Thirteen New Plastid Genomes from Mixotrophic and Autotrophic Species Provide Insights into Heterotrophy Evolution in Neottieae Orchids

Abstract

Mixotrophic species use both organic and mineral carbon sources. Some mixotrophic plants combine photosynthesis and a nutrition called mycoheterotrophy, where carbon is obtained from fungi forming mycorrhizal symbiosis with their roots. These species can lose photosynthetic abilities and evolve full mycoheterotrophy. Besides morphological changes, the latter transition is associated with a deep alteration of the plastid genome. Photosynthesis-related genes are lost first, followed by housekeeping genes, eventually resulting in a highly reduced genome. Whether relaxation of selective constraints already occurs for the plastid genome of mixotrophic species, which remain photosynthetic, is unclear. This is partly due to the difficulty of comparing plastid genomes of autotrophic, mixotrophic, and mycoheterotrophic species in a narrow phylogenetic framework. We address this question in the orchid tribe Neottieae, where this large assortment of nutrition types occurs. We sequenced 13 new plastid genomes, including 9 mixotrophic species and covering all 6 Neottieae genera. We investigated selective pressure on plastid genes in each nutrition type and conducted a phylogenetic inference of the group. Surprisingly, photosynthesis-related genes did not experience selection relaxation in mixotrophic species compared with autotrophic relatives. Conversely, we observed evidence for selection intensification for some plastid genes. Photosynthesis is thus still under purifying selection, maybe because of its role in fruit formation and thus reproductive success. Phylogenetic analysis resolved most relationships, but short branches at the base of the tree suggest an evolutionary radiation at the beginning of Neottieae history, which, we hypothesize, may be linked to mixotrophy emergence.

Three-year pot culture of Epipactis helleborine reveals autotrophic survival, without mycorrhizal networks, in a mixotrophic species

“…We may have here an extreme of the continuum from mycohetero-to autotrophy, leading to undetectable mycoheterotrophy because of light level and lack of fungal resources. The possibility of autotrophic survival in E. helleborine is also congruent with the recent report that its plastid genome retains a full set of photosynthetic genes without any evidence of selective relaxation (Lallemand et al 2019b) and has intact photosynthetic abilities. Moreover, the phylogenetically related mixotrophic Limodorum abortivum displayed some photosynthetic compensation (higher chlorophyll content and possibly higher photosynthetic activity) after experimental eradication of its fungal partners in situ (Bellino et al 2014).…”

“…These Epipactis species belong to rhizoctonia-associated, putatively autotrophic orchids, and thus, an autotrophy-to-mixotrophy transition (or vice-versa) occurred in the evolution of the genus Epipactis. In the framework of Neottieae evolution as a whole, it is still unclear in which direction this transition occurred, and a reversion from mixo-to autotrophy is also possible (Lallemand et al 2019b, c). Autotrophic survival in E. helleborine, combining the intact plastid genomes of mixotrophic orchids (retaining all photosynthetic genes; (Feng et al 2016;Lallemand et al 2019b), makes a reversion possible, even if the physiology of mixotrophs is deeply rooted in their dependence on two carbon sources, as mentioned above (Gonneau et al 2014;Lallemand et al 2019a).…”

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

“…For examples, extensive gene losses have been reported in several independent mycoheterotrophic orchid lineages-i.e., Aphyllorchis (Feng et al, 2016), Cyrtosia (Kim et al, 2019), Epipogium (Schelkunov et al, 2015), Gastrodia (Yuan et al, 2018), Hexalectris (Barrett and Kennedy, 2018) and Rhizanthella (Delannoy et al, 2011). In addition, ndh deletion and pseudogenization are assumed to be phenomena that occur independently in many orchid lineages such as Apostasia (Lin et al, 2017;Niu et al, 2017a), Calypso , Cattleya (da Rocha Perini et al, 2016), Cephalanthera (Feng et al, 2016), Cremastra (Dong et al, 2018), Cymbidium (Yang et al, 2013;Kim et al, 2018;Wang et al, 2018), Dendrobium (Niu et al, 2017b), Epipactis (Dong et al, 2018), Eulophia (Huo et al, 2017), Holcoglossum (Li et al, 2019), Limodorum (Lallemand et al, 2019), Liparis (Krawczyk et al, 2018), Neuwiedia (Niu et al, 2017a), Oncidium (Wu et al, 2010;Kim et al, 2015a), Paphiopedilum (Niu et al, 2017b;Hou et al, 2018), Phalaenopsis (Chang et al, 2006), Phragmipedium (Kim et al, 2015a), Platanthera (Dong et al, 2018), Vanilla (Lin et al, 2015), and Vanda (Li et al, 2019). On the other hand, full ndh genes have been reported in members of Anoectochilus (Yu et al, 2016), Calanthe (Dong et al, 2018), Cypripedium (Kim et al, 2015b;Lin et al, 2015), Habenaria…”

Mycorrhizal Communities and Isotope Signatures in Two Partially Mycoheterotrophic Orchids

“…Given that E. helleborine is a very widespread species that occurs in many different habitats and associates with a wide variety of fungi (Xing et al, 2020 ), selection on these genes is probably limited. Recent research has indeed shown that the plastid genome of E. helleborine retains a full set of photosynthetic genes without any evidence of selective relaxation (Lallemand et al, 2019a ) and has intact photosynthetic abilities. In contrast, E. neglecta usually occurs in the understory of beech and oak forests, where very little light penetrates to the forest soil.…”