Extensive Losses of Photosynthesis Genes in the Plastome of a Mycoheterotrophic Orchid, Cyrtosia septentrionalis (Vanilloideae: Orchidaceae).

Young-Kee Kim,Myoung Hai Kwak,Sangjin Jo,Ki-Joong Kim,Ja-Ram Hong,Se-Hwan Cheon,Min-Jung Joo,Shu-Miaw Chaw

doi:10.1093/gbe/evz024

Young-Kee Kim, Myoung Hai Kwak + Show 6 more

Open Access

https://doi.org/10.1093/gbe/evz024

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Abstract

Cyrtosia septentrionalis is an achlorophyllous mycoheterotrophic orchid in the subfamily Vanilloideae (Orchidaceae). This article reports C. septentrionalis’s complete plastome sequence and compare it with other orchid plastomes with a same mycoheterotrophic nutritional mode. The C. septentrionalis plastome has decreased to 96,859 bp in length, but it still maintains a quadripartite structure. The C. septentrionalis plastome contains 38 protein-coding genes, 25 tRNA genes, and four ribosomal RNA genes. Most genes related to photosynthesis have been lost, whereas the majority of housekeeping genes remain; this pattern corresponds to the end of stage 3 gene degradation. The inverted repeat regions of the C. septentrionalis plastome have decreased to 10,414 bp and mainly contain the gene ycf2. A block consisting of four rrn genes and rps7 and rps12 has shifted to a small single-copy region. As a result, the small single-copy region was found to be expanded, despite the loss of all ndh genes in the region. Three inversion mutations are required to explain the C. septentrionalis plastome’s current gene order. The species is endangered, and these results have implications for its conservation.

Highlights

The family Orchidaceae consists of 736 genera, comprising 28,000 species (Christenhusz and Byng 2016), of which the plastome sequences of 116 species from 38 genera have been completely decoded (NCBI database, July 7, 2018)
The inverted repeat regions of the C. septentrionalis plastome have decreased to 10,414 bp and mainly contain the gene ycf2
Most Orchidaceae species have a photosynthetic nutritional mode that is generally similar to other plants, 232 species belonging to 43 genera do not photosynthesize—or they photosynthesize at insignificant levels— and instead rely on mycoheterotrophy for nutrition (Merckx et al 2013)

Summary

Introduction

The family Orchidaceae consists of 736 genera, comprising 28,000 species (Christenhusz and Byng 2016), of which the plastome sequences of 116 species from 38 genera have been completely decoded (NCBI database, July 7, 2018). Plastome studies on mycoheterotrophic orchids have been performed for 20 species from 10 genera. All of these genera belong to the Epidendroideae subfamily, except for one Rhizanthella species (Delannoy et al 2011), which belongs to Orchidoideae. These include one Aphyllorchis species (Feng et al 2016), one Cephalanthera species (Feng et al 2016), seven Corallorhiza species (Barrett and Davis 2012; Barrett et al 2018), one Cymbidium species (Kim et al 2017; Kim et al 2018), two Epipogium species (Schelkunov et al 2015), one Eulophia species (Huo et al 2017), one Gastrodia species (Yuan et al 2018), one Hexalectris species (Barrett and Kennedy 2018), and four Neottia species (Logacheva et al 2011; Feng et al 2016). The plastomes of Platanthera japonica and Cremastra appendiculata have been decoded (Dong et al 2018), revealing typical photosynthetic plastomes, even some other congeneric species are mycoheterotrophy

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