Abstract
The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.
Highlights
Zingiberales are a diverse group of tropical monocots, including important tropical crop plants and ornamentals
DNA was extracted using an SDS and salt extraction protocol (Edwards, Johnstone & Thompson, 1991; Konieczny & Ausubel, 1993) from freshly collected leaves dried in silica, eluted in TE buffer, and sonicated with a BioruptorÒ (Diagenode, Liege, Belgium) or qSonica Q800R machine to an average size of approximately 250bp
Sequence capture, sequencing To generate a nuclear probe set, the Musa acuminata CDS was downloaded from the banana genome hub and split into annotated exons
Summary
Zingiberales are a diverse group of tropical monocots, including important tropical crop plants (e.g., ginger, turmeric, cardamom, bananas) and ornamentals (e.g., cannas, birdof-paradise, prayer plants). Zingiberales are thought to have diverged from the sister order Commelinales (sensu Angiosperm Phylogeny Group, 2003) between 80–124 Ma, with diversification into the major lineages occurring from ca. Relationships among the families are not well-resolved using multi-gene phylogenies (Kress et al, 2001; Barrett et al, 2014), likely due to this early rapid radiation. Whole plastid data for 14 taxa spanning the eight families still failed to resolve the early diverging branches of the phylogeny, perhaps owing to limited sampling and a lack of phylogenetic signal in the plastome (Barrett et al, 2014). Rapid evolutionary radiations are thought to be a common theme across the tree of life and are thought to explain poorly resolved phylogenies in many groups including insects, birds, bees, turtles, mammals, and angiosperms (Whitfield & Lockhart, 2007; Whitfield & Kjer, 2008)
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