A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Berthelier, Jérémy; Casse, Nathalie; Daccord, Nicolas; Jamilloux, Véronique; Saint‐Jean, Bruno; Carrier, Grégory

doi:10.1186/s12864-018-4763-1

Cited by 44 publications

(56 citation statements)

References 98 publications

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“…Several programs and pipelines are now available to detect and annotate repetitive sequences, mainly using detection based on similarity, structure or repetitiveness [63]. These tools are crucial for large-scale approaches and for providing an overall view of the TE composition of genomes.…”

Section: Discussionmentioning

confidence: 99%

“…To evaluate our analysis strategy, mainly avoiding erroneous determination of element limits, we also used an automated pipeline to search for VIPER in T. cruzi Dm28c and TATE in L. braziliensis MHOM/BR/75/ M2904. We used the detection TE programs (based on assembled genomes) from PiRATE, as automated in Galaxy platform [63,85].…”

Section: Characterization Of Copiesmentioning

confidence: 99%

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Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

et al. 2019

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Background Kinetoplastids are a flagellated group of protists, including some parasites, such as Trypanosoma and Leishmania species, that can cause diseases in humans and other animals. The genomes of these species enclose a fraction of retrotransposons including VIPER and TATE , two poorly studied transposable elements that encode a tyrosine recombinase (YR) and were previously classified as DIRS elements. This study investigated the distribution and evolution of VIPER and TATE in kinetoplastids to understand the relationships of these elements with other retrotransposons. Results We observed that VIPER and TATE have a discontinuous distribution among Trypanosomatidae, with several events of loss and degeneration occurring during a vertical transfer evolution. We were able to identify the terminal repeats of these elements for the first time, and we showed that these elements are potentially active in some species, including T. cruzi copies of VIPER . We found that VIPER and TATE are strictly related elements, which were named in this study as VIPER-like . The reverse transcriptase (RT) tree presented a low resolution, and the origin and relationships among YR groups remain uncertain. Conversely, for RH, VIPER-like grouped with Hepadnavirus , whereas for YR, VIPER-like sequences constituted two different clades that are closely allied to Crypton . Distinct topologies among RT, RH and YR trees suggest ancient rearrangements/exchanges in domains and a modular pattern of evolution with putative independent origins for each ORF. Conclusions Due to the presence of both elements in Bodo saltans, a nontrypanosomatid species, we suggested that VIPER and TATE have survived and remained active for more than 400 million years or were reactivated during the evolution of the host species. We did not find clear evidence of independent origins of VIPER-like from the other YR retroelements, supporting the maintenance of the DIRS group of retrotransposons. Nevertheless, according to phylogenetic findings and sequence structure obtained by this study and other works, we proposed separating DIRS elements into four subgroups: DIRS-like, PAT-like, Ngaro-like, and VIPER-like. Electronic supplementary material The online version of this article (10.1186/s13100-019-0175-2) contains supplementary material, which is available to authori...

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Section: Discussionmentioning

confidence: 99%

Section: Characterization Of Copiesmentioning

confidence: 99%

Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

et al. 2019

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“…Other TE discovery programs exist, but either focus on finding instances in the genome instead of family consensus sequence building (e.g. Berthelier et al 2018, Ou et al 2019, or are challenging to install and use (Flutre et al 2011). RepeatModeler2 is easy to install and run, as we provide a container version to avoid installing independently all dependencies.…”

Section: Speciesmentioning

confidence: 99%

RepeatModeler2: automated genomic discovery of transposable element families

Flynn

Hubley

Goubert

et al. 2019

Preprint

152

128

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AbstractThe accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a new pipeline that greatly facilitates this process. This new program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete LTR retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately three times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. The program had an extremely low false positive rate when applied to simulated genomes devoid of TEs. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, https://github.com/Dfam-consortium/TETools).SignificanceGenome sequences are being produced for more and more eukaryotic species. The bulk of these genomes is composed of parasitic, self-mobilizing transposable elements (TEs) that play important roles in organismal evolution. Thus there is a pressing need for developing software that can accurately identify the diverse set of TEs dispersed in genome sequences. Here we introduce RepeatModeler2, an easy-to-use package for the curation of reference TE libraries which can be applied to any eukaryotic species. Through several major improvements over the previous version, RepeatModeler2 is able to produce libraries that recapitulate the known composition of three model species with some of the most complex TE landscapes. Thus RepeatModeler2 will greatly enhance the discovery and annotation of TEs in genome sequences.

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“…Bam files were later submitted to the package PINDEL (version 0.2.5, parameters: -T 4, -x 5, -r false, -t false, -A 35) (Ye et al 2009) to identify deletions in samples. Transposable elements (TE) were annotated in P. dulcis and P. persica assemblies using TEdenovo and TEannot pipelines of the REPET package (Quesneville et al, 2005;Flutré et al, 2011) installed in the PiRATE virtual machine (Berthelier et al, 2018). Classification of TEdenovo consensus sequences at the order level was done with PASTEC (Hoede et al, 2014).…”

Section: Annotation and Analysis Of Transposable Elements In Genome Amentioning

confidence: 99%

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Alioto

Alexiou

Bardil

et al. 2019

Preprint

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Combining both short and long-read sequencing, we have estimated the almond Prunus dulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified.Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.3

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A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Cited by 44 publications

References 98 publications

Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

RepeatModeler2: automated genomic discovery of transposable element families

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

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