The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae

An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?

Microsatellites (SSRs) are tandem repeat sequences in eukaryote genomes, including plant cytoplasmic genomes. The mitochondrial genome (mtDNA) has been shown to vary in size, number, and distribution of SSRs among different plant groups. Thus, SSRs contribute with genomic diversity in mtDNAs. However, the abundance, distribution, and evolutionary significance of SSRs in mtDNA from a wide range of algae and plants have not been explored. In this study, the mtDNAs of 204 plant and algal species were investigated related to the presence of SSRs. The number of SSRs was positively correlated with genome size. Its distribution is dependent on plant and algal groups analyzed, although the cluster analysis indicates the conservation of some common motifs in algal and terrestrial plants that reflect common ancestry of groups. Many SSRs in coding and non-coding regions can be useful for molecular markers. Moreover, mitochondrial SSRs are highly abundant, representing an important source for natural or induced genetic variation, i.e., for biotechnological approaches that can modulate mtDNA gene regulation. Thus, this comparative study increases the understanding of the plant and algal SSR evolution and brings perspectives for further studies.

The complete mitochondrial genome of the Caulerpa lentillifera (Ulvophyceae, Chlorophyta): Sequence, genome content, organization structure and phylogenetic consideration

The complete mitochondrial genome is greatly important for studies on genetic structure and phylogenetic relationship at various taxonomic levels. To obtain information about the evolutionary trends of mtDNA in the Ulvophyceae and also to gain insights into the phylogenetic relationships between ulvophytes and other chlorophytes, we determined the mtDNA sequence of Caulerpa lentillifera (sea grape) using de novo mitochondrial genome sequencing. The complete genomic DNA of C. lentillifera was circular and 209,034 bp in length, and it was the largest green-algal mitochondrial genome sequenced to date, with a low gene density of 65.2%, which is reminiscent of the "expanded" pattern of evolution exhibited by embryophyte mtDNAs. The C. lentillifera mtDNA consisted of a typical set of 17 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 42 putative open reading frames (ORFs) and 29 introns, which had homologs in green-algal mtDNAs displaying an "ancestral" or a "reduced-derived" pattern of evolution. The overall base composition of its mitochondrial genome was 24.19% for A, 24.94% for T, 25.80% for G, 25.07% for C and 50.87% for GC. The mitochondrial genome of C. lentillifera was characterized by numerous small intergenic regions and introns, which was clearly different from other green algae. With the exception of the NADH dehydrogenase subunit 6 (ND6), ND1, ATP and three tRNA genes (tRNA-His, tRNA-Thr and tRNA-Ala), all other mitochondrial genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we inferred the complete mtDNA sequence of C. lentillifera, an ulvophyte belonging to a distinct, early-diverging lineage. Taken together, our data offered useful information for the studies on phylogenetic hypotheses and phylogenetic relationships of C. lentillifera within the Chlorophyta.

Mitochondrial genomes of the green macroalga Ulva pertusa (Ulvophyceae, Chlorophyta): novel insights into the evolution of mitogenomes in the Ulvophyceae

To further understand the trends in the evolution of mitochondrial genomes (mitogenomes or mtDNAs) in the Ulvophyceae, the mitogenomes of two separate thalli of Ulva pertusa were sequenced. Two U. pertusa mitogenomes (Up1 and Up2) were 69,333 bp and 64,602 bp in length. These mitogenomes shared two ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein-coding genes, and 12 open reading frames. The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions. A total of six introns were present in the smaller U. pertusa mtDNA (Up2), while the larger mtDNA (Up1) had eight. The larger mtDNA had two additional group II introns in two genes (cox1 and cox2) and tandem duplication mutations in noncoding regions. Our results showed the first case of intraspecific variation in chlorophytan mitogenomes and provided further genomic data for the undersampled Ulvophyceae.

Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis

Mitochondria are archetypal eukaryotic organelles that were acquired by endosymbiosis of an ancient species of alpha-proteobacteria by the last eukaryotic common ancestor. The genetic information contained within the mitochondrial genome has been an important source of information for resolving relationships among eukaryotic taxa. In this study, we utilized mitochondrial and chloroplast genomes to explore relationships among prasinophytes. Prasinophytes are represented by diverse early-diverging green algae whose physical structures and genomes have the potential to elucidate the traits of the last common ancestor of the Viridiplantae (or Chloroplastida). We constructed de novo mitochondrial genomes for two prasinophyte algal species, Pyramimonas parkeae and Cymbomonas tetramitiformis, representing the prasinophyte clade. Comparisons of genome structure and gene order between these species and to those of other prasinophytes revealed that the mitochondrial genomes of P. parkeae and C. tetramitiformis are more similar to each other than to other prasinophytes, consistent with other molecular inferences of the close relationship between these two species. Phylogenetic analyses using the inferred amino acid sequences of mitochondrial and chloroplast protein-coding genes resolved a clade consisting of P. parkeae and C. tetramitiformis; and this group (representing the prasinophyte clade I) branched with the clade II, consistent with previous studies based on the use of nuclear gene markers.

Mitochondrial Genome of Prasinophyte Alga Pyramimonas parkeae

Prasinophytes are a paraphyletic assemblage of nine heterogeneous lineages in the Chlorophyta clade of Archaeplastida. Until now, seven complete mitochondrial genomes have been sequenced from four prasinophyte lineages. Here, we report the mitochondrial genome of Pyramimonas parkeae, the first representative of the prasinophyte clade I. The circular-mapping molecule is 43,294 bp long, AT rich (68.8%), very compact and it comprises two 6,671 bp long inverted repeat regions. The gene content is slightly smaller than the gene-richest prasinophyte mitochondrial genomes. The single identified intron is located in the cytochrome c oxidase subunit 1 gene (cox1). Interestingly, two exons of cox1 are encoded on the same strand of DNA in the reverse order and the mature mRNA is formed by trans-splicing. The phylogenetic analysis using the data set of 6,037 positions assembled from 34 mtDNA-encoded proteins of 48 green algae and plants is not in compliance with the branching order of prasinophyte clades revealed on the basis of 18S rRNA genes and cpDNA-encoded proteins. However, the phylogenetic analyses based on all three genomic elements support the sister position of prasinophyte clades Pyramimonadales and Mamiellales.

Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta)

Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.

Complete mitochondrial genome of Ulva prolifera, the dominant species of green macroalgal blooms in Yellow Sea, China

Ulva prolifera (U. prolifera), a green macroalgae, is widely known as the dominant species of the world's largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U. prolifera (GenBank accession number: KU161104). The genome consists of circular chromosomes of 61 962 bp and encodes a total of 26 protein-coding genes include nine ribosomal protein genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. prolifera clustered into Ulvo phyceae clade and had close genetic relationship with algae Ulva fasciata.

Complete mitochondrial genome of Ulva linza, one of the causal species of green macroalgal blooms in Yellow Sea, China

Ulva linza, a green macroalgae, is one of the causal species of the world's largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U.linza (GenBank accession no. KU189740). The genome consists of circular chromosomes of 70 858 bp and encodes a total of 28 protein-coding genes including eight rps genes, three rpl genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. linza clustered into Ulvophyceae clade and had close genetic relationship with algae Ulva prolifera.

Draft Plastid and Mitochondrial Genome Sequences from Antarctic Alga Prasiola crispa

The organelle genomes of the Antarctic alga Prasiola crispa (Lightfoot) Kützing have been sequenced. The plastid and mitochondrial genomes have a total length of 196,502 bp and 89,819 bp, respectively. These genomes have 19 putative photosynthesis-related genes and 17 oxidative metabolism-related genes, respectively.

The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat

Background

Lobosphaera incisa, formerly known as Myrmecia incisa and then Parietochloris incisa, is an oleaginous unicellular green alga belonging to the class Trebouxiophyceae (Chlorophyta). It is the richest known plant source of arachidonic acid, an ω-6 poly-unsaturated fatty acid valued by the pharmaceutical and baby-food industries. It is therefore an organism of high biotechnological interest, and we recently reported the sequence of its chloroplast genome.

Results

We now report the complete sequence of the mitochondrial genome of L. incisa from high-throughput Illumina short-read sequencing. The circular chromosome of 69,997 bp is predicted to encode a total of 64 genes, some harboring specific self-splicing group I and group II introns. Overall, the gene content is highly similar to that of the mitochondrial genomes of other Trebouxiophyceae, with 34 protein-coding, 3 rRNA, and 27 tRNA genes. Genes are distributed in two clusters located on different DNA strands, a bipartite arrangement that suggests expression from two divergent promoters yielding polycistronic primary transcripts. The L. incisa mitochondrial genome contains families of intergenic dispersed DNA repeat sequences that are not shared with other known mitochondrial genomes of Trebouxiophyceae. The most peculiar feature of the genome is a repetitive palindromic repeat, the LIMP (L. Incisa Mitochondrial Palindrome), found 19 times in the genome. It is formed by repetitions of an AACCA pentanucleotide, followed by an invariant 7-nt loop and a complementary repeat of the TGGTT motif. Analysis of the genome sequencing reads indicates that the LIMP can be a substrate for large-scale genomic rearrangements. We speculate that LIMPs can act as origins of replication. Deep sequencing of the L. incisa transcriptome also suggests that the LIMPs with long stems are sites of transcript processing. The genome also contains five copies of a related palindromic repeat, the HyLIMP, with a 10-nt motif related to that of the LIMP.

Conclusions

The mitochondrial genome of L. incisa encodes a unique type of repetitive palindromic repeat sequence, the LIMP, which can mediate genome rearrangements and play a role in mitochondrial gene expression. Experimental studies are needed to confirm and further characterize the functional role(s) of the LIMP.

The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta)

Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping molecule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid genome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes). Additionally, five introns were annotated in four genes: atpA (1), petB (1), psbB (2), and rrl (1). The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and follows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA genes for a total of 56 identifiable genes. Ten introns were annotated in this mtDNA: cox1 (4), atp1 (1), nad3 (1), nad5 (1), and rrs (3). Double-cut-and-join (DCJ) values showed that organellar genomes across Chlorophyta are highly rearranged, in contrast to the highly conserved organellar genomes of the red algae (Rhodophyta). A phylogenomic investigation of 51 plastid protein-coding genes showed that Ulvophyceae is not monophyletic, and also placed Oltmannsiellopsis (Oltmannsiellopsidales) and Tetraselmis (Chlorodendrophyceae) closely to Ulva (Ulvales) and Pseudendoclonium (Ulothrichales).

The mitochondrial genome of the prasinophyte Prasinoderma coloniale reveals two trans-spliced group I introns in the large subunit rRNA gene

Organelle genes are often interrupted by group I and or group II introns. Splicing of these mobile genetic occurs at the RNA level via serial transesterification steps catalyzed by the introns'own tertiary structures and, sometimes, with the help of external factors. These catalytic ribozymes can be found in cis or trans configuration, and although trans-arrayed group II introns have been known for decades, trans-spliced group I introns have been reported only recently. In the course of sequencing the complete mitochondrial genome of the prasinophyte picoplanktonic green alga Prasinoderma coloniale CCMP 1220 (Prasinococcales, clade VI), we uncovered two additional cases of trans-spliced group I introns. Here, we describe these introns and compare the 54,546 bp-long mitochondrial genome of Prasinoderma with those of four other prasinophytes (clades II, III and V). This comparison underscores the highly variable mitochondrial genome architecture in these ancient chlorophyte lineages. Both Prasinoderma trans-spliced introns reside within the large subunit rRNA gene (rnl) at positions where cis-spliced relatives, often containing homing endonuclease genes, have been found in other organelles. In contrast, all previously reported trans-spliced group I introns occur in different mitochondrial genes (rns or coxI). Each Prasinoderma intron is fragmented into two pieces, forming at the RNA level a secondary structure that resembles those of its cis-spliced counterparts. As observed for other trans-spliced group I introns, the breakpoint of the first intron maps to the variable loop L8, whereas that of the second is uniquely located downstream of P9.1. The breakpoint In each Prasinoderma intron corresponds to the same region where the open reading frame (ORF) occurs when present in cis-spliced orthologs. This correlation between the intron breakpoint and the ORF location in cis-spliced orthologs also holds for other trans-spliced introns; we discuss the possible implications of this interesting observation for trans-splicing of group I introns.

Lineage-specific fragmentation and nuclear relocation of the mitochondrial cox2 gene in chlorophycean green algae (Chlorophyta)

In most eukaryotes the subunit 2 of cytochrome c oxidase (COX2) is encoded in intact mitochondrial genes. Some green algae, however, exhibit split cox2 genes (cox2a and cox2b) encoding two polypeptides (COX2A and COX2B) that form a heterodimeric COX2 subunit. Here, we analyzed the distribution of intact and split cox2 gene sequences in 39 phylogenetically diverse green algae in phylum Chlorophyta obtained from databases (28 sequences from 22 taxa) and from new cox2 data generated in this work (23 sequences from 18 taxa). Our results support previous observations based on a smaller number of taxa, indicating that algae in classes Prasinophyceae, Ulvophyceae, and Trebouxiophyceae contain orthodox, intact mitochondrial cox2 genes. In contrast, all of the algae in Chlorophyceae that we examined exhibited split cox2 genes, and could be separated into two groups: one that has a mitochondrion-localized cox2a gene and a nucleus-localized cox2b gene ("Scenedesmus-like"), and another that has both cox2a and cox2b genes in the nucleus ("Chlamydomonas-like"). The location of the split cox2a and cox2b genes was inferred using five different criteria: differences in amino acid sequences, codon usage (mitochondrial vs. nuclear), codon preference (third position frequencies), presence of nucleotide sequences encoding mitochondrial targeting sequences and presence of spliceosomal introns. Distinct green algae could be grouped according to the form of cox2 gene they contain: intact or fragmented, mitochondrion- or nucleus-localized, and intron-containing or intron-less. We present a model describing the events that led to mitochondrial cox2 gene fragmentation and the independent and sequential migration of cox2a and cox2b genes to the nucleus in chlorophycean green algae. We also suggest that the distribution of the different forms of the cox2 gene provides important insights into the phylogenetic relationships among major groups of Chlorophyceae.

Nested in the Chlorellales or independent class? Phylogeny and classification of the Pedinophyceae (Viridiplantae) revealed by molecular phylogenetic analyses of complete nuclear and plastid-encoded rRNA operons

The class Pedinophyceae was established for asymmetric uniflagellate green algae, and was originally considered as an ancestral lineage of viridiplants. However, analyses of 71 concatenated plastid proteins [Turmel et al. (2009): Mol. Biol. Evol. 26: 2317-2331] recovered Pedinomonas within the Chlorellales (Trebouxiophyceae), thereby questioning the Pedinophyceae as an independent class. For the present study, complete nuclear and plastid-encoded rRNA operon sequences have been determined for 37 taxa of green algae including 6 members of the Pedinophyceae, providing 9272 aligned nucleotide positions. Phylogenies using both rRNA operons consistently rejected any relationship between Pedinophyceae and the Chlorellales. Instead, the Pedinophyceae were significantly resolved as sister of all phycoplast-containing 'core' chlorophytes, i.e. Chlorodendrophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Reinvestigation of plastid proteins discovered biased phylogenetic signal among protein partitions, indicating the published Pedinomonas + Chlorellales association as likely artificial. Marine pedinophytes (Resultomonas and Marsupiomonas; Marsupiomonadales ord. nov.), formed a sister clade to the order Pedinomonadales, occurring in freshwater and soil habitats. Synapomorphies in rRNA secondary structures were integrated in taxonomic diagnoses of the Pedinophyceae and were also used for BLAST searches targeting environmental sequence databases. The latter approach revealed conserved habitat preferences for the Marsupiomonadales and Pedinomonadales, and identified several novel pedinophyte lineages.

The mitochondrial genome of the entomoparasitic green alga helicosporidium

BACKGROUND

Helicosporidia are achlorophyllous, non-photosynthetic protists that are obligate parasites of invertebrates. Highly specialized, these pathogens feature an unusual cyst stage that dehisces inside the infected organism and releases a filamentous cell displaying surface projections, which will penetrate the host gut wall and eventually reproduce in the hemolymph. Long classified as incertae sedis or as relatives of other parasites such as Apicomplexa or Microsporidia, the Helicosporidia were surprisingly identified through molecular phylogeny as belonging to the Chlorophyta, a phylum of green algae. Most phylogenetic analyses involving Helicosporidia have placed them within the subgroup Trebouxiophyceae and further suggested a close affiliation between the Helicosporidia and the genus Prototheca. Prototheca species are also achlorophyllous and pathogenic, but they infect vertebrate hosts, inducing protothecosis in humans. The complete plastid genome of an Helicosporidium species was recently described and is a model of compaction and reduction. Here we describe the complete mitochondrial genome sequence of the same strain, Helicosporidium sp. ATCC 50920 isolated from the black fly Simulium jonesi.

METHODOLOGY/PRINCIPAL FINDINGS

The circular mapping 49343 bp mitochondrial genome of Helicosporidium closely resembles that of the vertebrate parasite Prototheca wickerhamii. The two genomes share an almost identical gene complement and display a level of synteny that is higher than any other sequenced chlorophyte mitochondrial DNAs. Interestingly, the Helicosporidium mtDNA feature a trans-spliced group I intron, and a second group I intron that contains two open reading frames that appear to be degenerate maturase/endonuclease genes, both rare characteristics for this type of intron.

CONCLUSIONS/SIGNIFICANCE

The architecture, genome content, and phylogeny of the Helicosporidium mitochondrial genome are all congruent with its close relationship to Prototheca within the Trebouxiophyceae. The Helicosporidium mitochondrial genome does, however, contain a number of novel features, particularly relating to its introns.

Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture

Background

The magnitude of intronic and intergenic DNA can vary substantially both within and among evolutionary lineages; however, the forces responsible for this disparity in genome compactness are conjectural. One explanation, termed the mutational-burden hypothesis, posits that genome compactness is primarily driven by two nonadaptive processes: mutation and random genetic drift – the effects of which can be discerned by measuring the nucleotide diversity at silent sites (π_silent), defined as noncoding sites and the synonymous sites of protein-coding regions. The mutational-burden hypothesis holds that π_silent is negatively correlated to genome compactness. We used the model organism Chlamydomonas reinhardtii, which has a streamlined, coding-dense mitochondrial genome and an noncompact, intron-rich nuclear genome, to investigate the mutational-burden hypothesis. For measuring π_silent we sequenced the complete mitochondrial genome and portions of 7 nuclear genes from 7 geographical isolates of C. reinhardtii.

Results

We found significantly more nucleotide diversity in the nuclear compartment of C. reinhardtii than in the mitochondrial compartment: net values of π_silent for the nuclear and mitochondrial genomes were 32 × 10^-3 and 8.5 × 10^-3, respectively; and when insertions and deletions (indels) are factored in, these values become 49 × 10^-3 for the nuclear DNA and 11 × 10^-3 for the mitochondrial DNA (mtDNA). Furthermore, our investigations of C. reinhardtii revealed 4 previously undiscovered mitochondrial introns, one of which contains a fragment of the large-subunit (LSU) rRNA gene and another of which is found in a region of the LSU-rRNA gene not previously reported (for any taxon) to contain introns.

Conclusion

At first glance our results are in opposition to the mutational-burden hypothesis: π_silent was approximately 4 times greater in the nuclear compartment of C. reinhardtii relative to the mitochondrial compartment. However, when we consider the encumbrance of noncoding DNA in each of these C. reinhardtii compartments, we conclude that introns in the mtDNA impose a greater burden than those in the nuclear DNA and suggest that the same may be true for the intergenic regions. Overall, we cannot reject the mutational-burden hypothesis and feel that more data on nucleotide diversity from green algae and other protists are needed.

The Culture Collection of Algae and Protozoa (CCAP): a biological resource for protistan genomics

CCAP, the largest European protistan culture collection, is based at the Scottish Association for Marine Science near Oban, Scotland (http://www.ccap.ac.uk). The Collection comprises more than 2700 strains in the public domain, of which 1050 are marine algae, 1300 freshwater algae, and 350 protozoa. The primary mission of CCAP is to maintain and distribute defined cultures and their associated information to its customers. It also has a support and advisory function on all aspects of protistan science. In addition, it is involved in the training of students and researchers in algal identification and culture techniques. In light of the increasing number of fully sequenced protists, the CCAP is striving to provide targeted services and support to workers involved in all aspects of genomic research. At present, the Collection holds several hundred strains of genomic model taxa including: Acanthamoeba, Cafeteria, Cercomonas, Chlamydomonas, Chlorella, Cyanophora, Dictyostelium, Dunaliella, Ectocarpus, Emiliania, Euglena, Micromonas, Naegleria, Nephroselmis, Paramecium, Pavlova, Phaeodactylum, Porphyra, Pseudendoclonium, Pylaiella, Rhodomonas, Scenedesmus, Staurastrum, Tetrahymena, Thalassiosira, Volvox and Zygnema. These strains provide a defined representation of natural variation within model organisms, an increasingly useful resource for post-genomics approaches. Our aim over the next 2-5 years is to add value to the Collection by increasing the number of genome model species, and by offering an integrated, up-to-date, easy-to-use resource that would provide curated information on our strain holdings. In collaboration with other major Biological Resource Centres worldwide, we intend to build a hub providing access to both protistan cultures and their associated bioinformatics data.

An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus

Background

The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA) of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens.

Results

The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL(gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara, Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma, due to analytical problems arising from accelerated sequence evolution in this lineage.

Conclusion

The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean evolution is no longer tenable. Our data raise the possibility that the emergence of land plants was not associated with a substantial gain of intergenic sequences by the mitochondrial genome.

The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction

The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most gene-dense mt genome of all Chlorophyta. Furthermore, it is characterized by a unique segmental duplication, encompassing 22 genes and covering 44% of the genome. Such a duplication has not been observed before in green algae, although it is also present in the mt genomes of higher plants. The quadripartite cp genome forms a circle of 71,666 bp, containing 86 genes divided over a larger and a smaller single-copy region, separated by 2 inverted repeat sequences. Based on genome size and number of genes, the Ostreococcus cp genome is the smallest known among the green algae. Phylogenetic analyses based on a concatenated alignment of cp, mt, and nuclear genes confirm the position of O. tauri within the Prasinophyceae, an early branch of the Chlorophyta.

Mitochondrial genome sequence evolution in Chlamydomonas

The mitochondrial genomes of the Chlorophyta exhibit significant diversity with respect to gene content and genome compactness; however, quantitative data on the rates of nucleotide substitution in mitochondrial DNA, which might help explain the origin of this diversity, are lacking. To gain insight into the evolutionary forces responsible for mitochondrial genome diversification, we sequenced to near completion the mitochondrial genome of the chlorophyte Chlamydomonas incerta, estimated the evolutionary divergence between Chlamydomonas reinhardtii and C. incerta mitochondrial protein-coding genes and rRNA-coding regions, and compared the relative evolutionary rates in mitochondrial and nuclear genes. Synonymous and nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear protein-coding genes. The mitochondrial rRNA-coding regions, however, are evolving much faster than their nuclear counterparts, and this difference might be explained by relaxed functional constraints on the mitochondrial translational apparatus due to the small number of proteins synthesized in Chlamydomonas mitochondria. Substitution rates at synonymous sites in a nonstandard mitochondrial gene (rtl) and at intronic and synonymous sites in nuclear genes expressed at low levels suggest that the mutation rate is similar in these two genetic compartments. Potential evolutionary forces shaping mitochondrial genome evolution in Chlamydomonas are discussed.