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1. Evolutionary genomics of the cold-Adapted diatom Fragilariopsis cylindrus

Author

Mock, T., Otillar, R. P., Strauss, Jan, 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, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., Grigoriev, I. V., Mock, T., Otillar, R. P., Strauss, Jan, 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, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., and Grigoriev, I. V.

Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Published
2017
Full Text
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2. Evolutionary genomics of the cold-Adapted diatom Fragilariopsis cylindrus

Author

Mock, T., Otillar, R. P., Strauss, Jan, 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, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., Grigoriev, I. V., Mock, T., Otillar, R. P., Strauss, Jan, 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, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., and Grigoriev, I. V.

Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Published
2017
Full Text
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3. Evolutionary genomics of the cold-Adapted diatom Fragilariopsis cylindrus

Author

Mock, T., Otillar, R. P., Strauss, Jan, 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, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., Grigoriev, I. V., Mock, T., Otillar, R. P., Strauss, Jan, 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, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., and Grigoriev, I. V.

Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Published
2017
Full Text
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4. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Author

Riley, R., Riley, R., Salamov, A. A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., Lindquist, E. A., Sun, H., LaButti, K. M., Schmutz, J., Jabbour, D., Luo, H., Baker, S. E., Pisabarro, A. G., Walton, J. D., Blanchette, R. A., Henrissat, B., Martin, F., Cullen, D., Hibbett, D. S., Grigoriev, I. V., Riley, R., Riley, R., Salamov, A. A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., Lindquist, E. A., Sun, H., LaButti, K. M., Schmutz, J., Jabbour, D., Luo, H., Baker, S. E., Pisabarro, A. G., Walton, J. D., Blanchette, R. A., Henrissat, B., Martin, F., Cullen, D., Hibbett, D. S., and Grigoriev, I. V.

Published
2014

5. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Author

Riley, R., Riley, R., Salamov, A. A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., Lindquist, E. A., Sun, H., LaButti, K. M., Schmutz, J., Jabbour, D., Luo, H., Baker, S. E., Pisabarro, A. G., Walton, J. D., Blanchette, R. A., Henrissat, B., Martin, F., Cullen, D., Hibbett, D. S., Grigoriev, I. V., Riley, R., Riley, R., Salamov, A. A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., Lindquist, E. A., Sun, H., LaButti, K. M., Schmutz, J., Jabbour, D., Luo, H., Baker, S. E., Pisabarro, A. G., Walton, J. D., Blanchette, R. A., Henrissat, B., Martin, F., Cullen, D., Hibbett, D. S., and Grigoriev, I. V.

Published
2014

6. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Author

Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martinez, A.T., Otillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Foster, B., Gaskell, J., Glotzer, D., Gorecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N., Kersten, P., Kohler, A., Kues, U., Kumar, T.K., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lombard, V., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nagy, L.G., Nolan, M., Ohm, R.A., Patyshakuliyeva, A, Rokas, A., Ruiz-Duenas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St John, F., Stenlid, J., Sun, H., Sun, S., Syed, K., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V., Hibbett, D.S., Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martinez, A.T., Otillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Foster, B., Gaskell, J., Glotzer, D., Gorecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N., Kersten, P., Kohler, A., Kues, U., Kumar, T.K., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lombard, V., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nagy, L.G., Nolan, M., Ohm, R.A., Patyshakuliyeva, A, Rokas, A., Ruiz-Duenas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St John, F., Stenlid, J., Sun, H., Sun, S., Syed, K., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V., and Hibbett, D.S.

Published
2012

7. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Author

Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martinez, A.T., Otillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Foster, B., Gaskell, J., Glotzer, D., Gorecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N., Kersten, P., Kohler, A., Kues, U., Kumar, T.K., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lombard, V., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nagy, L.G., Nolan, M., Ohm, R.A., Patyshakuliyeva, A, Rokas, A., Ruiz-Duenas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St John, F., Stenlid, J., Sun, H., Sun, S., Syed, K., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V., Hibbett, D.S., Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martinez, A.T., Otillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Foster, B., Gaskell, J., Glotzer, D., Gorecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N., Kersten, P., Kohler, A., Kues, U., Kumar, T.K., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lombard, V., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nagy, L.G., Nolan, M., Ohm, R.A., Patyshakuliyeva, A, Rokas, A., Ruiz-Duenas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St John, F., Stenlid, J., Sun, H., Sun, S., Syed, K., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V., and Hibbett, D.S.

Published
2012

8. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.

Author

Worden, A. Z., Lee, J.-H., Mock, Thomas, Rouzé, P., Simmson, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, Uwe, Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y., Grigoriev, I. V., Worden, A. Z., Lee, J.-H., Mock, Thomas, Rouzé, P., Simmson, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, Uwe, Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y., and Grigoriev, I. V.

Published
2009

9. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.

Author

Worden, A. Z., Lee, J.-H., Mock, Thomas, Rouzé, P., Simmson, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, Uwe, Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y., Grigoriev, I. V., Worden, A. Z., Lee, J.-H., Mock, Thomas, Rouzé, P., Simmson, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, Uwe, Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y., and Grigoriev, I. V.

Published
2009

10. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes micromonas

Author

Worden, Alexandra Z., Lee, J.-H., Mock, T., Rouzé, P., Simmons, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Von Dassow, P., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, U., Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van De Peer, Y., Grigoriev, I.V., Worden, Alexandra Z., Lee, J.-H., Mock, T., Rouzé, P., Simmons, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Von Dassow, P., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, U., Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van De Peer, Y., and Grigoriev, I.V.

Abstract

Picoeukaryotes are a taxonomically diverse group of organism less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90 of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

Published
2009
Full Text
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11. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes micromonas

Author

Worden, Alexandra Z., Lee, J.-H., Mock, T., Rouzé, P., Simmons, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Von Dassow, P., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, U., Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van De Peer, Y., Grigoriev, I.V., Worden, Alexandra Z., Lee, J.-H., Mock, T., Rouzé, P., Simmons, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Von Dassow, P., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, U., Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van De Peer, Y., and Grigoriev, I.V.

Abstract

Picoeukaryotes are a taxonomically diverse group of organism less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90 of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

Published
2009
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12. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, Grigoriev Iv, Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, and Grigoriev Iv

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008
Full Text
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13. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, Grigoriev Iv, Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, and Grigoriev Iv

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008
Full Text
View/download PDF

14. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., 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., Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., 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., and Grigoriev, I. V.

Published
2008

15. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, Grigoriev Iv, Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, and Grigoriev Iv

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008
Full Text
View/download PDF

16. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., 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., Cadoret, J.-P., Bowler, C., Allan, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheshwari, U., Martens, C., Maumus, F., Otillar, R. P., Rayko, E., Salamov, A., Vandepoele, K., Beszeri, B., Gruber, A., Heijde, M., Katinka, M., Mock, Thomas, Valentin, Klaus-Ulrich, Verret, F., Berges, J. A., Brownlee, C., Chiovitti, A., Jae Choi, C., Coesel, S., De Martino, A., Detter, J. C., Durkin, C., Falciatore, A., Fournet, J., Haruta, M., Huysman, M. J. J., Jenkins, B. D., Jiroutova, K., Jorgensen, R. E., Joubert, Y., Kaplan, A., Kröger, N., Kroth, P. G., La Roche, J., Lindquiste, E., Lommer, M., Martin-Jézéquel, V., Lopez, P. J., Lucas, S., Mangogna, M., McGinnis, K., Medlin, Linda, Monsant, A., Oudot-Le Secq, M.-P., Napoli, C., Obornik, M., Petit, J.-L., Porcel, B. M., Poulsen, N., Robison, M., Rychlewski, L., Rynearson, T. A., Schmutz, J., Schnitzler Parker, M., Shapiro, H., Siaur, M., Stanley, M., Sussman, M. J., 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., and Grigoriev, I. V.

Published
2008

17. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, Grigoriev Iv, Bowler, C, Allen, A, Badger, J, Grimwood, J, Jabbari, K, Kuo, A, Maheswari, U, Martens, C, Maumus, F, Otillar, R, Rayko, E, Salamov, A, Vandepoele, K, Beszteri, B, Gruber, A, Heijde, M, Katinka, M, Mock, T, Valentin, K, Verret, F, Berges, J, Brownlee, C, Cadoret, Jean-paul, Chiovitti, A, Choi, C, Coesel, S, De Martino, A, Detter, J, Durkin, C, Falciatore, A, Fournet, J, Haruta, M, Huysman, M, Jenkins, B, Jiroutova, K, Jorgensen, R, Joubert, Y, Kaplan, A, Kroger, N, Kroth, P, La Roche, J, Lindquist, E, Lommer, M, Martin Jezequel, V, Lopez, P, Lucas, S, Mangogna, M, Mcginnis, K, Medlin, L, Montsant, A, Oudot Le Secq, M, Napoli, C, Obornik, M, Parker, M, Petit, J, Porcel, B, Poulsen, N, Robison, M, Rychlewski, L, Rynearson, T, Schmutz, J, Shapiro, H, Siaut, M, Stanley, M, Sussman, M, Taylor, A, Vardi, A, Von Dassow, P, Vyverman, W, Willis, A, Wyrwicz, L, Rokhsar, D, Weissenbach, J, Armbrust, E, Green, B, Van De Peer, Y, and Grigoriev Iv

Abstract

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Published
2008
Full Text
View/download PDF

18. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Author

Mock, Thomas, Otillar, Robert P., Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J., Allen, Andrew E., Dupont, Christopher L, Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang, Barry, Kerrie W., Falciatore, Angela, Ferrante, Maria I., Fortunato, Antonio E., Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G., Kroth, Peter G., Leese, Florian, Lindquist, Erika A., Lyon, Barbara R., Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A., Uhlig, Christiane, Valas, Ruben E., Valentin, Klaus, Worden, Alexandra Z., Armbrust, E. Virginia, Clark, Matthew D., Bowler, Chris, Green, Beverley R., Moulton, Vincent, van Oosterhout, Cock, Grigoriev, Igor V., Mock, Thomas, Otillar, Robert P., Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J., Allen, Andrew E., Dupont, Christopher L, Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang, Barry, Kerrie W., Falciatore, Angela, Ferrante, Maria I., Fortunato, Antonio E., Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G., Kroth, Peter G., Leese, Florian, Lindquist, Erika A., Lyon, Barbara R., Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A., Uhlig, Christiane, Valas, Ruben E., Valentin, Klaus, Worden, Alexandra Z., Armbrust, E. Virginia, Clark, Matthew D., Bowler, Chris, Green, Beverley R., Moulton, Vincent, van Oosterhout, Cock, and Grigoriev, Igor V.

Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent from those of temperate diatoms (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Published
2017

19. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Author

Mock, Thomas, Otillar, Robert P., Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J., Allen, Andrew E., Dupont, Christopher L, Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang, Barry, Kerrie W., Falciatore, Angela, Ferrante, Maria I., Fortunato, Antonio E., Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G., Kroth, Peter G., Leese, Florian, Lindquist, Erika A., Lyon, Barbara R., Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A., Uhlig, Christiane, Valas, Ruben E., Valentin, Klaus, Worden, Alexandra Z., Armbrust, E. Virginia, Clark, Matthew D., Bowler, Chris, Green, Beverley R., Moulton, Vincent, van Oosterhout, Cock, Grigoriev, Igor V., Mock, Thomas, Otillar, Robert P., Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J., Allen, Andrew E., Dupont, Christopher L, Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang, Barry, Kerrie W., Falciatore, Angela, Ferrante, Maria I., Fortunato, Antonio E., Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G., Kroth, Peter G., Leese, Florian, Lindquist, Erika A., Lyon, Barbara R., Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A., Uhlig, Christiane, Valas, Ruben E., Valentin, Klaus, Worden, Alexandra Z., Armbrust, E. Virginia, Clark, Matthew D., Bowler, Chris, Green, Beverley R., Moulton, Vincent, van Oosterhout, Cock, and Grigoriev, Igor V.

Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent from those of temperate diatoms (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Published
2017

20. Comparative genomics of biotechnologically important yeasts

Author

Sub Molecular Microbiology, Molecular Microbiology, Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H, Lopes, Mariana R, Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A, Wisecaver, Jennifer H, Long, Tanya M, Calvey, Christopher H, Aerts, Andrea L, Barry, Kerrie W, Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y, Deshpande, Shweta, Douglass, Alexander P, Hanson, Sara J, Klenk, Hans-Peter, LaButti, Kurt M, Lapidus, Alla, Lindquist, Erika A, Lipzen, Anna M, Meier-Kolthoff, Jan P, Ohm, Robin A, Otillar, Robert P, Pangilinan, Jasmyn L, Peng, Yi, Rokas, Antonis, Rosa, Carlos A, Scheuner, Carmen, Sibirny, Andriy A, Slot, Jason C, Stielow, J Benjamin, Sun, Hui, Kurtzman, Cletus P, Blackwell, Meredith, Grigoriev, Igor V, Jeffries, Thomas W, Sub Molecular Microbiology, Molecular Microbiology, Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H, Lopes, Mariana R, Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A, Wisecaver, Jennifer H, Long, Tanya M, Calvey, Christopher H, Aerts, Andrea L, Barry, Kerrie W, Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y, Deshpande, Shweta, Douglass, Alexander P, Hanson, Sara J, Klenk, Hans-Peter, LaButti, Kurt M, Lapidus, Alla, Lindquist, Erika A, Lipzen, Anna M, Meier-Kolthoff, Jan P, Ohm, Robin A, Otillar, Robert P, Pangilinan, Jasmyn L, Peng, Yi, Rokas, Antonis, Rosa, Carlos A, Scheuner, Carmen, Sibirny, Andriy A, Slot, Jason C, Stielow, J Benjamin, Sun, Hui, Kurtzman, Cletus P, Blackwell, Meredith, Grigoriev, Igor V, and Jeffries, Thomas W

Published
2016

21. Comparative genomics of biotechnologically important yeasts

Author

Sub Molecular Microbiology, Molecular Microbiology, Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H, Lopes, Mariana R, Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A, Wisecaver, Jennifer H, Long, Tanya M, Calvey, Christopher H, Aerts, Andrea L, Barry, Kerrie W, Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y, Deshpande, Shweta, Douglass, Alexander P, Hanson, Sara J, Klenk, Hans-Peter, LaButti, Kurt M, Lapidus, Alla, Lindquist, Erika A, Lipzen, Anna M, Meier-Kolthoff, Jan P, Ohm, Robin A, Otillar, Robert P, Pangilinan, Jasmyn L, Peng, Yi, Rokas, Antonis, Rosa, Carlos A, Scheuner, Carmen, Sibirny, Andriy A, Slot, Jason C, Stielow, J Benjamin, Sun, Hui, Kurtzman, Cletus P, Blackwell, Meredith, Grigoriev, Igor V, Jeffries, Thomas W, Sub Molecular Microbiology, Molecular Microbiology, Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H, Lopes, Mariana R, Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A, Wisecaver, Jennifer H, Long, Tanya M, Calvey, Christopher H, Aerts, Andrea L, Barry, Kerrie W, Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y, Deshpande, Shweta, Douglass, Alexander P, Hanson, Sara J, Klenk, Hans-Peter, LaButti, Kurt M, Lapidus, Alla, Lindquist, Erika A, Lipzen, Anna M, Meier-Kolthoff, Jan P, Ohm, Robin A, Otillar, Robert P, Pangilinan, Jasmyn L, Peng, Yi, Rokas, Antonis, Rosa, Carlos A, Scheuner, Carmen, Sibirny, Andriy A, Slot, Jason C, Stielow, J Benjamin, Sun, Hui, Kurtzman, Cletus P, Blackwell, Meredith, Grigoriev, Igor V, and Jeffries, Thomas W

Published
2016

22. Comparative genomics of biotechnologically important yeasts

Author

Sub Molecular Microbiology, Molecular Microbiology, Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H, Lopes, Mariana R, Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A, Wisecaver, Jennifer H, Long, Tanya M, Calvey, Christopher H, Aerts, Andrea L, Barry, Kerrie W, Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y, Deshpande, Shweta, Douglass, Alexander P, Hanson, Sara J, Klenk, Hans-Peter, LaButti, Kurt M, Lapidus, Alla, Lindquist, Erika A, Lipzen, Anna M, Meier-Kolthoff, Jan P, Ohm, Robin A, Otillar, Robert P, Pangilinan, Jasmyn L, Peng, Yi, Rokas, Antonis, Rosa, Carlos A, Scheuner, Carmen, Sibirny, Andriy A, Slot, Jason C, Stielow, J Benjamin, Sun, Hui, Kurtzman, Cletus P, Blackwell, Meredith, Grigoriev, Igor V, Jeffries, Thomas W, Sub Molecular Microbiology, Molecular Microbiology, Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H, Lopes, Mariana R, Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A, Wisecaver, Jennifer H, Long, Tanya M, Calvey, Christopher H, Aerts, Andrea L, Barry, Kerrie W, Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y, Deshpande, Shweta, Douglass, Alexander P, Hanson, Sara J, Klenk, Hans-Peter, LaButti, Kurt M, Lapidus, Alla, Lindquist, Erika A, Lipzen, Anna M, Meier-Kolthoff, Jan P, Ohm, Robin A, Otillar, Robert P, Pangilinan, Jasmyn L, Peng, Yi, Rokas, Antonis, Rosa, Carlos A, Scheuner, Carmen, Sibirny, Andriy A, Slot, Jason C, Stielow, J Benjamin, Sun, Hui, Kurtzman, Cletus P, Blackwell, Meredith, Grigoriev, Igor V, and Jeffries, Thomas W

Published
2016

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