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De Novo Characterization of the Timema Cristinae Transcriptome Facilitates Marker Discovery and Inference of Genetic Divergence

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De Novo Characterization of the Timema Cristinae Transcriptome Facilitates Marker Discovery and Inference of Genetic Divergence Molecular Ecology Resources (2012) doi: 10.1111/j.1755-0998.2012.03121.x De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence AARON A. COMEAULT,* MATHEW SOMMERS,* TANJA SCHWANDER,† C. ALEX BUERKLE,‡ TIMOTHY E. FARKAS,* PATRIK NOSIL* and THOMAS L. PARCHMAN‡ *Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80303, USA, †Center for Ecology and Evolutionary Studies, University of Groningen, 9700CC Groningen, The Netherlands, ‡Department of Botany, University of Wyoming, Laramie, WY 82071, USA Abstract Adaptation to different ecological environments can promote speciation. Although numerous examples of such ‘ecological speciation’ now exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study, we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms of ecological speciation, but for which genomic resources have not been previously developed. Specifically, we obtained >1 million 454 sequencing readsthatassembledinto84937contigsrepresenting approximately 18 282 unique genes and tens of thousands of potential molecular markers. Second, as an illustration of their utility, we used these geno- mic resources to assess multilocus genetic divergence within both an ecotype pair and a species pair of Timema stick insects. The results suggest variable levels of genetic divergence and gene flow among taxon pairs and genes and illustrate afirststeptowardsfuturegenomicworkinTimema. Keywords: gene flow, isolation with migration, next-generation sequencing, speciation, transcriptome Received 3 November 2011; revision received 6 January 2012; accepted 13 January 2012 Introduction resources (some notable exceptions aside, such as three- spine stickleback; Peichel et al. 2001; Colosimo et al. The causes of speciation are a central and long-standing 2005; Chan et al. 2010). Thus, although we now have topic in evolutionary biology (Darwin 1859; Dobzhansky convincing evidence for ecological speciation in nature, 1937, 1940; Mayr 1947, 1963) and have received renewed and the number of systems with genomic resources is interest over the last two decades (Coyne & Orr 2004). growing, the genetic basis of ecological speciation One hypothesis that has received particular attention is remains relatively poorly understood (reviewed in Sch- that adaptation to different ecological environments, via luter & Conte 2009). Here, we take steps towards filling divergent natural selection, can drive the evolution of this gap by developing genomic resources for Timema reproductive isolation. This hypothesis of ‘ecological cristinae walking stick insects. The genus Timema is com- speciation’ (for reviews see Schluter 2001; Rundle & Nosil prised of approximately 20 species of herbivourous 2005; Schluter 2009; Nosil 2012) has now seen widespread walking stick insects found throughout California (Vic- support from theoretical work (Kirkpatrick 2001; Kirk- kery 1993; Sandoval et al. 1998; Crespi & Sandoval 2000). patrick & Ravigne´ 2002; Gavrilets 2004), laboratory Numerous studies of Timema have focused on the role of evolution experiments (reviewed in Rice & Hostert 1993), ecology, such as adaptation to different host plant spe- comparative studies (Funk et al. 2006) and detailed case cies, in processes such as adaptive radiation and specia- studies in nature (Funk 1998; Rundle et al. 2000; Jiggins tion (Crespi & Sandoval 2000; Nosil 2007; Supporting et al. 2001; Rundle & Nosil 2005 for review; Langerhans information for more detail on species included in this et al. 2007; Nosil 2007). study). Timema cristinae, in particular, has been studied The systems used to study ecological speciation tend intensively in terms of adaptive divergence and ecologi- to be ecologically well characterized, but lack genomic cal speciation (see Nosil 2007 for review), but to date has Correspondence: Aaron A. Comeault, Fax: (303) 492 8699; largely lacked genomic resources (160 sequences E-mail: [email protected] currently at NCBI). Ó 2012 Blackwell Publishing Ltd 2 A. A. COMEAULT ET AL. The study presented here has two main objectives. specimens of Timema cristinae. The specimens were col- First, we characterize the transcriptome of T. cristinae lected from ten different localities spanning the species’ using sequences obtained from 454 pyrosequencing of a range in the vicinity of Santa Barbara, California. Five normalized cDNA library (Margulies et al. 2005; Ellegren specimens were from the host Adenostoma (population 2008; Holt & Jones 2008; Hudson 2008; Vera et al. 2008; abbreviations following past work, HVA, OUTA, OGA, Wheat 2010). The de novo assembly of transcriptome BTA, OCA) and five specimens from the host Ceanothus sequences is facilitated by greater coverage depth for the (population abbreviations, PC, R12C, PRC, MC, PEC) much smaller number of nucleotides in the transcriptome (Nosil 2007). Procedures were as follows. To minimize than in the whole genome (Bouck & Vision 2007; Emrich sequencing of gut microbes, live insects had their gut et al. 2007). Indeed, recent studies have demonstrated intestinal tracts removed. Specimens were then immedi- highly successful de novo assemblies of 454 EST data for ately placed in a tared 2-mL tube containing 300 lL RLT organisms with few or no prior genomic resources (e.g. Buffer (Qiagen RNeasy Mini Kit), 1% 2BME and a 5-mm Novaes et al. 2008; Vera et al. 2008; Hahn et al. 2009; Kris- steel bead. Upon placing each tissue sample in a tube, it tiansson et al. 2009; Meyer et al. 2009; Schwarz et al. 2009; was subject to disruption and homogenization using the Parchman et al. 2010; Fraser et al. 2011; Garg et al. 2011; TissueLyserII at 20 Hz for 6 min. Total RNA was isolated Martin & Wang 2011). Transcriptome sequencing projects using the Qiagen RNeasy protocol. RNA was quantified also have the advantage of focusing on the protein-cod- using NanoDrop spectrophotometry, and RNA integrity ing fraction of the genome where much of the functional was verified through analysis using BioRad Experion variation might be expected to reside (Bouck & Vision RNA Standard Sensitivity Chip (BioRad, Inc.). For cDNA 2007). The generation of such large-scale sequence data synthesis, 1 lg of total RNA was used as per Evrogen’s will enable the application of genome-wide analyses to Mint Universal cDNA Synthesis Kit Protocol II. taxa that are of ecological interest, but that previously Approximately 750 ng of double-stranded cDNA was have lacked genomic resources (Wheat 2010). used for normalization as per the specifications of the Second, we utilize the T. cristinae transcriptome Evrogen Trimmer Direct cDNA Normalization Kit. Fol- assembly to develop primers for nuclear loci that can be lowing normalization, gene-specific primers were amplified, by PCR, in different species of Timema. We designed for amplification in real-time PCR assays of then gather Sanger sequence data from these loci to char- Actin (a highly expressed gene) and HSP70 (a gene with acterize the nature of genetic divergence and gene flow low expression). These assays were used as an indicator within an ecotype pair and a species pair of Timema stick of normalization. Initially, PCR assays were optimized insects. Such multilocus data sets can provide powerful using RT reagents, conditions and 5 ng of normalized insight into speciation, for example, by providing infor- cDNA with reaction products run on a 2% agarose gel. mation on the extent to which genetic divergence Real-time PCR assays were carried out on Roche 480 occurred in the presence of substantial gene flow, as well Light cycler using Roche LightCycler 480 Sybr Green I as information on the effective population size and the Master Mix. Differences in the Ct values of HSP70 rela- time since population divergence was initiated (Wakeley tive to Actin for both control cDNA (hybridized but not & Hey 1997; Hey 2006; Wakeley 2008). normalized) and normalized cDNA were calculated. The analyses presented here add to a growing body of Results indicate a change as a result of normalization of literature that takes advantage of closely related taxon 5.2 cycles between Actin and HSP70. The normalized pairs, which differ in levels of reproductive isolation, to cDNA collection was then sequenced on a preliminary make inferences on how the process of speciation unfolds quarter-plate run and a final full-plate run on a 454 GS (Coyne & Orr 1989; Funk et al. 2006; Berner et al. 2009; XLR Titanium platform at the Roy Carver Center for Nosil et al. 2009; Stelkens et al. 2010; Merrill et al. 2011; Genomics, University of Iowa. Rosenblum & Harmon 2011). The overall results demon- 454 primer sequences and all sequences resulting from strate the feasibility of rapidly and inexpensively develop- cDNA synthesis reagents were trimmed from reads prior ing novel genomic resources and show how such to assembly. In addition, long poly(A) regions were resources can readily be utilized for population-level screened from reads prior to assembly. As for past stud- insights in evolution. ies involving de novo transcriptome assembly (Weber et al. 2007; Vera et al. 2008; Parchman et al. 2010; Wheat 2010), we used Seqman Ngen (DNAstar, Inc.) to assemble Methods reads into contigs. The assembly was run with a mini- mum match size
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