Chloroplast genome evolution in New Zealand mycoheterotrophic Orchidaceae : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Manawatu, New Zealand

Abstract

The plastid genomes, or plastomes, of most photosynthetic land plants are highly similar. In contrast, those of non-photosynthetic, heterotrophic land plants are often reduced in both size and gene content. The apparent degradation of mycoheterotrophic plant plastomes has been attributed to a functionally-driven stepwise pattern of loss. However, the number of complete plastome sequences available for mycoheterotrophic plants is small and taxonomic coverage is biased. In this thesis, the plastomes of two mycoheterotrophic orchid species endemic to New Zealand, 𝘊𝘰𝘳𝘺𝘣𝘢𝘴 𝘤𝘳𝘺𝘱𝘵𝘢𝘯𝘵𝘩𝘶𝘴 Hatch (Diurideae) and 𝘋𝘢𝘯𝘩𝘢𝘵𝘤𝘩𝘪𝘢 𝘢𝘶𝘴𝘵𝘳𝘢𝘭𝘪𝘴 Garay & Christenson (Goodyerinae), as well as those of an albino and several photosynthetic representatives of 𝘊𝘰𝘳𝘺𝘣𝘢𝘴 are reported. Beyond increasing the number of mycoheterotrophic plastomes available for evaluating broad hypotheses about plastome evolution in non-photosynthetic plants, these data also provide insights into two little studied aspects of plastome evolution in mycoheterotrophs; intraspecific variation in the plastomes of mycoheterotrophs and the differences between mycoheterotrophs and their closest photosynthetic relatives.

The plastomes of 𝘊. 𝘤𝘳𝘺𝘱𝘵𝘢𝘯𝘵𝘩𝘶𝘴 and 𝘋. 𝘢𝘶𝘴𝘵𝘳𝘢𝘭𝘪𝘴 differ in the extent to which they are degraded. Perhaps unexpectedly, the plastome of 𝘊. 𝘤𝘳𝘺𝘱𝘵𝘢𝘯𝘵𝘩𝘶𝘴, which has close photosynthetic relatives and therefore is likely to have arisen more recently than the taxonomically isolated 𝘋. 𝘢𝘶𝘴𝘵𝘳𝘢𝘭𝘪𝘴, is more reduced. Specifically, the plastomes of 𝘊. 𝘤𝘳𝘺𝘱𝘵𝘢𝘯𝘵𝘩𝘶𝘴 are approximately half the size and have half the gene content of the other 𝘊𝘰𝘳𝘺𝘣𝘢𝘴 sequenced whereas the plastome of 𝘋. 𝘢𝘶𝘴𝘵𝘳𝘢𝘭𝘪𝘴 is similar to those available for photosynthetic relatives. This contrast may reflect underlying differences between the two genera; the photosynthetic relatives of D. australis have plastomes containing NADH dehydrogenase (𝘯𝘥𝘩) genes whereas those of photosynthetic 𝘊𝘰𝘳𝘺𝘣𝘢𝘴 have lost their 𝘯𝘥𝘩 genes and their small single copy regions are highly reduced. These features may have predisposed the ancestor of 𝘊. 𝘤𝘳𝘺𝘱𝘵𝘢𝘯𝘵𝘩𝘶𝘴 to rapid genome degradation. Finally, observations on these results strongly suggest that plastome degradation follows, rather than precedes, the shift to mycoheterotrophy.