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Analysis of Transposable Elements and Protein Divergence Across Diatoms

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Analysis of Transposable Elements and Protein Divergence Across Diatoms Analysis of Transposable Elements and Protein Divergence across Diatoms Nina Denne, Illinois Mathematics and Science Academy Matthew Parks, Norm Wickett, & Matthew Johnson, Chicago Botanic Garden IMSAloquium – 4/26/2017 IMSAloquium 2017 1 Outline • Topic 1: Introduction to Diatoms • Topic 2: Introduction to Transposable Elements • Topic 3: Introduction to Protein Divergence • Topic 4: Methods • Topic 5: Transposable Element Results • Topic 6: Protein Divergence Results • Topic 7: Discussion IMSAloquium 2017 2 Diatoms • Responsible for up to 20% of total global photosynthesis • 3 diatom genomes have been sequenced: Thalassiosira pseudonana, Phaeodactylum tricornutum, Fragiliariopsis cylindrus (closest relative: Nannochloropsis gaditana) • How do these diatom genomes compare to Psammoneis japonica in terms of transposable elements and protein divergence? Topic: Introduction to Diatoms - IMSAloquium 2017 3 Diatoms Us! Topic: Introduction to Diatoms IMSAloquium 2017 4 Nannochloropsis gaditana Thalassiosira pseudonana Psammoneis japonica Phaeodactylum tricornutum Fragilariopsis cylindrus Topic: Introduction to Diatoms - IMSAloquium 2017 5 Transposable Elements • DNA sequences that can excise themselves and reinsert themselves in the genome • Regulate gene expression • Two main classes: • 1. Class 1 transposons (retrotransposons) • 2. Class 2 transposons (DNA transposons) • Diatom-specific lineages: CoDiI and CoDiII • Important in understanding genome function and evolution Topic: Transposable Element Introduction - IMSAloquium 2017 6 Protein Divergence -ATCG--ACTG-A • Quantifying divergence between protein sequences of all 4 diatom genomes -TTCA--GCTGCG • 3 methods -ATCG--ACTG-A -TTCA--GCTGCG -ATCG--ACTG-A -TTCA--GCTGCG Topic: Protein Divergence Introduction - IMSAloquium 2017 7 Distribution of CoDi elements in Diatoms Species Psammoneis Thalassiosira Phaeodactylum Nannochloropsis Fragilariopsis japonica pseudonana tricornutum gaditana cylindrus CoDi-1 16 1 87 0 0 CoDi-2 2,030 0 375 0 84 CoDi-3 38 0 163 0 15 CoDi-4 784 51 404 0 57 CoDi-5 5 34 116 0 288 CoDi-6 580 54 170 5 35 CoDi-7 7 0 63 0 3 Total 3,453 140 1,176 5 482 Topic: Methods - IMSAloquium 2017 8 Percent of total genome size represented by transposable elements Species Psammoneis Phaeodactylum Thalassiosira Nannochloropsis Fragilariopsis japonica tricornutum pseudonana gaditana cylindrus Percent 3.26% 4.12% 1.66 % 2.39% 2.47% TEs Topic: Transposable Element Results - IMSAloquium 2017 9 Transposable Element Distribution Distribution of Transposable Elements across Heterokonts 3500 3000 2500 2000 1500 1000 500 0 LINEs Ty1/Copia Gyspy/DIRS1 CoDi DNA transposons Psammoneis Thalassiosira Phaeodactylum Nannochloropsis Fragilariopsis Topic: Transposable Element Results - IMSAloquium 2017 10 1000 Number of Hits 1200 600 400 800 200 0 RT_1731 RT_17_6 HMM Hits from the RT Gypsy Database RT_412_mdg1 RT_a_clade RT_alpharetrovirida Nannochloropsis RT_athila RT_badnavirus RT_b_clade RT_bel RT_betaretroviridae RT_caulimovirus RT_cavemovirus RT_cer2_3 RT_codi_c RT_codi_d RT_codi_I Thalassiosira RT_codi_II Topic: Transposable Element Results - RT_copia RT_crm RT_csrn1 RT_del RT_deltaretroviridae RT_epsilonretrovirid RT_galadriel RT_galea Fragilariopsis RT_gammaretroviri RT_gmr1 RT_gypsy RT_hydra IMSAloquium RT_lentiviridae RT_maggy RT_micropia RT_oryco 2017 RT_osvaldo Phaeodactylum RT_pao RT_pCretro RT_pseudovirus RT_pyggy RT_pyret RT_reina RT_retrofit RT_sinbad RT_sire RT_soymovirus Psammoneis RT_spumaretrovirid RT_suzu RT_tas RT_tat 11 RT_TF RT_tork RT_v_clade Hidden Markov Model Hits Total number of hits per species modeled 3500 3000 2500 2000 1500 Number of Hits 1000 500 0 Nannochloropsis Psammoneis Thalassiosira Phaeodactylum Fragilariopsis Psammoneis Thalassiosira Fragilariopsis Phaeodactylum Nannochloropsis Topic: Transposable Element Results - IMSAloquium 2017 12 Protein Divergence Topic: Protein Divergence Results - IMSAloquium 2017 13 Discussion • Transposable Elements • CoDi elements found in all diatom species • Including CoDi elements thought to be specific to Phaeodactylum tricornutum • Some CoDi hits found in Nannochloropsis • Psammoneis japonica had the most total CoDi matches and HMM hits • Protein Divergence • Proteins on average are around 40% similar • Levels of divergence in different species pairwise comparisons were very similar • Amount of evolutionary change between any two species is roughly equal for conserved proteins Topic: Discussion - IMSAloquium 2017 14 References • Armbrust, E.V., Berges, J.A., Bowler, C., Green, B.R., Martinez, D., Putnam, N.H., Zhou, S., Allen, A.E., Apt, K.E., Bechner, M., Brzezinski, M.A., Chaal, B.K., Chiovitti, A., Davis, A.K., Demarest, M.S., Detter, J.C., Glavina, T., Goodstein, D., Hadi, M.Z., Hellsten, U., Hildebrand, M., Jenkins, B.D., Jurka, J., Kapitonov, V.V., Kröger, N., Lau, W.W., Lane, T.W., Larimer, F.W., Lippmeier, J.C., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M.S., Palenik, B., Pazour, G.J., Richardson, P.M., Rynearson, T.A., Saito, M.A., Schwartz, D.C., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F.P., Rokhsar, D.S., 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306(5693), 79-86. • Bowler, C., Allen, A.E., Badger, J.H., Grimwood, J., Jabbari, K., Kuo, A., Maheswari, U., Martens, C., Maumus, F., Otillar, R.P., Rayko, E., Salamov, A., Vandepoele, K., Beszteri, B., Gruber, A., Heijde, M., Katinka, M., Mock, T., Valentin, K., Verret, F., Berges, J.A., Brownlee, C., Cadoret, J.P., Chiovitti, A., Choi, C.J., Coesel, S., De Martino, A., Detter, J.C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M.J., Jenkins, B.D., Jiroutova, K., Jorgensen, R.E., Joubert, Y., Kaplan, A., Kroger, N., Kroth, P.G., La Roche, J., Lindquist, E., Lommer, M., Martin-Jezequel, V., Lopez, P.J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, L.K., Montsant, A., Oudot-Le Secq, M.P., Napoli, C., Obornik, M., Parker, M.S., Petit, J.L., Porcel, B.M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T.A., Schmutz, J., Shapiro, H., Siaut, M., Stanley, M., Sussman, M.R., Taylor, A.R., Vardi, A., von Dassow, P., Vyverman, W., Willis, A., Wyrwicz, L.S., Rokhsar, D.S., Weissenbach, J., Armbrust, E.V., Green, B.R., Van de Peer, Y., Grigoriev, I.V., 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456, 239-244. • Eisenberg, L. (2012, September 20). The Great Tree of Life. Retrieved April 11, 2017, from http://visual.ly/great-tree-life • Genetic manipulation of competition for nitrate between heterotrophic bacteria and diatoms. (n.d.). Retrieved April 12, 2017, from https://scripps.ucsd.edu/biblio/genetic-manipulation-competition-nitrate-between- heterotrophic-bacteria-and-diatoms • Li, C.L., Ashworth, M.P., Witkowski. A., Dabek, P., Medlin, L.K., Kooistra, C.K., Sato, S., Zglobicka, I., Kurzydlowski, K.J., Theriot, E.C., Sabir, J.S.M., Khiyami, M., Mutwakil M., Sabit, M., Alharbi, N., Hajarah, N., Qing, S., Jansen, R.K., 2015. New Insights into Plagiogrammaceae (Bacillariophyta) Based on Multigene Phylogenies and Morphological Characteristics with the Description of a New Genus and Three New Species. PLOS https://doi.org/10.1371/journal.pone.0139300. • Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A., 2011. The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0. Nucleic Acids Research 39 (suppl 1): D70-D74. DOI: 10.1093/nar/gkq1061 • Maumus, F., Allen, A.E., Mhiri, C., Hu, H., Kamel, J., Vardi, A., Grandbastien, M., Bowler, C., 2009. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics 10:624. DOI: 10.1186/1471-2164-10-624. • Mock, T., Otillar, R.P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B.J., Allen, A.E., Dupont, C.L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K.W., Falciatore, A., Ferrante, M.I., Fortunato, A.E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M.G., Kroth, P.G., Leese, F., Lindquist, E.A., Lyon, B.R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J.A., Uhlig, C., Valas, R.E., Valentin, K.U., Worden, A.Z., Armbrust, E.V., Clark, M.D., Bowler, C., Green, B.R., Moulton, V., Oosterhout. C.V., Grigoriev, I.V., 2017. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541, 536-540. • Mock, T., Parker, M., Armbrust, E. Why Sequence Fragilariopsis cylindrus? (2013, November 07). Retrieved April 12, 2017, from http://jgi.doe.gov/why-sequence-fragilariopsis-cylindrus/ • Norton TA, Melkonian M, Andersen RA. 1996. Algal biodiversity. Phycologia 35: 308-326. • Pray, L., 2008. Transposons, or jumping genes: Not junk DNA? Nature Education 1, 32. • Radakovits, R., Jinkerson, R.E., Fuerstenberg, S.I., Tae, H., Settlage, R.E., Boore, J.L., Posewitz, M.C., 2012. Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana. Nature Communications 3:686. DOI: 10.1038/ncomms1688. • Samiksha, S. (2014, February 23). 6 Most Important Characteristics of Transposable Elements | Biology. Retrieved April 12, 2017, from http://www.yourarticlelibrary.com/biology/6-most-important-characteristics-of- transposable-elements-biology/6348/ • Smit AFA, Hubley R, Green P. 2013-2015. Repeatmasker Open-4.0, http://www.repeatmasker.org. IMSAloquium 2017 15 Thank you! • Matthew Parks • Norm Wickett • Matthew Johnson • The Chicago Botanic Garden • The SIR Department • Contact Info: Nina Denne, [email protected] IMSAloquium 2017 16 .
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