Genomic Resources for Erysimum spp. (Brassicaceae): Transcriptome and Chloroplast Genomes

Funding was provided by the Spanish Ministry of Science and Competitiveness (CGL2016-79950-R; CGL2017-86626-C22-P), including FEDER funds. This research was also funded by the Consejeria de Economia, Conocimiento, Empresas y Universidad, and European Regional Development Fund (ERDF), ref. SOMM17/6109/UGR and A-RNM-505-UGR18. COM was supported by the Ministry of Economy and Competitiveness (BES-2014-069022).
We are grateful to Modesto Berbel Cascales and José M. Gómez for their help in sampling and DNA/RNA extractions.
Erysimum (Brassicaceae) is a genus of more than 200 species (Al-Shehbaz, 2012). It is widely distributed in the Northern Hemisphere and has been the focus of active research in ecology, evolution, and genetics (Gómez and Perfectti, 2010; Gómez, 2012; Valverde et al., 2016). Despite long-standing interest in Erysimum, its taxonomy has yet to be properly established, partly due to a complex and reticulated evolutionary history that renders phylogenetic reconstructions highly challenging (Ancev, 2006; Marhold and Lihová, 2006; Abdelaziz et al., 2014; Gomez et al., 2014; Moazzeni et al., 2014; Züst et al., 2020). The Baetic Mountains (South-Eastern Iberia) are among the most critical glacial refugia in Europe. The waxing and waning of plant populations following climatic fluctuations have likely complicated the distribution and genetic variation of extant diversity in this region. Isolation and posterior secondary contact between taxa may have favored hybridization and introgression (Médail and Diadema, 2009). The Erysimum species that inhabit these mountains have been a particularly fruitful system for plant evolutionary ecology [e.g., Gómez et al., 2006, 2008; Gómez and Perfectti, 2010; Gómez, 2012; Valverde et al., 2016]. However, the relationships among these species remain unresolved, hampering comparative and evolutionary studies. Genome duplications, incomplete lineage sorting, and hybridization have compromised the phylogenetic reconstructions within Erysimum (Marhold and Lihová, 2006; Osuna-Mascaró, 2020). Additionally, clarifying this group's complex evolution requires extensive genomic resources, which are currently being produced but are mostly lacking. The fast development of high-throughput sequencing technologies has led to a rapid increase in genomic and transcriptomic for many plant species (Dong et al., 2004; Duvick et al., 2007; Sundell et al., 2015; Boyles et al., 2019). However, obtaining complete genome sequencing remains a challenge with large, repetitive-DNA enriched genomes. Transcriptome sequencing is comparatively more accessible, providing a relatively cheap and fast method to obtain large amounts of functional genomic data (Timme et al., 2012; Yang and Smith, 2013; Wickett et al., 2014; Léveillé-Bourret et al., 2017). Accordingly, global initiatives such as the 1,000 plants (1KP) project have generated transcriptomic resources for over 1,000 plant species (Matasci et al., 2014; Leebens-Mack et al., 2019). In addition, the use of RNA-Seq could be useful in obtaining complete chloroplast genomes in a reliable and accessible way, making possible the use of complete molecules in phylogenomic analyses (Smith, 2013; Osuna-Mascaró et al., 2018; Morales-Briones et al., 2021). Here, we report the annotation of 18 floral transcriptomes assembled de novo from total RNA-Seq libraries and nine chloroplast genomes from seven Erysimum species inhabiting the Baetic Mountains. The chloroplast genomes were assembled from total RNA-Seq data following a previously-validated reference assemble approach (Osuna-Mascaró et al., 2018). The data presented here represent reliable genomic resources for transcriptomic, proteomic, and phylotranscriptomic studies. These data contribute to the ecological and genetic resources available for Brassicaceae in general and the genus Erysimum in particular, being the only genomic resources for these species coming from flower buds.
Spanish Ministry of Science and Competitiveness CGL2016-79950-R CGL2017-86626-C22-P
European Commission
Consejeria de Economia, Conocimiento, Empresas y Universidad
European Commission SOMM17/6109/UGR A-RNM-505-UGR18
Ministry of Economy and Competitiveness BES-2014-069022