Mots-Clés

genomics viruses brown algae bioinformatics

Description

Integrated viral DNA has been found in the genomes of diverse eukaryotes and this integrated DNA is thought to play an important role in genome evolution1,2. Viruses in the phylum Nucleocytoviricota (also known as Nucleo-cytoplasmic large DNA viruses, NCLDVs) are a particularly interesting group of viruses as they have large complex genomes that contain many genes. The NCLDVs that infect brown algae (phaeoviruses) are the only members of this phylum of viruses that have been shown to integrate into their host's genome as part of their infection cycle3,4. The phaeoviruses are therefore expected to have a particularly marked influence on their host genomes but experimental analysis of their effect has been hampered by a lack of genome data for the brown algae. The Phaeoexplorer project (https://phaeoexplorer.sb-roscoff.fr/home/), coordinated by Mark Cock, has recently generated genome assemblies for 67 strains of brown algae plus four closely-related sister species. Ongoing analysis of these genomes is identifing a broad range of inserted phaeovirus genomes in diverse brown algal species.

The aim of this masters project will be to further characterise these inserted viral sequences and, in particular, to analyse how the viral sequences have been exploited by the host to become part of the host genetic toolkit (a process known as endogenisation).

The student will have full access to the unpublished Phaeoexplorer genomic resources and will use a broad range of bioinformatic approaches (comparative genomics, phylogenetic analysis, transcriptomics, synteny, network analysis) to identify and characterise endogenisation events.

References

1. Moniruzzaman, M., Weinheimer, A. R., Martinez-Gutierrez, C. A. & Aylward, F. O. (2020). Widespread endogenization of giant viruses shapes genomes of green algae. Nature 588, 141–145

2. Feschotte, C. & Gilbert, C. (2012). Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 13, 283–296

3. Delaroque, N., Maier, I., Knippers, R. & Müller, D. (1999). Persistent virus integration into the genome of its algal host, Ectocarpus siliculosus (Phaeophyceae). J Gen Virol 80 ( Pt 6), 1367–70

4. Cock, J. M. et al. (2010). The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465, 617–621

Supervisor for the internship : J. Mark Cock and Erwan Corre

Contact e-mail: cock@sb-roscoff.fr, corre@sb-roscoff.fr

Lab publications or recommended review on the subject :

• Bourdareau, S., Tirichine, L., Lombard, B., Loew, D., Scornet, D., Wu, Y., Coelho, S.M. and Cock, J.M. (2021). Histone modifications during the life cycle of the brown alga Ectocarpus. Genome Biology, 22, 12. doi: 10.1186/s13059-020-02216-8.
• Coelho, S.M., Cock, J.M. (2020). Brown algal model organisms. Annual Review of Genetics, 54, 71–92. doi.org/10.1146/annurev-genet-030620- 093031.
• Arun, A., Coelho, S.M., Peters, A.F., Bourdareau, S., Pérès, L., Scornet, D., Strittmatter, M., Lipinska, A.P., Yao, H., Godfroy, O., Montecinos, G.J., Avia, K., Macaisne, N., Troadec, C., Bendahmane, A. and Cock J.M. (2019). Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae. eLife, 8, e43101. doi: 10.7554/eLife.43101.
• Ahmed, S.*, Cock, J.M.*, Pessia, E.*, Luthringer, R., Cormier, A., Robuchon, M. Sterck, L., Peters, A.F., Dittami, S.M., Corre, E., Valero, M., Aury, J.-M., Roze, D., Van de Peer, Y., Bothwell, J., Marais, G.A.B., Coelho, S.M. (2014). A haploid system of sex determination in the brown alga Ectocarpus sp. Current Biology, 24, 1-13. *joint first authors.
• Cock, J.M., Sterck, L., Rouzé, P., Scornet, D., Allen, A.E., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J.-M., Badger, J.H., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J.H.F., Bowler, C., Boyen, C., Brownlee, C., Carrano, C.J., Charrier, B., Cho, G.Y., Coelho, S.M., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S.M., Doulbeau, S., Elias, M., Farnham, G., Gachon, C.M.M., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C, Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P.J., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C.A., Nelson, D.R., Nyvall-Collén, P., Peters, A.F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., A. Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D.C., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Van de Peer, Y. and Wincker, P. (2010). The Ectocarpus genome and the independent evolution of multicellularity in the brown algae. Nature, 465, 617-621.