scholarly journals LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

2019 ◽  
Author(s):  
Shujun Ou ◽  
Ning Jiang
Keyword(s):  
Triticum Aestivum ◽  
Long Terminal Repeat ◽  
Bread Wheat ◽  
Repetitive Sequences ◽  
Long Terminal Repeat Retrotransposons ◽  
Rapid Identification ◽  
Terminal Repeat ◽  
Parallel Operation ◽  
Ltr Retrotransposons ◽  
Plant Genomes

AbstractSummaryAnnotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for identification of LTR retrotransposons but its application on large genomes is hindered by its single threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting up to 8,500X faster identification of LTR elements. It takes only 72 minutes to process the 14.5 Gb bread wheat (Triticum aestivum) genome in comparison to 1.16 years required by the original sequential version.AvailabilityLTR_FINDER_parallel is freely available at https://github.com/oushujun/[email protected]

scholarly journals LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shujun Ou ◽  
Ning Jiang
Keyword(s):  
Triticum Aestivum ◽  
Long Terminal Repeat ◽  
Bread Wheat ◽  
Repetitive Sequences ◽  
Long Terminal Repeat Retrotransposons ◽  
Rapid Identification ◽  
Terminal Repeat ◽  
Parallel Operation ◽  
Ltr Retrotransposons ◽  
Plant Genomes

AbstractAnnotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for the identification of LTR retrotransposons but its application on large genomes is hindered by its single-threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting in up to 8500X faster identification of LTR elements. It takes only 72 min to process the 14.5 Gb bread wheat (Triticum aestivum) genome in comparison to 1.16 years required by the original sequential version. LTR_FINDER_parallel is freely available at https://github.com/oushujun/LTR_FINDER_parallel.

scholarly journals Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

2021 ◽  
Author(s):  
Nusrat Sultana ◽  
Gerhard Menzel ◽  
Kathrin M. Seibt ◽  
Sonia Garcia ◽  
Beatrice Weber ◽  
...  
Keyword(s):  
Long Terminal Repeat ◽  
Genome Assembly ◽  
In Silico ◽  
Transcriptional Activity ◽  
Long Terminal Repeat Retrotransposons ◽  
Genomic Variation ◽  
Terminal Repeat ◽  
Vaccinium Macrocarpon ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons

BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. OBJECTIVE: Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. METHODS: Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. RESULTS: We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsyin silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. CONCLUSIONS: We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.

scholarly journals New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 285 ◽  
Author(s):  
Bi Ma ◽  
Lulu Kuang ◽  
Youchao Xin ◽  
Ningjia He
Keyword(s):  
Long Terminal Repeat ◽  
Life Histories ◽  
Evolutionary Dynamics ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Ltr Retrotransposons ◽  
Positive Selection Pressure ◽  
Insertion And Deletion ◽  
Mulberry Tree ◽  
Dominant Influence

The evolutionary dynamics of long terminal repeat (LTR) retrotransposons in tree genomes has remained largely unknown. The availability of the complete genome sequences of the mulberry tree (Morus notabilis) has offered an unprecedented opportunity for us to characterize these retrotransposon elements. We investigated 202 and 114 families of Copia and Gypsy superfamilies, respectively, comprising 2916 intact elements in the mulberry genome. The tRNAMet was the most frequently used type of tRNA in both superfamilies. Phylogenetic analysis suggested that Copia and Gypsy from mulberry can be grouped into eight and six lineages, respectively. All previously characterized families of such elements could also be found in the mulberry genome. About 95% of the identified Copia and Gypsy full elements were estimated to have been inserted into the mulberry genome within the past 2–3 million years. Meanwhile, the estimated insertion times of members of the three most abundant families of the Copia superfamily (908 members from the three most abundant families) and Gypsy superfamily (783 members from the three most abundant families) revealed divergent life histories. Compared with the situation in Gypsy elements, three families of Copia elements are under positive selection pressure, which suggested that Copia elements may have a dominant influence in the evolution of mulberry genes. Analysis of insertion and deletion dynamics suggested that Copia and Gypsy elements exhibited a very long half-life in the mulberry genome. The present work provides new insights into the insertion and deletion dynamics of LTR retrotransposons, and it will greatly improve our understanding of the important roles transposable elements play in the architecture of the mulberry genome.

scholarly journals Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

2021 ◽  
pp. 1-21
Author(s):  
Nusrat Sultana ◽  
Gerhard Menzel ◽  
Kathrin M. Seibt ◽  
Sònia Garcia ◽  
Beatrice Weber ◽  
...  
Keyword(s):  
Long Terminal Repeat ◽  
Genome Assembly ◽  
In Silico ◽  
Transcriptional Activity ◽  
Long Terminal Repeat Retrotransposons ◽  
Genomic Variation ◽  
Terminal Repeat ◽  
Vaccinium Macrocarpon ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons

BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. OBJECTIVE: Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. METHODS: Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. RESULTS: We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsy in silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. CONCLUSIONS: We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.

scholarly journals LtrDetector: A modern tool-suite for detecting long terminal repeat retrotransposons de-novo on the genomic scale

2018 ◽  
Author(s):  
Joseph D Valencia ◽  
Hani Z Girgis
Keyword(s):  
Long Terminal Repeat ◽  
Large Scale ◽  
De Novo ◽  
False Positive Rate ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Plant Genomes ◽  
Positive Rate ◽  
Genomic Scale ◽  
Species Specific

AbstractLong terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and genomic evolution. Large-scale sequencing projects for plant genomes are currently underway. Software tools are important for annotating long terminal repeat retrotransposons in these newly available genomes. However, the available tools are not very sensitive to known elements and perform inconsistently on different genomes. Some are hard to install or obsolete. They may struggle to process large plant genomes. None are concurrent or have features to support manual review of new elements. To overcome these limitations, we developed LtrDetector, which uses signal-processing techniques. LtrDetector is easy to install and use. It is not species specific. It utilizes multi-core processors available in personal computers. It is more sensitive than other tools by 14.4%–50.8% while maintaining a low false positive rate on six plant genomes.

scholarly journals Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

2006 ◽  
Vol 26 (22) ◽  
pp. 8242-8251 ◽  
Author(s):  
Oliver Siol ◽  
Moustapha Boutliliss ◽  
Thanh Chung ◽  
Gernot Glöckner ◽  
Theodor Dingermann ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Long Terminal Repeat ◽  
Integration Site ◽  
Rna Polymerase Iii ◽  
Terminal Repeat ◽  
Trna Genes ◽  
Ltr Retrotransposons ◽  
Polymerase Iii

ABSTRACT In the compact Dictyostelium discoideum genome, non-long terminal repeat (non-LTR) retrotransposons known as TREs avoid accidental integration-mediated gene disruption by targeting the vicinity of tRNA genes. In this study we provide the first evidence that proteins of a non-LTR retrotransposon interact with a target-specific transcription factor to direct its integration. We applied an in vivo selection system that allows for the isolation of natural TRE5-A integrations into a known genomic location upstream of tRNA genes. TRE5-A frequently modified the integration site in a way characteristic of other non-LTR retrotransposons by adding nontemplated extra nucleotides and generating small and extended target site deletions. Mutations within the B-box promoter of the targeted tRNA genes interfered with both the in vitro binding of RNA polymerase III transcription factor TFIIIC and the ability of TRE5-A to target these genes. An isolated B box was sufficient to enhance TRE5-A integration in the absence of a surrounding tRNA gene. The RNA polymerase III-transcribed ribosomal 5S gene recruits TFIIIC in a B-box-independent manner, yet it was readily targeted by TRE5-A in our assay. These results suggest a direct role of an RNA polymerase III transcription factor in the targeting process.

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