RESEARCH ARTICLE Independent degradation in genes of the plastid ndh gene family in species of the orchid genus Cymbidium (Orchidaceae; Epidendroideae) Hyoung Tae Kim1, Mark W. Chase2* 1 College of Agriculture and Life Sciences, Kyungpook University, Daegu, Korea, 2 Jodrell Laboratory, Royal a1111111111 Botanic Gardens, Kew, Richmond, Surrey, United Kingdom a1111111111 *
[email protected] a1111111111 a1111111111 a1111111111 Abstract In this paper, we compare ndh genes in the plastid genome of many Cymbidium species and three closely related taxa in Orchidaceae looking for evidence of ndh gene degradation. OPEN ACCESS Among the 11 ndh genes, there were frequently large deletions in directly repeated or AT- Citation: Kim HT, Chase MW (2017) Independent rich regions. Variation in these degraded ndh genes occurs between individual plants, degradation in genes of the plastid ndh gene family apparently at population levels in these Cymbidium species. It is likely that ndh gene trans- in species of the orchid genus Cymbidium fers from the plastome to mitochondrial genome (chondriome) occurred independently in (Orchidaceae; Epidendroideae). PLoS ONE 12(11): e0187318. https://doi.org/10.1371/journal. Orchidaceae and that ndh genes in the chondriome were also relatively recently transferred pone.0187318 between distantly related species in Orchidaceae. Four variants of the ycf1-rpl32 region, Editor: Zhong-Jian Liu, The National Orchid which normally includes the ndhF genes in the plastome, were identified, and some Cymbid- Conservation Center of China; The Orchid ium species contained at least two copies of that region in their organellar genomes. The Conservation & Research Center of Shenzhen, four ycf1-rpl32 variants seem to have a clear pattern of close relationships.