EST-SSRs as a resource for population genetic analyses

Ellis, Jennifer R.; Burke, John M.

doi:10.1038/sj.hdy.6801001

Cited by 518 publications

(420 citation statements)

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“…Transcriptome sequencing has been an effective method of developing new SSR markers. The expressed sequencing tag SSR could be used for not only the source species but also, related species (22). The molecular markers identified from the transcriptome and primers designed could be used in the future for population genetics study (23), such as population diversity study, genome mapping, gene tagging, and quantitative trait loci analyses (24).…”

Section: Resultsmentioning

confidence: 99%

Sympatric speciation of spiny mice, Acomys , unfolded transcriptomically at Evolution Canyon, Israel

Wang

Cai

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Spiny mice, Acomys cahirinus, colonized Israel 30,000 y ago from dry tropical Africa and inhabited rocky habitats across Israel. Earlier, we had shown by mtDNA that A. cahirinus incipiently sympatrically speciates at Evolution Canyon I (EC I) in Mount Carmel, Israel because of microclimatic interslope divergence. The EC I microsite consists of a dry and hot savannoid "African" slope (AS) and an abutting humid and cool-forested "European" slope (ES). Here, we substantiate incipient SS in A. cahirinus at EC I based on the entire transcriptome, showing that multiple slope-specific adaptive complexes across the transcriptome result in two divergent clusters. Tajima's D distribution of the abutting Acomys interslope populations shows that the ES population is under stronger positive selection, whereas the AS population is under balancing selection, harboring higher genetic polymorphisms. Considerable sites of the two populations were differentiated with a coefficient of F ST = 0.25-0.75. Remarkably, 24 and 37 putatively adaptively selected genes were detected in the AS and ES populations, respectively. The AS genes involved DNA repair, growth arrest, neural cell differentiation, and heat-shock proteins adapting to the local AS stresses of high solar radiation, drought, and high temperature. In contrast, the ES genes involved high ATP associated with energetics stress. The sharp ecological interslope divergence led to strong slope-specific selection overruling the interslope gene flow. Earlier tests suggested slope-specific mate choice. Habitat interslope-adaptive selection across the transcriptome and mate choice substantiate sympatric speciation (SS), suggesting its prevalence at EC I and commonality in nature.adaptive ecological speciation | microclimate | natural selection | RNA-seq

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Section: Resultsmentioning

confidence: 99%

Sympatric speciation of spiny mice, Acomys , unfolded transcriptomically at Evolution Canyon, Israel

Wang

Cai

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…The main concern about coding sequence markers is that they may be acting in a non-neutral manner, and the subject of selection, biasing calculations of population genetic parameters (Ellis and Burke, 2007). The assumption that they are not subject to selection is rarely tested, and an in-depth comparison between estimates of genetic diversity with coding sequence markers and anonymous markers in natural systems would validate this assumption.…”

Section: How Can Ngs Technologies Help Us To Get Around These Limitatmentioning

confidence: 99%

“…The assumption that they are not subject to selection is rarely tested, and an in-depth comparison between estimates of genetic diversity with coding sequence markers and anonymous markers in natural systems would validate this assumption. In addition to concerns about selection, we anticipate that EST markers are less likely to be polymorphic than anonymous markers owing to functional constraints in transcribed regions, and may contain less informative differences between the hybridizing taxa (Ellis and Burke, 2007). Woodhead et al (2005) compared genetic diversity in the fern Athyrium distentifolium using EST-SSRs, genomic SSRs and AFLPs, and all marker types showed similar rank orders of population diversity and comparable F ST values, suggesting polymorphism in EST-SSRs can often be considered effectively neutral.…”

Section: How Can Ngs Technologies Help Us To Get Around These Limitatmentioning

confidence: 99%

Next-generation hybridization and introgression

2011

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Hybridization has a major role in evolution-from the introgression of important phenotypic traits between species, to the creation of new species through hybrid speciation. Molecular studies of hybridization aim to understand the class of hybrids and the frequency of introgression, detect the signature of ancient hybridization, and understand the behaviour of introgressed loci in their new genomic background. This often involves a large investment in the design and application of molecular markers, leading to a compromise between the depth and breadth of genomic data. New techniques designed to assay a large sub-section of the genome, in association with next-generation sequencing (NGS) technologies, will allow genome-wide hybridization and introgression studies in organisms with no prior sequence data. These detailed genotypic data will unite the breadth of sampling of loci characteristic of population genetics with the depth of sequence information associated with molecular phylogenetics. In this review, we assess the theoretical and methodological constraints that limit our understanding of natural hybridization, and promote the use of NGS for detecting hybridization and introgression between non-model organisms. We also make recommendations for the ways in which emerging techniques, such as pooled barcoded amplicon sequencing and restriction site-associated DNA tags, should be used to overcome current limitations, and enhance our understanding of this evolutionary significant process. Heredity (2012) 108, 179-189; doi:10.1038/hdy.2011.68; published online 7 September 2011Keywords: next-generation sequencing; hybridization; introgression; reticulate evolution; single-nucleotide polymorphisms (SNPs); restriction site-associated DNA (RAD) tags INTRODUCTION Hybridization, the crossbreeding between individuals of different species, and introgression, the transfer of genes between species mediated primarily by backcrossing, have been the focus of evolutionary studies over many decades (see Anderson, 1949;Arnold, 1992;Rieseberg and Carney, 1998). Hybridization is potentially a creative evolutionary process, allowing genetic novelties to accumulate faster than through mutation alone (Anderson and Hubricht, 1938;Martinsen et al., 2001). This may increase allelic variation at selectively neutral loci, and transfer adaptively important genetic variation, which may increase the fitness of the introgressed lineage (Choler et al., 2004;Martin et al., 2006;Castric et al., 2008;Kim et al., 2008). Moreover, hybridization can have a role in speciation. Hybridization in association with whole-genome duplication (polyploidy) is considered a likely route to speciation, particularly in plants ( Hegarty and Hiscock, 2008). The difference in ploidy levels between the polyploid hybrid and diploid progenitors acts as a strong reproductive barrier (Soltis et al., 2004), although there are examples of introgression across ploidy levels (for example, Senecio; Chapman and Abbott, 2010). Hybrid speciation can also occur without a change i...

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“…Microsatellites are effectively randomly distributed throughout the genome and can represent transcribed elements. Although, SSRs derived from transcribed ESTs can still maintain allelic variability comparable with that in non-transcribed genomic DNA, they can serve as molecular markers for numerous applications [22,23]. EST databases have been a rich source of SSRs for the development of "genotyping" applications.…”

Section: Introductionmentioning

confidence: 99%

Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)

Hamarsheh

Amro

2011

Parasites Vectors

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BackgroundPhlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs), or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers.ResultsSimple sequence repeats (SSRs) were characterized in P. papatasi expressed sequence tags (ESTs) derived from a public database, National Center for Biotechnology Information (NCBI). A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AX)n repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation.ConclusionThe first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

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EST-SSRs as a resource for population genetic analyses

Cited by 518 publications

References 56 publications

Sympatric speciation of spiny mice, Acomys , unfolded transcriptomically at Evolution Canyon, Israel

Sympatric speciation of spiny mice, Acomys , unfolded transcriptomically at Evolution Canyon, Israel

Next-generation hybridization and introgression

Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)

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