Plant Diversity ›› 2022, Vol. 44 ›› Issue (03): 316-321.DOI: 10.1016/j.pld.2021.07.002

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Plastid RNA editing reduction accompanied with genetic variations in Cymbidium, a genus with diverse lifestyle modes

Mengqing Zhea,b, Le Zhanga,c, Fang Liua,b, Yiwei Huanga,b, Weishu Fana, Junbo Yanga, Andan Zhua   

  1. a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China;
    b University of Chinese Academy of Sciences, Beijing 100049, China;
    c School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China
  • Received:2021-03-31 Revised:2021-06-30 Online:2022-05-25 Published:2022-06-21
  • Contact: Andan Zhu,
  • Supported by:
    This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDB31010000), by the Large-scale Scientific Facilities of the Chinese Academy of Sciences (grant no. 2017-LSF-GBOWS-02), by an open research project for “Cross-Cooperative Team” of the Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, and by the CAS Pioneer Hundred Talents Program (to A.Z.).

Abstract: Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes (plastomes) of flowering plants in diverse habitats, yet our knowledge of the evolution of plastid posttranscriptional modifications is limited. In this study, we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium, a genus with diverse trophic lifestyles. Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives. This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex, but independent pseudogenization of ndh genes has also occurred in the epiphyte C.?mannii, which was reported to use strong crassulacean acid metabolism photosynthesis. RNA editing sites are abundant but variable in number among Cymbidium plastomes. The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial, mycoheterotrophic, and C.?mannii plastomes. The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed, leading to nonrandom loss of ancestral edited sites via reduced editing efficiency. This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus. We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium.

Key words: RNA editing, Plastomes, ndh genes, Lifestyle