurate assemblies of the yeast and fruit fly genomes compared to state-of-the-art pipelines but also requires much less computational effort. Conclusions is new low-cost genome assembler that copes well with large genomes and low coverage. It is based on a novel approach for reducing the overlap graph to a collection of paths, thus opening new avenues for future improvements. Availability The prototype is available at https://github.com/TGatter/LazyB.

scholarly journals The genetic and epigenetic landscape of the Arabidopsis centromeres

2021 ◽  
Author(s):  
Matthew Naish ◽  
Michael Alonge ◽  
Piotr Wlodzimierz ◽  
Andrew J Tock ◽  
Bradley W Abramson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Arabidopsis Thaliana ◽  
Cell Division ◽  
Rapid Evolution ◽  
Epigenetic Landscape ◽  
Meiotic Dsbs ◽  
Long Read ◽  
Spindle Microtubules ◽  
Low Levels ◽  
Arabidopsis Thaliana Genome

Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used ultra-long-read sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support high CENH3 occupancy and are densely DNA methylated, with satellite variants private to each chromosome. CENH3 preferentially occupies satellites with least divergence and greatest higher-order repetition. The centromeres are invaded by ATHILA retrotransposons, which disrupt genetic and epigenetic organization of the centromeres. Crossover recombination is suppressed within the centromeres, yet low levels of meiotic DSBs occur that are regulated by DNA methylation. We propose that Arabidopsis centromeres are evolving via cycles of satellite homogenization and retrotransposon-driven diversification.

scholarly journals A critical comparison of technologies for a plant genome sequencing project

2017 ◽  
Author(s):  
Pirita Paajanen ◽  
George Kettleborough ◽  
Elena López-Girona ◽  
Michael Giolai ◽  
Darren Heavens ◽  
...  
Keyword(s):  
Genome Assembly ◽  
New Technologies ◽  
Model Organism ◽  
Plant Genome ◽  
High Quality ◽  
Short Read ◽  
Sequencing Project ◽  
Assembly Algorithm ◽  
Starting Point ◽  
Long Read

A high quality genome sequence of your model organism is an essential starting point for many studies. Old clone based methods are slow and expensive, whereas faster, cheaper short read only assemblies can be incomplete and highly fragmented, which minimises their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, human. However, plant genomes can be much more repetitive and larger than human, and plant biology makes obtaining high quality DNA free from contaminants difficult. Reflecting their challenging nature we observe that plant genome assembly statistics are typically poorer than for vertebrates. Here we compare Illumina short read, PacBio long read, 10x Genomics linked reads, Dovetail Hi-C and BioNano Genomics optical maps, singly and combined, in producing high quality long range genome assemblies of the potato species S. verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA, compute requirements and sequencing costs. We expect our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.

scholarly journals ARBitR: An overlap-aware genome assembly scaffolder for linked reads

2020 ◽  
Author(s):  
Markus Hiltunen ◽  
Martin Ryberg ◽  
Hanna Johannesson
Keyword(s):  
Genome Assembly ◽  
General Public ◽  
Source Code ◽  
Draft Genome ◽  
Supplementary Information ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Long Read ◽  
Genome Assemblies ◽  
General Public License

Abstract10X Genomics Chromium linked reads contain information that can be used to link sequences together into scaffolds in draft genome assemblies. Existing software for this purpose perform the scaffolding by joining sequences together with a gap between them, not considering potential contig overlaps. Such overlaps can be particularly prominent in genome drafts assembled from long-read sequencing data where an overlap-layout-consensus (OLC) algorithm has been used. Ignoring overlapping contig ends may result in genes and other features being incomplete or fragmented in the resulting scaffolds. We developed the application ARBitR to generate scaffolds from genome drafts using 10X Chromium data, with a focus on minimizing the number of gaps in resulting scaffolds by incorporating an OLC step to resolve junctions between linked contigs. We tested the performance of ARBitR on three published and simulated datasets and compared to the previously published tools ARCS and ARKS. The results revealed that ARBitR performed similarly considering contiguity statistics, and the advantage of the overlapping step was revealed by fewer long and short variants in ARBitR produced scaffolds, in addition to a higher proportion of completely assembled LTR retrotransposons. We expect ARBitR to have broad applicability in genome assembly projects that utilize 10X Chromium linked reads.Availability and implementationARBitR is written and implemented in Python3 for Unix-like operative systems. All source code is available at https://github.com/markhilt/ARBitR under the GNU General Public License [email protected] informationavailable online

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