Plastome Reduction, Gene Loss, and Phylogenetic Position of the Fully Mycoheterotrophic Orchid Neottia kiusiana (Orchidaceae)

Abstract

Fully mycoheterotrophic orchids provide a powerful system for examining plastome degradation following the loss of dependence on photosynthesis. Here, we assembled and characterized the complete plastome of Neottia kiusiana and compared its structure, gene content, inverted-repeat boundaries, and phylogenetic position with those of ten congeners. The N. kiusiana plastome is 87,068 bp long, comprising a 34,673-bp large single-copy region, a 5523-bp small single-copy region, and two 23,436-bp inverted repeats. Among 76 plastid protein-coding loci examined, only 24 remain intact, whereas 14 are pseudogenized and 38 are absent. Losses are concentrated in photosynthesis-related functions, while degradation also extends to ATP synthase, plastid-encoded RNA polymerase, and several ribosomal protein genes. Comparisons among Neottia species reveal substantial lineage-specific differences in plastome size, gene retention, pseudogene persistence, and inverted-repeat structure. A maximum-likelihood analysis of 22 plastid protein-coding genes strongly supports N. kiusiana as sister to N. nidus-avis. These results place N. kiusiana among the most strongly reduced Neottia plastomes and support a model in which trophic transition is associated with functionally biased but lineage-specific plastome degradation.