Lateral transfer of introns in the cryptophyte plastid genome

Cryptophytes are unicellular eukaryotic algae that acquired photosynthesis secondarily through the uptake and retention of a red-algal endosymbiont. The plastid genome of the cryptophyte Rhodomonas salina CCMP1319 was recently sequenced and found to contain a genetic element similar to a group II intron. Here, we explore the distribution, structure and function of group II introns in the plastid genomes of distantly and closely related cryptophytes. The predicted secondary structures of six introns contained in three different genes were examined and found to be generally similar to group II introns but unusually large in size (including the largest known noncoding intron). Phylogenetic analysis suggests that the cryptophyte group II introns were acquired via lateral gene transfer (LGT) from a euglenid-like species. Unexpectedly, the six introns occupy five distinct genomic locations, suggesting multiple LGT events or recent transposition (or both). Combined with structural considerations, RT–PCR experiments suggest that the transferred introns are degenerate ‘twintrons’ (i.e. nested group II/group III introns) in which the internal intron has lost its splicing capability, resulting in an amalgamation with the outer intron

A Gene in the Process of Endosymbiotic Transfer

BACKGROUND: The endosymbiotic birth of organelles is accompanied by massive transfer of endosymbiont genes to the eukaryotic host nucleus. In the centric diatom Thalassiosira pseudonana the Psb28 protein is encoded in the plastid genome while a second version is nuclear-encoded and possesses a bipartite N-terminal presequence necessary to target the protein into the diatom complex plastid. Thus it can represent a gene captured during endosymbiotic gene transfer. METHODOLOGY/PRINCIPAL FINDINGS: To specify the origin of nuclear- and plastid-encoded Psb28 in T. pseudonana we have performed extensive phylogenetic analyses of both mentioned genes. We have also experimentally tested the intracellular location of the nuclear-encoded Psb28 protein (nuPsb28) through transformation of the diatom Phaeodactylum tricornutum with the gene in question fused to EYFP. CONCLUSIONS/SIGNIFICANCE: We show here that both versions of the psb28 gene in T. pseudonana are transcribed. We also provide experimental evidence for successful targeting of the nuPsb28 fused with EYFP to the diatom complex plastid. Extensive phylogenetic analyses demonstrate that nucleotide composition of the analyzed genes deeply influences the tree topology and that appropriate methods designed to deal with a compositional bias of the sequences and the long branch attraction artefact (LBA) need to be used to overcome this obstacle. We propose that nuclear psb28 in T. pseudonana is a duplicate of a plastid localized version, and that it has been transferred from its endosymbiont

The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate

The cryptomonads are a group of unicellular algae that acquired photosynthesis through the engulfment of a red algal cell, a process called secondary endosymbiosis. Here, we present the complete plastid genome sequence of the secondarily nonphotosynthetic species Cryptomonas paramecium CCAP977/2a. The ∼78 kilobase pair (Kbp) C. paramecium genome contains 82 predicted protein genes, 29 transfer RNA genes, and a single pseudogene (atpF). The C. paramecium plastid genome is approximately 50 Kbp smaller than those of the photosynthetic cryptomonads Guillardia theta and Rhodomonas salina; 71 genes present in the G. theta and/or R. salina plastid genomes are missing in C. paramecium. The pet, psa, and psb photosynthetic gene families are almost entirely absent. Interestingly, the ribosomal RNA operon, present as inverted repeats in most plastid genomes (including G. theta and R. salina), exists as a single copy in C. paramecium. The G + C content (38%) is higher in C. paramecium than in other cryptomonad plastid genomes, and C. paramecium plastid genes are characterized by significantly different codon usage patterns and increased evolutionary rates. The content and structure of the C. paramecium plastid genome provides insight into the changes associated with recent loss of photosynthesis in a predominantly photosynthetic group of algae and reveals features shared with the plastid genomes of other secondarily nonphotosynthetic eukaryotes

Genome Evolution of a Tertiary Dinoflagellate Plastid

The dinoflagellates have repeatedly replaced their ancestral peridinin-plastid by plastids derived from a variety of algal lineages ranging from green algae to diatoms. Here, we have characterized the genome of a dinoflagellate plastid of tertiary origin in order to understand the evolutionary processes that have shaped the organelle since it was acquired as a symbiont cell. To address this, the genome of the haptophyte-derived plastid in Karlodinium veneficum was analyzed by Sanger sequencing of library clones and 454 pyrosequencing of plastid enriched DNA fractions. The sequences were assembled into a single contig of 143 kb, encoding 70 proteins, 3 rRNAs and a nearly full set of tRNAs. Comparative genomics revealed massive rearrangements and gene losses compared to the haptophyte plastid; only a small fraction of the gene clusters usually found in haptophytes as well as other types of plastids are present in K. veneficum. Despite the reduced number of genes, the K. veneficum plastid genome has retained a large size due to expanded intergenic regions. Some of the plastid genes are highly diverged and may be pseudogenes or subject to RNA editing. Gene losses and rearrangements are also features of the genomes of the peridinin-containing plastids, apicomplexa and Chromera, suggesting that the evolutionary processes that once shaped these plastids have occurred at multiple independent occasions over the history of the Alveolata

Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana

The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga

Organisation et structure des génomes mitochondriaux des algues brunes Pylaiella littoralis et Laminaria digitata

The mitochondrial genomes of two brown algae have been studied. The 1st is that of Pylaiella littoralis, which is thought to be primitive algae, the 2nd is that of Laminaria digitata, wich is expected to be an evolved alga, with the aim to compare their genomes. The 1st chapter describes the backgroundof the work: the endosymbiotic events that have given rise to mitochondria and plastids; an insight of what are brown algae and of what we know about mitochondria and their genome. The mitochondrial genomes of P. littoralis and L. digitata are circular DNA molecules of 58.507 bp about 36 kbp respectively. That of P. littoralis contains proteobacterial promoter regions and a T7-like RNA polymerase gene, at the same time. This genome also codes for quite a few ribosomal protein genes. One of them, rpl31, was only described in the mitochondrial DNA (mtDNA) of the primitive prostist Reclinomonas americana before. It also codes for group IIA and IIB introns with multidomaine encoded ORFs. The nad11 gene encodes only the 1st domain of the usual protein with the FeS-binding sequences important for the enzyme activity. The other part of the gene is not encoded in the mtDNA of P. littoralis, nor detected in the nuclear DNA. The cox2 gene exhibits an unusual in-frame insertion of 1006 amino acids within the gene, wich is 280 aa long only. P. littoralis mtDNA has conserved more primitive features than those of other eukaryotes, but has evolved beyond the stage represented by that of the protist R. americana. The sequenced part of the mitochondrial genome of L. digitata (60%) is surprisingly similar to that of P. littoralis. Gene order is nearly exactly the same, adn genesequences show very high homology. The main differences are the lack of introns and of the majority of ORFs. We have also made a few limited comparisons using other brown algae, wich could produce good tools for phylogenetic studies of the brown algae lineage, still mainly unraveled.Deux études de génomes mitochondriaux d'algues brunes sont présentées. La 1ère concerne celui d'une algue primitive Pylaiella littoralis. La 2nde est le début de la comparaison avec celui de Laminaria digitata, considérée comme évoluée. Le contexte de ces études est décrit : la 1ère partie traite des endosymbioses ayant conduit aux mitochondries et aux plastes ; une autre concerne la définition des algues brunes et la 3ème traite des mitochondries et de leur génome. L'ADN mitochondrial (ADNmt) de P. littoralis et de L. digitata consiste en molécules circulaires de 58507 pb et de 36k pb, respectivement. Celui de P. littoralis contient à la fois des promoteurs de type eubactérien et un gène d'ARN polymérase de type phagique. Ce génome code plusieurs gènes de protéines ribosomiques, dont rpl31, identifié avant uniquement dans l'ADNmt d'un protiste primitif, Reclinomonas americana. Il code aussi des introns des groupes IIA et IIB, avec des ORFs multidomaines complets. Le gène nad11 ne comporte que le 1er tiers du gène habituel, soit celui des domaines de liaison aux groupements FeS, dont l'importance a été montrée pour l'activité de l'enzyme. L'autre partie n'est pas codée dans l'ADNmt et n'a pas été détectée dans l'ADN nucléaire. Le gène cox2, lui, comporte une insertion de 1006 aa alors qu'il n'en code lui-même que 280. L'ADNmt de P. littoralis a conservé plus de caractères primitifs que ceux des autres eucaryotes tout en ayant plus évolué que celui de R. americana. Les 60% du génome mitochondrial de L. digitata qui sont séquencés ressemblent étonnamment à celui de P. littoralis. L'ordre des gènes est presque identique et leurs séquences ont de très fortes homologies. Les principales différences sont l'absence des introns et la plupart des ORFs. Nous avons aussi fait plusieurs comparaisons ponctuelles avec d'autres algues brunes qui pourraient être un outil utile dans l'étude des relations phylogénétiques de la lignée des algues brunes, encore peu connue

The mitochondrial genome of the brown alga Laminaria digitata: a comparative analysis

We report here the complete sequence of the mitochondrial genome of the brown alga Laminaria digitata (Hudson) J.V. Lamouroux. L. digitata mtDNA is a circular molecule of 38,007 bp (64.9 % A+ T), encoding 63 genes and 3 ORFs and with only 6-7 % of non-coding sequences. Based on gene content and order, its overall organization is very similar to that of the mitochondrial genome of Pylaiella littoralis, another brown alga belonging to a different sublineage of the Phaeophyceae. In particular, the two genomes share unusual features, which hence could be unique to brown algae among the heterokont lineage, namely the presence of a rn5 gene, a short nad I I gene, a cox2 gene with a large in-frame insertion and alpha-proteobacterial-like promoter sequences. On the other hand, L. digitata lacks the sequences which are thought to have been transmitted horizontally to the P. littoralis genome, that is, the group-II introns in the rnl and cox1 genes, and it features only traces of an ancestral T7-like RNA polymerase. Distance phylogenetic trees inferred from concatenated mitochondrial genes confirm that speciation of brown algae occurred recently compared to other heterokonts

A mtDNA-based phylogeny of the brown algal genus Fucus (Heterokontophyta; Phaeophyta)

Species of Fucus are among the dominant seaweeds along Northern Hemisphere shores, but taxonomic designations often are confounded by significant intraspecific morphological variability. We analyzed intra- and inter-specific phylogenetic relationships within the genus (275 individuals representing 16 taxa) using two regions of the mitochondrion: a variable intergenic spacer and a conserved portion of the 23S subunit. Bayesian ML and MP analyses verified a shallow phylogeny with two major lineages (previously reported) and resolved some intra-lineage relationships. Significant species-level paraphyly/polyphyly was observed within lineages 1A and 2. Despite higher species richness in the North Atlantic, a North Pacific origin of the genus is supported by a gradient of decreasing haplotype and nucleotide diversities in F. distichus from the North Pacific to the East Atlantic