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6 results on '"Everett, M. V."'

1. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

Author

Mckinney, G. J., Seeb, L. W., Larson, W. A., Gomez-Uchida, D., Limborg, Morten Tønsberg, Brieuc, M. S. O., Everett, M. V., Naish, K. A., Waples, R. K., Seeb, J. E., Mckinney, G. J., Seeb, L. W., Larson, W. A., Gomez-Uchida, D., Limborg, Morten Tønsberg, Brieuc, M. S. O., Everett, M. V., Naish, K. A., Waples, R. K., and Seeb, J. E.

Abstract

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.

Published
2016

3. 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

4. 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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6. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha).

Author

McKinney GJ, Seeb LW, Larson WA, Gomez-Uchida D, Limborg MT, Brieuc MS, Everett MV, Naish KA, Waples RK, and Seeb JE

Subjects
Animals, Expressed Sequence Tags, Genetics, Population, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Adaptation, Biological, Chromosome Mapping, Genetic Variation, Salmon classification, Salmon genetics
Abstract

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences., (© 2015 John Wiley & Sons Ltd.)

Published
2016
Full Text
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