23/01/2018. PiRATE: a Pipeline to Retrieve and Annotate TEs of non-model organisms. Transposable elements (TEs) Impact of TEs on genomes

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1 Transposable elements () PiRATE: a Pipeline to Retrieve and Annotate of non-model organisms are DNAsequences able to move (= transposition) into the host genome of eucaryotic and procaryotic organisms Two classes: Classe I named retrotransposons move by a copy-paste mechanism dsdna TE TE Classe II named DNA transposon move by a cut-paste mechanism Jérémy BERTHELIER, Ph.D. student N. Casse, N. Daccord, V. Jamilloux, B. Saint-Jean, G. Carrier dsdna TE 2 A huge diversity Impact of on genomes Wicker et al., 2007 Non-autonomous impact genome size Zea Mays Homo sapiens Classe I TRIM LARD >4000 bp <4000 bp can generate phenotype changes Proportion of in genomes (%) Chénais et al., 2012 (Non-autonomes) Vitis vinifera Citrus sinensis Kobayashi et al., 2004 Butelli et al., 2012 Classe II MITE <500 bp TE mutations can promote species adaptation 3 Darboux et al., How to conduct a de novo TE annotation Limitations with non-model organisms 1. Detection of Seq1 Seq2 1. Detection of Seq1 Seq2 Seq3 Seq3 Genome assembly is usually fragmented missassembly of repeated elements 2. Classification of detected No Class 2. Classification of detected No Class Comparaison (BLAST) Few knowledge in TE databanks difficulty to classify/recognize Comparaison (BLAST) TE1 TE1 3. TE annotation 3. TE annotation Genome assembly 5 Genome assembly 6 1

2 Limitations with non-model organisms 1. Detection of Seq1 Seq2 Seq3 PiRATE is implemented into a stand-alone Galaxy: Genome assembly is usually fragmented missassembly of repeated elements Improve the detection step 2. Classification of detected No Class Few knowledge in TE databanks difficulty to classify/recognize Comparaison (BLAST) Improve the classification step 3. TE annotation TE1 Genome assembly Download the PiRATE Virtual Machine (Virtual Linux) 2. Import the PiRATE Virtual Machine into a Virtual Machine Monitor (VirtualBox) Launch the PiRATE-Galaxy It s ready to use!!!

3 Tools RepeatMasker Censor Windowmasker Transposon-PSI TeClass RepClass TESeeker + Tools TRANSPO LTR_STRUC MAK LTR_MINER LTR_par/LTR_seq Find_LTR LTR_FINDER LTRharvest LTRdigest MUST Tools REPuter RepeatFinder RECON GROUPER PILER RepeatScout Repseek Tallymer TEdenovo Tool ReAS RepeatExplorer RepARK dnapipete Transposome REPdenovo HelSearch MITE-Hunter Sine-Finder RSPB MITE-Digger TIRfinder Helitron_scanner detectmite MGEScan-LTR MGEScan-nonLTR RepeatModeler Group every existing TE detection approach to: - promote the detection of every TE families - promote the detection of full-length To facilitate the classification step A priori de novo Build repeated sequences Detect repeated sequences Detect specific structure of Detect similare sequences

4 output Cluster identical sequences Remove redundancy Only keep the larger putative Concatenate the detected sequences Cluster identical sequences Remove redundancy Only keep the larger putative Automated classification Automated classification Using databanks Automated classification Using databanks 23 Improved by: - combining public TE databanks - adding non-invertoried sequences - Creating new profiles 24 4

5 Familly 1 Familly 2 Group TE sequences into families PiRATE-Galaxy: Annotation PiRATE-Galaxy: Annotation 3: Annotation 3: Annotation 3 annotations: Putative 27 3 annotations: Putative 28 PiRATE-Galaxy: Annotation Control with Arabidopsis thaliana Genome size: 157 Mb Arabidopsis thaliana 259 TE families - PiRATE detects 81% of the TE families of A. thaliana (difficulty to detect non-autonomous ) 3: Annotation - 75% of these detectes were correctly classified (difficulty to classify non-autonomous ) 3 annotations: Putative All All repeated elements 29 Berthelier et al. BMC Genomics Under Review 30 5

6 Use of PiRATE with T. lutea (Haptophyta) Use of PiRATE with T. lutea (Haptophyta) Example with the microalga Tisochrysis lutea Phylum: Haptophyte Genome size: 82 Mb 193 contigs Example with the microalga Tisochrysis lutea Phylum: Haptophyte Genome size: 82 Mb 193 contigs 17 TE families of Haptophytes 17 TE families of Haptophytes Putative non-autonomous Putative autonomous putative autonomous total LTR / Copia LTR / Gypsy LTR / LARD LTR / TRIM LINE / Tx1 SINE Total repeated elements Proportion of the genome (%) Berthelier et al. BMC Genomics Under Review 31 TIR / Tc1-Mariner TIR / hat TIR / PiggyBac TIR / PIF-Harbinger MITE Proportion of the genome (%) 32 Berthelier et al. BMC Genomics Under Review Thanks for your attention! Acknowledgements: How improve TE classification? PASTEClassifier Public TE databanks To improve: Combine public databanks and adding non-inventoried Non-inventoried - Nicolas Daccord - Véronique Jamilloux Public profil Grégory Carrier Funding: Bruno Saint-Jean Nathalie Casse New profiles done done for microalgal genomes Control Detection Control Classification Arabidopsis thaliana Arabidopsis thaliana % of classified TE families % of detected TE families 96% 94% 100% 79% 80% 62% 60% 60% 40% 27% 20% 0% LTR (173) LINE (19) SINE (22) TIR (69) Helitron n-a (5) Helitron (32) 81% 81% n-a TIR Total TE (58) families (359) 100% 80% 60% 40% 20% 0% 98% 91% 87% 50% 27% LTR (148) LINE (15) SINE (6) TIR (43) n-a TIR (48) Classification : Correct 100% Helitron (3) 7% n-a Helitron (29) 359 TE families