Concomitant loss of NDH complex‐related genes within chloroplast and nuclear genomes in some orchids

Abstract

These authors contributed equally to this work. SUMMARYThe chloroplast NAD(P)H dehydrogenase-like (NDH) complex consists of about 30 subunits from both the nuclear and chloroplast genomes and is ubiquitous across most land plants. In some orchids, such as Phalaenopsis equestris, Dendrobium officinale and Dendrobium catenatum, most of the 11 chloroplast genomeencoded ndh genes (cp-ndh) have been lost. Here we investigated whether functional cp-ndh genes have been completely lost in these orchids or whether they have been transferred and retained in the nuclear genome. Further, we assessed whether both cp-ndh genes and nucleus-encoded NDH-related genes can be lost, resulting in the absence of the NDH complex. Comparative analyses of the genome of Apostasia odorata, an orchid species with a complete complement of cp-ndh genes which represents the sister lineage to all other orchids, and three published orchid genome sequences for P. equestris, D. officinale and D. catenatum, which are all missing cp-ndh genes, indicated that copies of cp-ndh genes are not present in any of these four nuclear genomes. This observation suggests that the NDH complex is not necessary for some plants. Comparative genomic/transcriptomic analyses of currently available plastid genome sequences and nuclear transcriptome data showed that 47 out of 660 photoautotrophic plants and all the heterotrophic plants are missing plastid-encoded cp-ndh genes and exhibit no evidence for maintenance of a functional NDH complex. Our data indicate that the NDH complex can be lost in photoautotrophic plant species. Further, the loss of the NDH complex may increase the probability of transition from a photoautotrophic to a heterotrophic life history.

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

“…squamar i a 23 . This degree of ndh gene degradation is not only observed in heterotrophic organisms, but also in many autotrophic plants, including Orchidaceae 57,58 , Geraniaceae 59 and Cactaceae 60 . Kim et al .…”

Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex

“…Alternatively, the idiosyncratic losses of these genes in some leafy taxa, but not in others, may be explained by their tendency to inhabit low-or variable-light environments. It is clear that mycoheterotrophy can be implicated in relaxed selection on this gene complex (Wicke et al, 2013;Barrett et al, 2014;Kim et al, 2015;Kim & Chase, 2017;Lin et al, 2017). -related (ccsA, cemA, psa, psb, rbcL, ycf3&4 Housekeeping' genes (rpl, rps, accD, clpP, matK, ycf1&2, rrn, tRNA…”

Bioinformatic Analysis of Strawberry NDH-H Gene

“…As the endosymbiont evolved into an organelle, the plastid retained a greatly reduced genome with many of the cyanobacterial genes being transferred to the host nuclear genome. Although most functional cp-tonuclear gene transfers occurred early in plastid evolution [2], such transfers have been a continual evolutionary process [3] , and the cp genome (plastome) of photosynthetic land plants typically encodes 68-82 conserved protein-coding genes [4][5][6][7]. The study chosen NDH-H-like gene of 13 kinds species, downloaded their nucleotide and protein sequence from NCBI as the research object, found strawberry NDH-H gene via bioinformation analyze so as to provide reference for further study and utilization.…”