Annotation of the genome assembly (version 2) of the microalga Tisochrysis lutea

Date 2018
Author(s) Berthelier JérémyORCID1, Casse Nathalie2, Daccord Nicolas3, Jamilloux Véronique3, Saint-Jean Bruno1, Carrier GregoryORCID1
Affiliation(s) 1 : Ifremer, France
2 : Université du Mans
3 : INRA, France
DOI 10.17882/52231
Publisher SEANOE
Keyword(s) Tisochrysis lutea, genome, assembly, transposable elements, mobile elements, Haptophyte, algae
Abstract

We recently published the first draft genome of T. lutea obtained with the Illumina short-read technology. While this technology has a very low sequencing error rates, the assemblers are known to misassemble the long repeated sequences, resulting into the fragmentation of the genome assembly. The genome of T. lutea was re-sequenced with the long-read technology Pacific Bioscience. Indeed, long-read assemblers show efficiency to resolve the assembly of long repeated elements such as TEs. However, this technology have to date a high sequencing error rates and its combination with short-read Illumina data is became a common method to overcome this error rate. A de novo genome assembly was perform from the long-reads and was improved with Illumina short-read data, used in the first genome assembly version.

The de novo genome of T. lutea is composed of 193 contigs and has a size of 82 Mb. A gain of around 30 Mb was obtained (+34%), compared to the previous genome assembly, having a size of 54 Mb and composed of 7,659 contigs. The size of the coding regions has fewly increased between the both genome versions. While the de novo genome assembly encodes for ~16,000 genes, corresponding to a coding region length of 28 Mb, the previous gene proportion of the draft genome version was of 25 Mb. This suggest that the new assembled regions are mostly repeated elements. This new genome version is by far away more accurate than the previous one and was suitable to properly detect and annotate the TE content.

To identify potential autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate TEs) and conducted an accurate TE annotation in a de novo genome of T. lutea. We established that its genome is composed of 15.9% and 4.9% of Class I and Class II TEs respectively. Among them 3.8% and 15.95% correspond to potentially autonomous and non-autonomous TEs respectively.

Licence CC0
Acknowledgments This work was supported by the French region of Pays de la Loire with the AMI (Atlantic Microalgue) program and the French Research Institute for Exploitation of the Sea (IFREMER).
Data
File Size Format Processing Access
Contigs Genome Tiso V2 78 MB TEXTE Quality controlled data Open access
Annotation Potentially Autonomous Transposable Elements Tiso 102 KB TEXTE Quality controlled data Open access
Annotation Transposable Elements Tiso 4 MB TEXTE Quality controlled data Open access
Annotation Repeated Elements Tiso 8 MB TEXTE Quality controlled data Open access
Annotation Simple Repeats Tiso 6 MB TEXTE Quality controlled data Open access
Sequences used for the annotation of TEs and repeated elements 1 MB XLS, XLSX Quality controlled data Open access
Annotation of the genes coding 1 MB TEXTE Quality controlled data Open access
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How to cite 

Berthelier Jérémy, Casse Nathalie, Daccord Nicolas, Jamilloux Véronique, Saint-Jean Bruno, Carrier Gregory (2018). Annotation of the genome assembly (version 2) of the microalga Tisochrysis lutea. SEANOE. https://doi.org/10.17882/52231