Severe Plastid Genome Size Reduction in a Mycoheterotrophic Orchid, <i>Danxiaorchis singchiana</i>, Reveals Heavy Gene Loss and Gene Relocations
Lee, Shiou Yih | Meng, Kaikai | Wang, Haowei | Zhou, Renchao | Liao, Wenbo | Chen, Fang | Zhang, Shouzhou | Fan, Qiang
<i>Danxiaorchis singchiana</i> (Orchidaceae) is a leafless mycoheterotrophic orchid in the subfamily Epidendroideae. We sequenced the complete plastome of <i>D. singchiana</i>. The plastome has a reduced size of 87,931 bp, which includes a pair of inverted repeat (IR) regions of 13,762 bp each that are separated by a large single copy (LSC) region of 42,575 bp and a small single copy (SSC) region of 17,831 bp. When compared to its sister taxa, <i>Cremastra appendiculata</i> and <i>Corallorhiza striata</i> var. <i>involuta</i>, <i>D. singchiana</i> showed an inverted gene block in the LSC and SSC regions. A total of 61 genes were predicted, including 21 tRNA, 4 rRNA, and 36 protein-coding genes. While most of the housekeeping genes were still intact and seem to be protein-coding, only four photosynthesis-related genes appeared presumably intact. The majority of the presumably intact protein-coding genes seem to have undergone purifying selection (d<i>N</i>/d<i>S</i> < 1), and only the <i>psa</i>C gene was positively selected (d<i>N</i>/d<i>S</i> > 1) when compared to that in <i>Cr. appendiculata</i>. Phylogenetic analysis of 26 complete plastome sequences from 24 species of the tribe Epidendreae had revealed that <i>D. singchiana</i> diverged after <i>Cr. appendiculata</i> and is sister to the genus <i>Corallorhiza</i> with strong bootstrap support (100%).
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