Abstract
The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia, Paphiopedilum armeniacum, Paphiopedilum niveum, Cypripedium formosanum, Habenaria longidenticulata, Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla, at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh-deleted orchids and also in ndh containing species.
Highlights
The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast genomes
Four orchid cp genome sequences were found to contain a complete set of ndh genes
There was a massive transfer of genes from the endosymbiont genomes into the nuclear genome of the host cell[3]. Plant chloroplasts possess their own genomes, which contain genes that are involved in photosynthesis, transcription and translation[4]
Summary
Correspondence and requests for materials should be addressed to M.-C.S. The cp genome of E. pusilla contains truncated versions of ndhJ, C, D, B, G, and H and lacks sequences for ndhK, F, E, A, and I16 These results indicate that deletion and truncation of ndh gene fragments are common to orchid cp genomes. There were eight ndh genes in G. fumata and nine in M. picturata, whose cp genomes contained a complete ndh profile (Supplementary Table S3) These results showed that the number of transferred ndh gene fragments did not correlate with ndh deletions in the cp genome. As more mt genomes are sequenced and completed, the taxonomic relationship between the ndh regions and the cp genome sequences can be further studied Of all of these mt ndh genes, only mt-ndhD in Vitis vinifera, mtndhJ in Phoenix dactylifera, B. oldhamii, and Oryza and mt-ndhB in Triticum aestivum and Zea are full length (Supplementary Table S3)[32]. These results indicate that these gene fragments can be transcribed but translation requires further investigation
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