AUTHOR=Zhou Lisi , Chen Tongyao , Qiu Xiandan , Liu Jinxin , Guo Shunxing 

TITLE=Evolutionary differences in gene loss and pseudogenization among mycoheterotrophic orchids in the tribe Vanilleae (subfamily Vanilloideae)

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1160446

DOI=10.3389/fpls.2023.1160446

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p><italic>Galeola lindleyana</italic> is a mycoheterotrophic orchid belonging to the tribe Vanilleae within the subfamily Vanilloideae.</p></sec><sec><title>Methods</title><p>In this study, the <italic>G. lindleyana</italic> plastome was assembled and annotated, and compared with other Vanilleae orchids, revealing the evolutionary variations between the photoautotrophic and mycoheterotrophic plastomes.</p></sec><sec><title>Results</title><p>The <italic>G. lindleyana</italic> plastome was found to include 32 protein-coding genes, 16 tRNA genes and four ribosomal RNA genes, including 11 pseudogenes. Almost all of the genes encoding photosynthesis have been lost physically or functionally, with the exception of six genes encoding ATP synthase and <italic>psaJ</italic> in photosystem I. The length of the <italic>G. lindleyana</italic> plastome has decreased to 100,749 bp, while still retaining its typical quadripartite structure. Compared with the photoautotrophic Vanilloideae plastomes, the inverted repeat (IR) regions and the large single copy (LSC) region of the mycoheterotrophic orchid’s plastome have contracted, while the small single copy (SSC) region has expanded significantly. Moreover, the difference in length between the two <italic>ndh</italic>B genes was found to be 682 bp, with one of them spanning the IRb/SSC boundary. The Vanilloideae plastomes were varied in their structural organization, gene arrangement, and gene content. Even the <italic>Cyrtosia septentrionalis</italic> plastome which was found to be closest in length to the <italic>G. lindleyana</italic> plastome, differed in terms of its gene arrangement and gene content. In the LSC region, the <italic>psb</italic>A, <italic>psb</italic>K, <italic>atp</italic>A and <italic>psa</italic>B retained in the <italic>G. lindleyana</italic> plastome were missing in the <italic>C. septentrionalis</italic> plastome, while, the <italic>mat</italic>K, <italic>rps</italic>16, and <italic>atp</italic>F were incomplete in the <italic>C. septentrionalis</italic> plastome, yet still complete in that of the <italic>G. lindleyana</italic>. Lastly, compared with the <italic>G. lindleyana</italic> plastome, a 15 kb region located in the SSC area between <italic>ndh</italic>B<italic>-rrn</italic>16S was found to be inverted in the <italic>C. septentrionalis</italic> plastome. These changes in gene content, gene arrangment and gene structure shed light on the polyphyletic evolution of photoautotrophic orchid plastomes to mycoheterotrophic orchid plastomes.</p></sec><sec><title>Discussion</title><p>Thus, this study’s decoding of the mycoheterotrophic <italic>G. lindleyana</italic> plastome provides valuable resource data for future research and conservation of endangered orchids.</p></sec>