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

Type Article
Date 2018-05
Language English
Author(s) Berthelier Jeremy1, 2, Casse Nathalie2, Daccord Nicolas3, 5, Jamilloux Veronique4, Saint-Jean Bruno1, Carrier GregoryORCID1
Affiliation(s) 1 : IFREMER, Physiol & Biotechnol Algae Lab, Rue Ille Yeu, F-44311 Nantes, France.
2 : Le Mans Univ, CNRS, EA IUML FR 3473 2160, Mer Mol Sante, Le Mans, France.
3 : Univ Angers, QUASAV SFR4207, AGROCAMPUS Ouest, Inst Rech Hort & Semences,INRA Angers, Angers, France.
4 : INRA Versailles, Res Unit Genom Info, Versailles, France.
5 : Univ Bretagne Loire, Angers, France.
Source Bmc Genomics (1471-2164) (Biomed Central Ltd), 2018-05 , Vol. 19 , N. 1 , P. 378 (14p.)
DOI 10.1186/s12864-018-4763-1
WOS© Times Cited 2
Keyword(s) Transposable elements, Genome assembly, Pipeline, Tool, Annotation, Algae, Haptophyte, Tisochrysis lutea
Abstract

Background

Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution.

Results

To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi.org/10.17882/51795), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements.

Conclusion

This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae.

Full Text
File Pages Size Access
Publisher's official version 14 1 MB Open access
Additional file 1: Additional supporting information. This file contains the additional supporting figures, tables, results and materials and methods 8 571 KB Open access
Additional file 2: Percentage of identity between copies of the expressed TE families. This file lists the percentage of identity between the TE copies of the 17 expressed TE families identified ... 19 KB Open access
Additional file 3: Sequences alignment of TE copies of the TIR/Mariner Luffy family. This file contains the sequence alignment of the copies belonging to the TIR/Mariner Luffy described in the genome 1 21 MB Open access
Additional file 4: Sequences alignment of the peptides matching on the predicted TE proteins. This file contains the alignment of the peptides matching on the predicted proteins of the TIR/Mariner... 3 991 KB Open access
Additional file 5: List of non-inventoried sequences added to the databanks used by the pipeline PiRATE. This file lists the non-inventoried sequences added to the databanks used by the pipeline... 23 KB Open access
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How to cite 

Berthelier Jeremy, Casse Nathalie, Daccord Nicolas, Jamilloux Veronique, Saint-Jean Bruno, Carrier Gregory (2018). A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. Bmc Genomics, 19(1), 378 (14p.). Publisher's official version : https://doi.org/10.1186/s12864-018-4763-1 , Open Access version : https://archimer.ifremer.fr/doc/00441/55250/