The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family

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.

Figure 1. Phylogenetic analysis of orchids.

The phylogenetic tree was based on the chloroplast rbcL, matK, psaA, psaB, and rpoC2 nucleotide sequences. The species names in red are ndh-complete and in black are ndh-deleted genomes. The asterisk (*) indicates that the cp genomes were sequenced in this report. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches.

Figure 2. Gene maps of Vanilla planifolia chloroplast genomes.

Genes on the outside of the map are transcribed clockwise whereas genes on the inside of the map are transcribed counterclockwise. Colors indicate genes with different functional groups.

Figure 3. Genome order of the chloroplast-coding regions in 4 orchid genera, Arabidopsis thaliana, Oryza sativa, and Musa acuminata.

The name in red indicates that the cp genome contains complete ndh genes. Black indicates that the ndh genes are deleted. The asterisk (*) indicates the cp genomes were sequenced in this study. P. niveum and P. armeniacum have the same genome structure and order. H. longidenticulata, M. picturata, and G. fumata have the same genome structure and gene order. The arrowheads indicate the direction of the genes. The pink arrows indicate that the rice psbC and psbD are inserted next to psbI but are located behind psbM in the other plant cp genomes. Blue indicates that the sequence region from atpA to psbM is reversed in the rice cp genome. The yellow arrow indicates that there is a full-length ycf1 gene in the IR region. Orange indicates that the atpA-petG region is reversed in C. formosanum. The lower panels are a zoom-in of the box regions. The arrowheads indicate the direction of sequences from 5′ to 3′. The numbers indicate the position in the cp genome.

Figure 4. Comparison of the Cypripedium formosanum cp, Erycina pusilla cp genomes, and the mt ndh regions.

The arrows indicate coding regions. The arrowheads indicate the direction of the genes.

Figure 5. Transfer of chloroplast DNA, including ndh genes, to mt genomes within Kingdom Plantae.

The published mitochondrial and chloroplast genomes were downloaded from NCBI. The species names in the boxes indicate that the cp genome is unavailable. The cp and mt genomes were compared using BLASTN. The names in gray indicate that no cp DNA sequences were found in the mt genome. The names that are underlined in black indicate that cp DNA was found in the mt genome but that the ndh genes were not. The names in green indicate the presence of ndh genes in the mt DNA.

Figure 6. BLASTN comparison of the Erycina pusilla mt DNA and the E. pusilla cp genome.

The numbers at the top are the positions of the E. pusilla cp genome. The red boxes indicate the aligned sequences. The numbers in the first column are the clone IDs in the E. pusilla BAC library. The circles indicate that the clones are circular chromosomes and have been confirmed by PCR. c1: contig 1; c2: contig 2.