Harnessing genomics for evolutionary insights

被引:101
作者
Rokas, Antonis [1 ]
Abbot, Patrick [1 ]
机构
[1] Vanderbilt Univ, Dept Biol Sci, Nashville, TN 37235 USA
基金
美国国家科学基金会;
关键词
PROTEIN-DNA INTERACTIONS; SEQUENCING TECHNOLOGY; MICROBIAL DIVERSITY; QUALITY SCORES; SNP DISCOVERY; RAST SERVER; GENE; METAGENOMICS; ACCURACY; BIOLOGY;
D O I
10.1016/j.tree.2008.11.004
中图分类号
Q14 [生态学(生物生态学)];
学科分类号
071012 ; 0713 ;
摘要
Next-generation DNA sequencing technologies can generate unprecedented amounts of genomic data, even for non-model organisms. Here we describe how these new technologies have facilitated recent key advances in ecology and evolutionary biology, and highlight several outstanding ecological and evolutionary questions that are distinctly suited to the innovations they provide. Importantly, using these technologies to their full potential requires careful experimental design and critical consideration of several caveats associated with them. Although several significant challenges remain to be resolved before the integration of next-generation sequencing technologies into single-investigator research programs, we argue that they will soon transform ecology and evolution by fundamentally changing the ranges and types of questions that can be addressed.
引用
收藏
页码:192 / 200
页数:9
相关论文
共 83 条
[41]   Parallel confocal detection of single molecules in real time [J].
Lundquist, Paul M. ;
Zhong, Cheng F. ;
Zhao, Peiqian ;
Tomaney, Austin B. ;
Peluso, Paul S. ;
Dixon, John ;
Bettman, Brad ;
Lacroix, Yves ;
Kwo, Deborah P. ;
McCullough, Etienne ;
Maxham, Mark ;
Hester, Kevin ;
McNitt, Paul ;
Grey, Donald M. ;
Henriquez, Carlos ;
Foquet, Mathieu ;
Turner, Stephen W. ;
Zaccarin, Denis .
OPTICS LETTERS, 2008, 33 (09) :1026-1028
[42]   A genome-wide view of the spectrum of spontaneous mutations in yeast [J].
Lynch, Michael ;
Sung, Way ;
Morris, Krystalynne ;
Coffey, Nicole ;
Landry, Christian R. ;
Dopman, Erik B. ;
Dickinson, W. Joseph ;
Okamoto, Kazufusa ;
Kulkarni, Shilpa ;
Hartl, Daniel L. ;
Thomas, W. Kelley .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (27) :9272-9277
[43]   The frailty of adaptive hypotheses for the origins of organismal complexity [J].
Lynch, Michael .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 :8597-8604
[44]   Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth [J].
Marcy, Yann ;
Ouverney, Cleber ;
Bik, Elisabeth M. ;
Loesekann, Tina ;
Ivanova, Natalia ;
Martin, Hector Garcia ;
Szeto, Ernest ;
Platt, Darren ;
Hugenholtz, Philip ;
Relman, David A. ;
Quake, Stephen R. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (29) :11889-11894
[45]   The impact of next-generation sequencing technology on genetics [J].
Mardis, Elaine R. .
TRENDS IN GENETICS, 2008, 24 (03) :133-141
[46]   Genome sequencing in microfabricated high-density picolitre reactors [J].
Margulies, M ;
Egholm, M ;
Altman, WE ;
Attiya, S ;
Bader, JS ;
Bemben, LA ;
Berka, J ;
Braverman, MS ;
Chen, YJ ;
Chen, ZT ;
Dewell, SB ;
Du, L ;
Fierro, JM ;
Gomes, XV ;
Godwin, BC ;
He, W ;
Helgesen, S ;
Ho, CH ;
Irzyk, GP ;
Jando, SC ;
Alenquer, MLI ;
Jarvie, TP ;
Jirage, KB ;
Kim, JB ;
Knight, JR ;
Lanza, JR ;
Leamon, JH ;
Lefkowitz, SM ;
Lei, M ;
Li, J ;
Lohman, KL ;
Lu, H ;
Makhijani, VB ;
McDade, KE ;
McKenna, MP ;
Myers, EW ;
Nickerson, E ;
Nobile, JR ;
Plant, R ;
Puc, BP ;
Ronan, MT ;
Roth, GT ;
Sarkis, GJ ;
Simons, JF ;
Simpson, JW ;
Srinivasan, M ;
Tartaro, KR ;
Tomasz, A ;
Vogt, KA ;
Volkmer, GA .
NATURE, 2005, 437 (7057) :376-380
[47]   Parallel genomic evolution and metabolic interdependence in an ancient symbiosis [J].
McCutcheon, John P. ;
Moran, Nancy A. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (49) :19392-19397
[48]   The Chlamydomonas genome reveals the evolution of key animal and plant functions [J].
Merchant, Sabeeha S. ;
Prochnik, Simon E. ;
Vallon, Olivier ;
Harris, Elizabeth H. ;
Karpowicz, Steven J. ;
Witman, George B. ;
Terry, Astrid ;
Salamov, Asaf ;
Fritz-Laylin, Lillian K. ;
Marechal-Drouard, Laurence ;
Marshall, Wallace F. ;
Qu, Liang-Hu ;
Nelson, David R. ;
Sanderfoot, Anton A. ;
Spalding, Martin H. ;
Kapitonov, Vladimir V. ;
Ren, Qinghu ;
Ferris, Patrick ;
Lindquist, Erika ;
Shapiro, Harris ;
Lucas, Susan M. ;
Grimwood, Jane ;
Schmutz, Jeremy ;
Cardol, Pierre ;
Cerutti, Heriberto ;
Chanfreau, Guillaume ;
Chen, Chun-Long ;
Cognat, Valerie ;
Croft, Martin T. ;
Dent, Rachel ;
Dutcher, Susan ;
Fernandez, Emilio ;
Fukuzawa, Hideya ;
Gonzalez-Ballester, David ;
Gonzalez-Halphen, Diego ;
Hallmann, Armin ;
Hanikenne, Marc ;
Hippler, Michael ;
Inwood, William ;
Jabbari, Kamel ;
Kalanon, Ming ;
Kuras, Richard ;
Lefebvre, Paul A. ;
Lemaire, Stephane D. ;
Lobanov, Alexey V. ;
Lohr, Martin ;
Manuell, Andrea ;
Meier, Iris ;
Mets, Laurens ;
Mittag, Maria .
SCIENCE, 2007, 318 (5848) :245-251
[49]   The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes [J].
Meyer, F. ;
Paarmann, D. ;
D'Souza, M. ;
Olson, R. ;
Glass, E. M. ;
Kubal, M. ;
Paczian, T. ;
Rodriguez, A. ;
Stevens, R. ;
Wilke, A. ;
Wilkening, J. ;
Edwards, R. A. .
BMC BIOINFORMATICS, 2008, 9 (1)
[50]   Parallel tagged sequencing on the 454 platform [J].
Meyer, Matthias ;
Stenzel, Udo ;
Hofreiter, Michael .
NATURE PROTOCOLS, 2008, 3 (02) :267-278