The Plastid Genome of Najas flexilis: Adaptation to Submersed Environments Is Accompanied by the Complete Loss of the NDH Complex in an Aquatic Angiosperm

Les DH (2013) The Plastid Genome of Najas flexilis: Adaptation to Submersed Environments Is Accompanied by the Complete Loss of the NDH Complex in an Aquatic Angiosperm. PLoS ONE 8(7): e68591. doi:10.1371/journal.pone.0068591 The Plastid Genome of Najas flexilis : Adaptation to Submersed Environments Is Accompanied by the Complete Loss of the NDH Complex in an Aquatic Angiosperm Elena L. Peredo 0 Ursula M. King 0 Donald H. Les 0 Ive De Smet, University of Nottingham, United Kingdom 0 Department of Ecology and Evolutionary Biology, University of Connecticut , Storrs, Connecticut , United States of America The re-colonization of aquatic habitats by angiosperms has presented a difficult challenge to plants whose long evolutionary history primarily reflects adaptations to terrestrial conditions. Many aquatics must complete vital stages of their life cycle on the water surface by means of floating or emergent leaves and flowers. Only a few species, mainly within the order Alismatales, are able to complete all aspects of their life cycle including pollination, entirely underwater. Waterpollinated Alismatales include seagrasses and water nymphs (Najas), the latter being the only freshwater genus in the family Hydrocharitaceae with subsurface water-pollination. We have determined the complete nucleotide sequence of the plastid genome of Najas flexilis. The plastid genome of N. flexilis is a circular AT-rich DNA molecule of 156 kb, which displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) from the small single copy (SSC) regions. In N. flexilis, as in other Alismatales, the rps19 and trnH genes are localized in the LSC region instead of within the IR regions as in other monocots. However, the N. flexilis plastid genome presents some anomalous modifications. The size of the SSC region is only one third of that reported for closely related species. The number of genes in the plastid is considerably less. Both features are due to loss of the eleven ndh genes in the Najas flexilis plastid. In angiosperms, the absence of ndh genes has been related mainly to the loss of photosynthetic function in parasitic plants. The ndh genes encode the NAD(P)H dehydrogenase complex, believed essential in terrestrial environments, where it increases photosynthetic efficiency in variable light intensities. The modified structure of the N. flexilis plastid genome suggests that adaptation to submersed environments, where light is scarce, has involved the loss of the NDH complex in at least some photosynthetic angiosperms. - Funding: Portions of this research were funded by grants from the National Science Foundation (NSF DEB0841658), Fulbright Foundation and Spanish MEC, Irish Research Council for Science, Engineering and Technology (IRCSET) and University of Connecticut CLAS. Publication costs were provided by the University of Connecticut Open Access Author Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Chloroplasts evolved from prokaryotic photosynthetic endosymbionts [1] as cell organelles that maintain their own genetic material in a double stranded DNA molecule ranging in size from 35 to 217 kb [2]. Compared to their cyanobacterium-like ancestors, plastid genomes have experienced a dramatic reduction in gene number from the +3 000 once present in free-living Cyanobacteria to only 120250 genes in photosynthetic eukaryotes. The plastid genes that have been retained encode products necessary for photosynthetic and housekeeping functions. During photosynthetic eukaryote evolution, cyanobacterial genes were transferred from the endosymbiont to the host nucleus or were lost entirely, in instances where the function of those genes was no longer essential [3]. The process of gene transfer has not stopped [4] but continues as a constant flood of plastid and mitochondrial genome fragments to the nucleus, where organelle DNA can be integrated as functional genes. However, over time, such genes usually are pseudogenized and lost, with only a small proportion of the transferred DNA integrated into functional areas and being conserved [4]. Red algal plastids retain the highest number of genes of any other group of photosynthetic eukaryotes (232252) [3]. In contrast, the chloroplast of land plants (Embryophyta), and of their ancestral green algae (Chlorophyta), retains only 120 genes. It usually consists of two copies of an inverted repeat (IRa, IRb) that separate a large single copy region (LSC) from a small single copy region (SSC). While missing in some algae (Glaucophyta, Rhodophyta), green plant plastids are rich in repeated regions and possess editing mechanisms [3]. Key photosynthetic elements are encoded in plastid genomes, such as photosystem I and II genes, RuBisCO and thylakoid NAD(P)H dehydrogenase. Independent of any former function of ndh genes in Cyanobacteria, ndh genes are essential for photosynthesis in land plants [5]. Lost in other algal divisions, the ndh genes probably were essential in the adaptation of green algae to the fluctuating conditions of shoreline environments [5] The eleven plastid ndh genes together with four nuclear genes (nhdL, ndhM, ndhN, and ndhO) encode the thylakoid NAD(P)H dehydrogenase complex which functions mainly in the electron transfer from NADH to plastoquinone, which protects the cell against photooxidative-related stress and maintains optimal rates of cyclic photophosphorylation [5]. In land plants, small changes in any of the ndh genes significantly decrease net photosynthesis [6]. As a consequence of such strong selective pressure, the ndh genes are highly conserved across all vascular plant divisions [7]. In angiosperms, ndh loss in plastomes is associated primarily with heterotrophic (i.e., parasitic) plants [8]. The plastid genome of non-photosynthetic organisms undergoes severe rearrangements and deletions that lead to losses of both photosynthetic and chlororespiratory genes, which no longer are needed to maintain metabolic functions. Convergent (homoplasious) losses of ndh genes are evident among unrelated parasitic plants; such as Epifagus (Lamiales) [9], Cuscuta (Solanales) [10,11] or the mycotrophic orchid Neottia [12]. Pseudogenization and loss of ndh genes in the parasitic bryophyte Aneura mirabilis [13] further substantiates the relationship between parasitism and ndh loss. Due to the mutual interaction between symbiotic fungi and orchids [14], it is understandable that the lack of functional ndh genes is widespread within the Orchidaceae, even green-leaved orchids [1517]. Recent data suggest pseudogenization of ndhB and even complete loss of ndhF for some taxa in the order Alismatales (seagrasses and water nymphs) [18]. Homoplasic loss of ndh genes in aquatic angioperms might be related to potential adaptations to the (...truncated)