Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)1

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC-BY-NC-SA 4.0), which permits unrestricted noncommercial use and redistribution provided that the original author and source are credited and the new work is distributed under the same license as the original. The understanding of the genetic basis of phenotypic and ecological divergences between species is a central question in evolutionary biology (Coyne and Orr, 2004). The investigation of these questions in nonmodel plant species is motivated by their patterns of ecological and phenotypic differentiation during lin-eage diversification (Elmer and Meyer, 2011), but represents a challenge due to the lack of genomic resources. This challenge can now be overcome with the advent of next-generation se-quencing (NGS) methods that allow a better integration of the patterns of molecular, chromosomal, and epigenetic evolution into plant speciation and diversification (Rieseberg and Wendel, 2004; Lexer and Widmer, 2008). Recent studies highlighted the value of genomic resources for the phylogenomics of highly diverse lineages (Yang et al., 2015) and the advances and future research of NGS into broad-scale patterns of diversification (Lexer et al., 2013). One of the strategies that has revolutionized NGS projects is whole-transcriptome sequencing, or RNA-Seq (Wang et al., 2009). This technique directly accesses the expressed protein-coding genes in a sample, allowing the investigation of differences in gene expression and sequence between conditions, populations, or species, without any previous knowledge of the biological system. The increased adoption of this technique to address ecological and evolutionary questions relies partially on its applicability to nonmodel organisms and its growing toolkit and bioinformatics support (Orsini et al., 2013; Wolf, 2013). The Ligeriinae subtribe, previously named Sinningieae (Weber et al., 2013), is a clade of Gesneriaceae endemic to the Brazilian Atlantic Forest, which includes three genera (Sinnin-gia Nees, Vanhouttea Lem., and Paliavana Vand.) and 91 species. Ligeriinae shows a large variation in habit, inflorescence form, and corolla shape that evolved during the ca. 30 Myr history of this clade (Perret et al., 2003, 2013). Previous studies on the mechanisms of speciation in Ligeriinae suggested that geographical isolation and repeated adaptations to different functional The authors thank Alain Chautems for sharing his expertise about the species and the Vital-IT facilities of the Swiss Institute of Bioinformatics for the computational support. The authors thank the staff of the Jardin botaniques de la Ville de Genève for the maintenance of the Gesneriaceae collection. Collection …