Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

被引:173
作者
Alvarez, Mariano [1 ]
Schrey, Aaron W. [2 ]
Richards, Christina L. [1 ]
机构
[1] Univ S Florida, Dept Integrat Biol, Tampa, FL 33620 USA
[2] Armstrong State Univ, Dept Biol, Ctr Sci, Savannah, GA 31419 USA
关键词
ecological transcriptome; gene expression; microarrays; RNAseq; transcriptomics; WHITEFISH COREGONUS-CLUPEAFORMIS; DIFFERENTIAL GENE-EXPRESSION; RNA-SEQ; PHENOTYPIC PLASTICITY; NATURAL VARIATION; DIVERGENCE; GENOMICS; CHALLENGES; ARABIDOPSIS; MECHANISMS;
D O I
10.1111/mec.13055
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
引用
收藏
页码:710 / 725
页数:16
相关论文
共 100 条
[1]   Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment [J].
Aikawa, Shinichiro ;
Kobayashi, Masaki J. ;
Satake, Akiko ;
Shimizu, Kentaro K. ;
Kudoh, Hiroshi .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (25) :11632-11637
[2]   Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis [J].
Akama, Satoru ;
Shimizu-Inatsugi, Rie ;
Shimizu, Kentaro K. ;
Sese, Jun .
NUCLEIC ACIDS RESEARCH, 2014, 42 (06)
[3]   Microarray data analysis: from disarray to consolidation and consensus [J].
Allison, DB ;
Cui, XQ ;
Page, GP ;
Sabripour, M .
NATURE REVIEWS GENETICS, 2006, 7 (01) :55-65
[4]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[5]   A road map for molecular ecology [J].
Andrew, Rose L. ;
Bernatchez, Louis ;
Bonin, Aurelie ;
Buerkle, C. Alex ;
Carstens, Bryan C. ;
Emerson, Brent C. ;
Garant, Dany ;
Giraud, Tatiana ;
Kane, Nolan C. ;
Rogers, Sean M. ;
Slate, Jon ;
Smith, Harry ;
Sork, Victoria L. ;
Stone, Graham N. ;
Vines, Timothy H. ;
Waits, Lisette ;
Widmer, Alex ;
Rieseberg, Loren H. .
MOLECULAR ECOLOGY, 2013, 22 (10) :2605-2626
[6]   Natural variation in the molecular stress network correlates with a behavioural syndrome [J].
Aubin-Horth, Nadia ;
Deschenes, Marilou ;
Cloutier, Sophie .
HORMONES AND BEHAVIOR, 2012, 61 (01) :140-146
[7]   Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity [J].
Aubin-Horth, Nadia ;
Renn, Susan C. P. .
MOLECULAR ECOLOGY, 2009, 18 (18) :3763-3780
[8]   Analysis of variance of microarray data [J].
Ayroles, Julien F. ;
Gibson, Greg .
DNA MICROARRAYS, PART B: DATABASES AND STATISTICS, 2006, 411 :214-+
[9]   Transcriptome Analysis of the Desert Locust Central Nervous System: Production and Annotation of a Schistocerca gregaria EST Database [J].
Badisco, Liesbeth ;
Huybrechts, Jurgen ;
Simonet, Gert ;
Verlinden, Heleen ;
Marchal, Elisabeth ;
Huybrechts, Roger ;
Schoofs, Liliane ;
De Loof, Arnold ;
Broeck, Jozef Vanden .
PLOS ONE, 2011, 6 (03)
[10]   INFLUENCE OF TEMPERATURE AND CURRENT SPEED ON THE SWIMMING CAPACITY OF LAKE WHITEFISH (COREGONUS-CLUPEAFORMIS) AND CISCO (C-ARTEDII) [J].
BERNATCHEZ, L ;
DODSON, JJ .
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES, 1985, 42 (09) :1522-1529