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...this, we aligned orthologous proteins with MUSCLE3.7 (Edgar 2004), reverse translated the alignments with RevTrans1.4 (Wernersson & Pedersen 2003) and used codeml from PAML4.5 to calculate Ks values (=-=Yang 1997-=-, 2007). We examined the average Ks values between crops and their wild relatives to determine if features of their domestication history, or reproductive barriers were associated with the degree of d...

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...program Trinity (http://trinityrnaseq.sourceforge.net/) using the butterfly parameters – ‘bfly_opts, edgethr=0.05’ – to increase its ability to distinguish close paralogs. We used MIRA version 3.2.1 (=-=Chevreux et al. 2004-=-) using the ‘accurate.est.denovo.454’ assembly mode to assemble the 454 data. As MIRA can split up high coverage contigs, we used CAP3 at 94% identity to further assemble the MIRA contigs and singleto...

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...ization of the transcriptome is desired, several factors have been shown to impact gene discovery including sequencing depth, normalization and the life stages/tissue types sampled (Wall et al. 2009; =-=Ekblom & Galindo 2011-=-; Lai et al. 2012a; Matvienko et al. 2013). A predominant factor in determining the number of unigenes identified in our study was sequencing depth, as evidenced by the correlation between sequencing ...

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...rhaps erroneous inclusion of some paralogs inflated the divergence estimates for these comparisons. Reproductive barriers should result in the accumulation of genetic differences between populations (=-=Dobzhansky 1940-=-; Coyne & Orr 1989; Hendry & Taylor 2004). We found that the two species with the greatest divergence between the crop and the putative progenitor (noug and sunflower) had evidence for postzygotic iso...

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...we included estimates of divergence and reproductive isolation of more distantly related congeners, this pattern was confirmed and is consistent with findings in many other plant and animal taxa (see =-=Edmands 2002-=- for review). Evidence for introgression Most comparisons of crops and their closest wild and weedy relatives revealed little divergence, suggesting ongoing gene flow or recent divergence. In our comp...

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...nclusion of some paralogs inflated the divergence estimates for these comparisons. Reproductive barriers should result in the accumulation of genetic differences between populations (Dobzhansky 1940; =-=Coyne & Orr 1989-=-; Hendry & Taylor 2004). We found that the two species with the greatest divergence between the crop and the putative progenitor (noug and sunflower) had evidence for postzygotic isolating barriers, a...

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...should be centred around a Ks value reflecting the time as the most recent common ancestor of the taxa involved, while a secondary peak at a lower Ks value can be attributed to more recent gene flow (=-=Wang & Hey 2010-=-). To identify significant peaks in the ortholog Ks distribution, we used SiZer (Chaudhuri & Marron 1999). Then, we used EMMIX (McLachlan et al. 1999) to determine the location of significant peaks in...

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...ssp. schimperi showed evidence of divergence followed by gene flow. There is limited postzygotic isolation and relatively high crossability between noug and this taxon as well as others in the genus (=-=Dagne 1994-=-). Also, unlike sunflower, another oilseed crop in the family, noug does not exhibit strong signs of artificial selection and resembles its wild relatives to a greater degree, suggesting ongoing gene ...

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...to their histories of domestication and invasiveness. Sunflower was domesticated in North America, yet today, H. annuus and many taxa in the genus are naturalized or invasive in Europe (Rehorek 1997; =-=Forman 2003-=-). High levels of gene flow between cultivated and weedy sunflower are known to occur (Arias & Rieseberg 1994; Linder et al. 1998; Burke et al. 2002) fuelling debates about transgene escape in the evo...

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...o, unlike sunflower, another oilseed crop in the family, noug does not exhibit strong signs of artificial selection and resembles its wild relatives to a greater degree, suggesting ongoing gene flow (=-=Dempewolf 2011-=-). However, population-level studies of noug and its putative progenitor using SSR markers have found little evidence of hybridization (Dempewolf 2011). The discrepancy between these results and ours ...

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... depth to G. scabra ssp. schimperii and S. rebaudiana, perhaps owing to the multiple tissue types sampled. However, polyploidy could have also contributed to the high number of contigs in both cases (=-=Gatt et al. 1998-=-; Viehmannova et al. 2009). One method to increase the breadth of the transcriptome coverage is normalization of the cDNA library (Ekblom & Galindo 2011; Lai et al. 2012a). With the exception of dahl...

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... with respect to their histories of domestication and invasiveness. Sunflower was domesticated in North America, yet today, H. annuus and many taxa in the genus are naturalized or invasive in Europe (=-=Rehorek 1997-=-; Forman 2003). High levels of gene flow between cultivated and weedy sunflower are known to occur (Arias & Rieseberg 1994; Linder et al. 1998; Burke et al. 2002) fuelling debates about transgene esca...

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...rosses between lettuce and bitter lettuce (Hayes & Ryder 2007). © 2013 John Wiley & Sons Ltd COMPOSITAE CROP GENOMIC RESOURCES 9 Bitter lettuce has been used occasionally in lettuce breeding efforts (=-=Ryder 1979-=-; Hayes & Ryder 2007). Also, the introgression identified in this analysis could reflect introgression from other species, or perhaps more ancient introgression, that occurred after the species diverg...

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...cory and endive in all comparisons. This finding is not unexpected as, although there is moderate sterility and reduced germination of the F1s, hybrids can be readily acquired under field conditions (=-=Rick 1953-=-). Similarly, noug and G. scabra ssp. schimperi showed evidence of divergence followed by gene flow. There is limited postzygotic isolation and relatively high crossability between noug and this taxon...