Abstract Detail

Phylogenomics

Barrett, Craig [1], Sass, Chodon [2].

A phylogeographic approach to assessing plastid genome evolution in a non-photosynthetic orchid using targeted sequence capture.

Studies of plastid genome (plastome) evolution have focused on single representatives of species, even in comparative investigations, yet few if any studies have addressed plastome evolution at the infraspecific level. Parasitic and mycoheterotrophic plants display accelerated rates of plastome evolution, often with drastic reduction in size and gene content due to relaxed selective constraints of photosynthesis. The leafless orchid genus Corallorhiza contains both partially and fully mycoheterotrophic species, and has thus become a model for understanding the relationship between plastome evolution, nutritional mode, and fungal host specificity. The C. striata complex, with three putative species (C. bentleyi; C. involuta; C. striata, with three varieties), displays the most evidence of plastome modification in the genus. However, plastomes in this complex have not been severely reduced as in other, well-studied parasites (e.g. holoparasitic Orobanchaceae), making it a useful system to address questions associated with the early stages of plastome degradation. For example, what is the degree of variation in plastome size and gene content among members of this complex? What is the tempo of plastome reduction? Do members of this complex follow a single trajectory of degradation, and is this similar to that observed in other parasites? Here we use genome skimming and targeted sequence capture via Agilent microarray to generate complete to nearly complete plastomes for 53 individuals across the geographic range of the C. striata complex, from Mexico to northern North America. Briefly, genome skimming was used to generate five annotated reference plastomes representing each putative taxonomic entity of the complex. Targeted sequence capture was then used to expand sampling of individuals, in a cost-effective manner. Plastome sizes vary widely from 124 kb to 141 kb among members of the complex, with the highest degree of reduction in the endangered C. bentleyi (eastern North America) and C. involuta (southern Mexico). Members of the complex show varying degrees of degradation of photosynthesis-related gene complexes. Based on patterns of deletions and pseudogenes, two distinct degradation pathways have occurred within the complex, in addition to that observed in the C. maculata complex. This suggests that C. bentleyi/C. involuta and C. striata sensu stricto represent two losses of photosynthesis from a putatively photosynthetic ancestor. Divergence times, rates of degradation, and ancestral plastome reconstructions are discussed in the context of phylogeographic history of the complex. Further, relative merits and challenges of targeted sequence capture are discussed for closely related taxa displaying rapid genome evolution.

1 - West Virginia University, Plant and Soil Sciences, G153 South Agricultural Sciences Building, Morgantown, WV, 26506, USA
2 - University of California, Berkeley, Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, Berkeley, CA, 94720, USA

Keywords:
Plastome
Next generation sequencing
phylogenomics
intraspecific variation
pseudogene
mycoheterotrophic
Orchidaceae
sequence capture
plastid
chloroplast
genome evolution.

Presentation Type: Oral Paper
Session: 1, Phylogenomics I
Location: 101/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 9:00 AM
Number: 1005
Abstract ID:170
Candidate for Awards:None