Repeat identification and comparative analysis
To identify the repeat elements of the S. ricini genome, a custom repeat library was constructed using RepeatModeler v1.0.11 (http://www.repeatmasker.org/RepeatModeler/) with RECON v1.0.8 (Bao, & Eddy, 2002), RepeatScout v1.0.5 (Price, Jones, & Pevzner, 2005) and TRF v4.0.4 (Benson, 1999). To mask and annotate repetitive sequences inS. ricini , the constructed custom repeat library was utilised by RepeatMasker v4.0.7 (http://www.repeatmasker.org/RMDownload.html; Tarailo-Graovac, & Chen, 2009) with Repbase (Jurka et al., 2005). RepeatMasker was conducted with RMBlast (http://www.repeatmasker.org/RMBlast.html).