Phylogenomics of Gesneriaceae using targeted capture of nuclear genes

• Published in: Molecular phylogenetics and evolution 2021-04, Vol.157, p.107068-107068, Article 107068
• Main Authors: Ogutcen, Ezgi, Christe, Camille, Nishii, Kanae, Salamin, Nicolas, Möller, Michael, Perret, Mathieu
• Format: Article
• Language: English
• Subjects: African violet; Base Sequence; Cell Nucleus - genetics; DNA, Plant - genetics; Genes, Plant; Lamiales; Likelihood Functions; Magnoliopsida - classification; Magnoliopsida - genetics; Phylogenetics; Phylogeny; Probe design; Sequence capture; Systematics; Target enrichment
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2021.107068

[Display omitted] •This is the first gene capture method developed for the family Gesneriaceae.•Our bait set targets 830 genes and has an average of 87.8% gene recovery rate.•The targeted loci include the genes from the Universal-Angiosperm-353 bait kit.•We selected a subset of 418 most informative genes for phylogenetic analyses.•The generated dataset performs well at different taxonomical levels. Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperms-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group.