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11 results on '"Sterck, L"'

1. Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting

Author

Tyrmi, J. S. (Jaakko S.), Vuosku, J. (Jaana), Acosta, J. J. (Juan J.), Li, Z. (Zhen), Sterck, L. (Lieven), Cervera, M. T. (Maria T.), Savolainen, O. (Outi), Pyhäjärvi, T. (Tanja), Tyrmi, J. S. (Jaakko S.), Vuosku, J. (Jaana), Acosta, J. J. (Juan J.), Li, Z. (Zhen), Sterck, L. (Lieven), Cervera, M. T. (Maria T.), Savolainen, O. (Outi), and Pyhäjärvi, T. (Tanja)

Abstract

Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.

Published
2020

2. Insights into the Evolution of Multicellularity from the Sea Lettuce Genome

Author

De Clerck, O, Kao, SM, Bogaert, KA, Blomme, J, Foflonker, F, Kwantes, M, Vancaester, E, Vanderstraeten, L, Aydogdu, E, Boesger, J, Califano, G, Charrier, B, Clewes, R, Del Cortona, A, D'Hondt, S, Fernandez-Pozo, N, Gachon, CM, Hanikenne, M, Lattermann, L, Leliaert, F, Liu, X, Maggs, CA, Popper, ZA, Raven, JA, Van Bel, M, Wilhelmsson, PKI, Bhattacharya, D, Coates, JC, Rensing, SA, Van Der Straeten, D, Vardi, A, Sterck, L, Vandepoele, K, Van de Peer, Y, Wichard, T, Bothwell, JH, De Clerck, O, Kao, SM, Bogaert, KA, Blomme, J, Foflonker, F, Kwantes, M, Vancaester, E, Vanderstraeten, L, Aydogdu, E, Boesger, J, Califano, G, Charrier, B, Clewes, R, Del Cortona, A, D'Hondt, S, Fernandez-Pozo, N, Gachon, CM, Hanikenne, M, Lattermann, L, Leliaert, F, Liu, X, Maggs, CA, Popper, ZA, Raven, JA, Van Bel, M, Wilhelmsson, PKI, Bhattacharya, D, Coates, JC, Rensing, SA, Van Der Straeten, D, Vardi, A, Sterck, L, Vandepoele, K, Van de Peer, Y, Wichard, T, and Bothwell, JH

Abstract

© 2018 Elsevier Ltd We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance “green tides.” Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage. De Clerck et al. present the first genome sequence of a green seaweed, a dominant group of primary producers in coastal environments. The Ulva genome informs on an independent acquisition of multicellularity, sheds light on adaptations to life in intertidal habitats, and identifies candidate genes involved in DMSP biosynthesis and conversion to DMS.

Published
2018

3. Insights into the Evolution of Multicellularity from the Sea Lettuce Genome

Author

De Clerck, O, Kao, SM, Bogaert, KA, Blomme, J, Foflonker, F, Kwantes, M, Vancaester, E, Vanderstraeten, L, Aydogdu, E, Boesger, J, Califano, G, Charrier, B, Clewes, R, Del Cortona, A, D'Hondt, S, Fernandez-Pozo, N, Gachon, CM, Hanikenne, M, Lattermann, L, Leliaert, F, Liu, X, Maggs, CA, Popper, ZA, Raven, JA, Van Bel, M, Wilhelmsson, PKI, Bhattacharya, D, Coates, JC, Rensing, SA, Van Der Straeten, D, Vardi, A, Sterck, L, Vandepoele, K, Van de Peer, Y, Wichard, T, Bothwell, JH, De Clerck, O, Kao, SM, Bogaert, KA, Blomme, J, Foflonker, F, Kwantes, M, Vancaester, E, Vanderstraeten, L, Aydogdu, E, Boesger, J, Califano, G, Charrier, B, Clewes, R, Del Cortona, A, D'Hondt, S, Fernandez-Pozo, N, Gachon, CM, Hanikenne, M, Lattermann, L, Leliaert, F, Liu, X, Maggs, CA, Popper, ZA, Raven, JA, Van Bel, M, Wilhelmsson, PKI, Bhattacharya, D, Coates, JC, Rensing, SA, Van Der Straeten, D, Vardi, A, Sterck, L, Vandepoele, K, Van de Peer, Y, Wichard, T, and Bothwell, JH

Abstract

© 2018 Elsevier Ltd We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance “green tides.” Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage. De Clerck et al. present the first genome sequence of a green seaweed, a dominant group of primary producers in coastal environments. The Ulva genome informs on an independent acquisition of multicellularity, sheds light on adaptations to life in intertidal habitats, and identifies candidate genes involved in DMSP biosynthesis and conversion to DMS.

Published
2018

4. The Ectocarpus genome and the independent evolution of multicellularity in the brown algae

Author

Cock, J. M., Sterck, L., Rouze, P., Scorne, D., Allen, A. E., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J. M., Badger, J. H., Beszteri, Bank, Billiau, K., Bonnet, E., Bothwell, J. H. F., Bowler, C., Boyen, C., Brownlee, C., Carrano, C. J., Charrier, B., Youn Cho, G., Coelho, S. M., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S. M., Doulbeau, S., Elias, M., Farnham, C., 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., Leblan, C., Lerouge, P., Lohr, M., López-González, 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, Pi, Peters, A. F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S. A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D. C., Séguren, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, Klaus-Ulrich, von Dassow, P., Yamagishi, T., Van de Peer, Y., Wincker, P., Cock, J. M., Sterck, L., Rouze, P., Scorne, D., Allen, A. E., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J. M., Badger, J. H., Beszteri, Bank, Billiau, K., Bonnet, E., Bothwell, J. H. F., Bowler, C., Boyen, C., Brownlee, C., Carrano, C. J., Charrier, B., Youn Cho, G., Coelho, S. M., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S. M., Doulbeau, S., Elias, M., Farnham, C., 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., Leblan, C., Lerouge, P., Lohr, M., López-González, 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, Pi, Peters, A. F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S. A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D. C., Séguren, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, Klaus-Ulrich, von Dassow, P., Yamagishi, T., Van de Peer, Y., and Wincker, P.

Published
2010

5. The Ectocarpus genome and the independent evolution of multicellularity in the brown algae

Author

Cock, J. M., Sterck, L., Rouze, P., Scorne, D., Allen, A. E., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J. M., Badger, J. H., Beszteri, Bank, Billiau, K., Bonnet, E., Bothwell, J. H. F., Bowler, C., Boyen, C., Brownlee, C., Carrano, C. J., Charrier, B., Youn Cho, G., Coelho, S. M., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S. M., Doulbeau, S., Elias, M., Farnham, C., 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., Leblan, C., Lerouge, P., Lohr, M., López-González, 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, Pi, Peters, A. F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S. A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D. C., Séguren, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, Klaus-Ulrich, von Dassow, P., Yamagishi, T., Van de Peer, Y., Wincker, P., Cock, J. M., Sterck, L., Rouze, P., Scorne, D., Allen, A. E., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J. M., Badger, J. H., Beszteri, Bank, Billiau, K., Bonnet, E., Bothwell, J. H. F., Bowler, C., Boyen, C., Brownlee, C., Carrano, C. J., Charrier, B., Youn Cho, G., Coelho, S. M., Collén, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S. M., Doulbeau, S., Elias, M., Farnham, C., 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., Leblan, C., Lerouge, P., Lohr, M., López-González, 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, Pi, Peters, A. F., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S. A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D. C., Séguren, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, Klaus-Ulrich, von Dassow, P., Yamagishi, T., Van de Peer, Y., and Wincker, P.

Published
2010

6. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Author

Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Sterky, Fredrik, et al, Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Sterky, Fredrik, and et al

Abstract

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport., QC 20100525

Published
2006
Full Text
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7. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).

Author

Tuskan, G A, Difazio, S, Jansson, Stefan, Bohlmann, J, Grigoriev, I, Hellsten, U, Putnam, N, Ralph, S, Rombauts, S, Salamov, A, Schein, J, Sterck, L, Aerts, A, Bhalerao, Rupali R, Bhalerao, Rishikesh P, Blaudez, D, Boerjan, W, Brun, A, Brunner, A, Busov, V, Campbell, M, Carlson, J, Chalot, M, Chapman, J, Chen, G-L, Cooper, D, Coutinho, P M, Couturier, J, Covert, S, Cronk, Q, Cunningham, R, Davis, J, Degroeve, S, Déjardin, A, Depamphilis, C, Detter, J, Dirks, B, Dubchak, I, Duplessis, S, Ehlting, J, Ellis, B, Gendler, K, Goodstein, D, Gribskov, M, Grimwood, J, Groover, A, Gunter, L, Hamberger, B, Heinze, B, Helariutta, Y, Henrissat, B, Holligan, D, Holt, R, Huang, W, Islam-Faridi, N, Jones, S, Jones-Rhoades, M, Jorgensen, R, Joshi, C, Kangasjärvi, J, Karlsson, Jan, Kelleher, C, Kirkpatrick, R, Kirst, M, Kohler, A, Kalluri, U, Larimer, F, Leebens-Mack, J, Leplé, J-C, Locascio, P, Lou, Y, Lucas, S, Martin, F, Montanini, B, Napoli, C, Nelson, D R, Nelson, C, Nieminen, K, Nilsson, Ove, Pereda, V, Peter, G, Philippe, R, Pilate, G, Poliakov, A, Razumovskaya, J, Richardson, P, Rinaldi, C, Ritland, K, Rouzé, P, Ryaboy, D, Schmutz, J, Schrader, J, Segerman, Bo, Shin, H, Siddiqui, A, Sterky, Fredrik, Terry, A, Tsai, C-J, Uberbacher, E, Unneberg, P, Vahala, J, Wall, K, Wessler, S, Yang, G, Yin, T, Douglas, C, Marra, M, Sandberg, Göran, Van de Peer, Y, Rokhsar, D, Tuskan, G A, Difazio, S, Jansson, Stefan, Bohlmann, J, Grigoriev, I, Hellsten, U, Putnam, N, Ralph, S, Rombauts, S, Salamov, A, Schein, J, Sterck, L, Aerts, A, Bhalerao, Rupali R, Bhalerao, Rishikesh P, Blaudez, D, Boerjan, W, Brun, A, Brunner, A, Busov, V, Campbell, M, Carlson, J, Chalot, M, Chapman, J, Chen, G-L, Cooper, D, Coutinho, P M, Couturier, J, Covert, S, Cronk, Q, Cunningham, R, Davis, J, Degroeve, S, Déjardin, A, Depamphilis, C, Detter, J, Dirks, B, Dubchak, I, Duplessis, S, Ehlting, J, Ellis, B, Gendler, K, Goodstein, D, Gribskov, M, Grimwood, J, Groover, A, Gunter, L, Hamberger, B, Heinze, B, Helariutta, Y, Henrissat, B, Holligan, D, Holt, R, Huang, W, Islam-Faridi, N, Jones, S, Jones-Rhoades, M, Jorgensen, R, Joshi, C, Kangasjärvi, J, Karlsson, Jan, Kelleher, C, Kirkpatrick, R, Kirst, M, Kohler, A, Kalluri, U, Larimer, F, Leebens-Mack, J, Leplé, J-C, Locascio, P, Lou, Y, Lucas, S, Martin, F, Montanini, B, Napoli, C, Nelson, D R, Nelson, C, Nieminen, K, Nilsson, Ove, Pereda, V, Peter, G, Philippe, R, Pilate, G, Poliakov, A, Razumovskaya, J, Richardson, P, Rinaldi, C, Ritland, K, Rouzé, P, Ryaboy, D, Schmutz, J, Schrader, J, Segerman, Bo, Shin, H, Siddiqui, A, Sterky, Fredrik, Terry, A, Tsai, C-J, Uberbacher, E, Unneberg, P, Vahala, J, Wall, K, Wessler, S, Yang, G, Yin, T, Douglas, C, Marra, M, Sandberg, Göran, Van de Peer, Y, and Rokhsar, D

Abstract

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Published
2006
Full Text
View/download PDF

8. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Author

Tuskan, G.A., Tuskan, G.A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphillis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehiting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.-C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, D., Nieminen, K., Nilsson, O., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., Vahala, J., Tuskan, G.A., Tuskan, G.A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphillis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehiting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.-C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, D., Nieminen, K., Nilsson, O., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., and Vahala, J.

Published
2006

9. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Author

Tuskan, G.A., Tuskan, G.A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphillis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehiting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.-C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, D., Nieminen, K., Nilsson, O., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., Vahala, J., Tuskan, G.A., Tuskan, G.A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphillis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehiting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.-C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, D., Nieminen, K., Nilsson, O., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., and Vahala, J.

Published
2006

10. EST data suggest that poplar is an ancient polyploid

Author

Sterck, L., Rombauts, S., Jansson, S., Sterky, Fredrik, Rouze, P., Van de Peer, Y., Sterck, L., Rombauts, S., Jansson, S., Sterky, Fredrik, Rouze, P., and Van de Peer, Y.

Abstract

We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and K-S dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the K-S values, which resulted in a distribution reflecting the age of duplicated genes in poplar. Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus., QC 20100525

Published
2005
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11. Insights into the Evolution of Multicellularity from the Sea Lettuce Genome.

Author

De Clerck, O., Kao, S-M., Bogaert, K.A., Blomme, J., Foflonker, F., Kwantes, M., Vancaester, E., Vanderstraeten, L., Aydogdu, E., Boesger, J., Califano, G., Charrier, B., Clewes, R., Del Cortona, A., D'Hondt, S., Fernandez-Pozo, N., Gachon, C.M., Hanikenne, M., Lattermann, L., Leliaert, F., Liu, X., Maggs, Christine, Popper, Z.A., Raven, J.A., Van Bel, M., Wilhelmsson, P.K.I., Bhattacharya, D., Coates, J.C., Rensing, S.A., Van Der Straeten, D., Vardi, A., Sterck, L., Vandepoele, K., Van de Peer, Y., Wichard, T., Bothwell, J.H, De Clerck, O., Kao, S-M., Bogaert, K.A., Blomme, J., Foflonker, F., Kwantes, M., Vancaester, E., Vanderstraeten, L., Aydogdu, E., Boesger, J., Califano, G., Charrier, B., Clewes, R., Del Cortona, A., D'Hondt, S., Fernandez-Pozo, N., Gachon, C.M., Hanikenne, M., Lattermann, L., Leliaert, F., Liu, X., Maggs, Christine, Popper, Z.A., Raven, J.A., Van Bel, M., Wilhelmsson, P.K.I., Bhattacharya, D., Coates, J.C., Rensing, S.A., Van Der Straeten, D., Vardi, A., Sterck, L., Vandepoele, K., Van de Peer, Y., Wichard, T., and Bothwell, J.H

Abstract

We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance "green tides." Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage.

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