Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus onDegranvillea dermaptera

Abstract

ABSTRACTPremiseLeafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. Yet, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants.MethodsWe sequenced and analyzed the plastome ofDegranvillea dermaptera, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities.Key ResultsWe revealed the most reduced plastome sequenced to date among the orchid subfamily Orchidoideae.Degranvilleahas lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement ofDegranvilleawithin the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and correlations among substitution rates and several other “traits” of the plastome among leafless members of orchid subfamily Orchidoideae.ConclusionsOur findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern.