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

<p>Abstract</p> <p>Background</p> <p>The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate <it>Mesostigma viride </it>(Mesostigmatales) and the sarcinoid <it>Chlorokybus atmophyticus </it>(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 <it>Chlorokybus </it>and compared this genome sequence with those of three other charophycean green algae and the bryophytes <it>Marchantia polymorpha </it>and <it>Physcomitrella patens</it>.</p> <p>Results</p> <p>The <it>Chlorokybus </it>genome differs radically from its 42,424-bp <it>Mesostigma </it>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 <it>nad10 </it>and <it>trnL</it>(gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the <it>Chlorokybus </it>genome shares with its <it>Chara</it>, <it>Chaetosphaeridium </it>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 <it>Mesostigma</it>, due to analytical problems arising from accelerated sequence evolution in this lineage.</p> <p>Conclusion</p> <p>The <it>Chlorokybus </it>and <it>Mesostigma </it>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.</p

The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales

BACKGROUND: The Streptophyta comprise all land plants and six monophyletic groups of charophycean green algae. Phylogenetic analyses of four genes from three cellular compartments support the following branching order for these algal lineages: Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales and Charales, with the last lineage being sister to land plants. Comparative analyses of the Mesostigma viride (Mesostigmatales) and land plant chloroplast genome sequences revealed that this genome experienced many gene losses, intron insertions and gene rearrangements during the evolution of charophyceans. On the other hand, the chloroplast genome of Chaetosphaeridium globosum (Coleochaetales) is highly similar to its land plant counterparts in terms of gene content, intron composition and gene order, indicating that most of the features characteristic of land plant chloroplast DNA (cpDNA) were acquired from charophycean green algae. To gain further insight into when the highly conservative pattern displayed by land plant cpDNAs originated in the Streptophyta, we have determined the cpDNA sequences of the distantly related zygnematalean algae Staurastrum punctulatum and Zygnema circumcarinatum. RESULTS: The 157,089 bp Staurastrum and 165,372 bp Zygnema cpDNAs encode 121 and 125 genes, respectively. Although both cpDNAs lack an rRNA-encoding inverted repeat (IR), they are substantially larger than Chaetosphaeridium and land plant cpDNAs. This increased size is explained by the expansion of intergenic spacers and introns. The Staurastrum and Zygnema genomes differ extensively from one another and from their streptophyte counterparts at the level of gene order, with the Staurastrum genome more closely resembling its land plant counterparts than does Zygnema cpDNA. Many intergenic regions in Zygnema cpDNA harbor tandem repeats. The introns in both Staurastrum (8 introns) and Zygnema (13 introns) cpDNAs represent subsets of those found in land plant cpDNAs. They represent 16 distinct insertion sites, only five of which are shared by the two zygnematalean genomes. Three of these insertions sites have not been identified in Chaetosphaeridium cpDNA. CONCLUSION: The chloroplast genome experienced substantial changes in overall structure, gene order, and intron content during the evolution of the Zygnematales. Most of the features considered earlier as typical of land plant cpDNAs probably originated before the emergence of the Zygnematales and Coleochaetales

The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes

BACKGROUND: The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae), in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR) featuring an inverted rRNA operon and a small single-copy (SSC) region containing 14 genes normally found in the large single-copy (LSC) region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis, a representative of a distinct, early diverging lineage. RESULTS: The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of Oltmannsiellopsis cpDNA more closely resembles that of Chlorella (Trebouxiophyceae) cpDNA. CONCLUSION: The chloroplast genome of the last common ancestor of Oltmannsiellopsis and Pseudendoclonium contained a minimum of 108 genes, carried only a few group I introns, and featured a distinctive quadripartite architecture. Numerous changes were experienced by the chloroplast genome in the lineages leading to Oltmannsiellopsis and Pseudendoclonium. Our comparative analyses of chlorophyte cpDNAs support the notion that the Ulvophyceae is sister to the Chlorophyceae

Chloroplast DNA sequence of the green alga <it>Oedogonium cardiacum </it>(Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer

<p>Abstract</p> <p>Background</p> <p>To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA) from representative taxa. The complete cpDNA sequences previously reported for <it>Chlamydomonas </it>(Chlamydomonadales), <it>Scenedesmus </it>(Sphaeropleales), and <it>Stigeoclonium </it>(Chaetophorales) revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by <it>Chlamydomonas </it>and <it>Scenedesmus</it>. Unexpectedly, our recent phylogenies inferred from these cpDNAs and the partial sequences of three other chlorophycean cpDNAs disclosed two major clades, one uniting the Chlamydomonadales and Sphaeropleales (CS clade) and the other uniting the Oedogoniales, Chaetophorales and Chaetopeltidales (OCC clade). Although molecular signatures provided strong support for this dichotomy and for the branching of the Oedogoniales as the earliest-diverging lineage of the OCC clade, more data are required to validate these phylogenies. We describe here the complete cpDNA sequence of <it>Oedogonium cardiacum </it>(Oedogoniales).</p> <p>Results</p> <p>Like its three chlorophycean homologues, the 196,547-bp <it>Oedogonium </it>chloroplast genome displays a distinctive architecture. This genome is one of the most compact among photosynthetic chlorophytes. It has an atypical quadripartite structure, is intron-rich (17 group I and 4 group II introns), and displays 99 different conserved genes and four long open reading frames (ORFs), three of which are clustered in the spacious inverted repeat of 35,493 bp. Intriguingly, two of these ORFs (<it>int </it>and <it>dpoB</it>) revealed high similarities to genes not usually found in cpDNA. At the gene content and gene order levels, the <it>Oedogonium </it>genome most closely resembles its <it>Stigeoclonium </it>counterpart. Characters shared by these chlorophyceans but missing in members of the CS clade include the retention of <it>psaM</it>, <it>rpl32 </it>and <it>trnL</it>(caa), the loss of <it>petA</it>, the disruption of three ancestral clusters and the presence of five derived gene clusters.</p> <p>Conclusion</p> <p>The <it>Oedogonium </it>chloroplast genome disclosed additional characters that bolster the evidence for a close alliance between the Oedogoniales and Chaetophorales. Our unprecedented finding of <it>int </it>and <it>dpoB </it>in this cpDNA provides a clear example that novel genes were acquired by the chloroplast genome through horizontal transfers, possibly from a mitochondrial genome donor.</p

Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dubia and Tetraselmis sp. CCMP 881

The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction

The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands

BACKGROUND: The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. While the basal position of the Prasinophyceae is well established, the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC) remains uncertain. The five complete chloroplast DNA (cpDNA) sequences currently available for representatives of these classes display considerable variability in overall structure, gene content, gene density, intron content and gene order. Among these genomes, that of the chlorophycean green alga Chlamydomonas reinhardtii has retained the least ancestral features. The two single-copy regions, which are separated from one another by the large inverted repeat (IR), have similar sizes, rather than unequal sizes, and differ radically in both gene contents and gene organizations relative to the single-copy regions of prasinophyte and ulvophyte cpDNAs. To gain insights into the various changes that underwent the chloroplast genome during the evolution of chlorophycean green algae, we have sequenced the cpDNA of Scenedesmus obliquus, a member of a distinct chlorophycean lineage. RESULTS: The 161,452 bp IR-containing genome of Scenedesmus features single-copy regions of similar sizes, encodes 96 genes, i.e. only two additional genes (infA and rpl12) relative to its Chlamydomonas homologue and contains seven group I and two group II introns. It is clearly more compact than the four UTC algal cpDNAs that have been examined so far, displays the lowest proportion of short repeats among these algae and shows a stronger bias in clustering of genes on the same DNA strand compared to Chlamydomonas cpDNA. Like the latter genome, Scenedesmus cpDNA displays only a few ancestral gene clusters. The two chlorophycean genomes share 11 gene clusters that are not found in previously sequenced trebouxiophyte and ulvophyte cpDNAs as well as a few genes that have an unusual structure; however, their single-copy regions differ considerably in gene content. CONCLUSION: Our results underscore the remarkable plasticity of the chlorophycean chloroplast genome. Owing to this plasticity, only a sketchy portrait could be drawn for the chloroplast genome of the last common ancestor of Scenedesmus and Chlamydomonas

The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae

<p>Abstract</p> <p>Background</p> <p>In the Chlorophyta – the green algal phylum comprising the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae – the chloroplast genome displays a highly variable architecture. While chlorophycean chloroplast DNAs (cpDNAs) deviate considerably from the ancestral pattern described for the prasinophyte <it>Nephroselmis olivacea</it>, the degree of remodelling sustained by the two ulvophyte cpDNAs completely sequenced to date is intermediate relative to those observed for chlorophycean and trebouxiophyte cpDNAs. <it>Chlorella vulgaris </it>(Chlorellales) is currently the only photosynthetic trebouxiophyte whose complete cpDNA sequence has been reported. To gain insights into the evolutionary trends of the chloroplast genome in the Trebouxiophyceae, we sequenced cpDNA from the filamentous alga <it>Leptosira terrestris </it>(Ctenocladales).</p> <p>Results</p> <p>The 195,081-bp <it>Leptosira </it>chloroplast genome resembles the 150,613-bp <it>Chlorella </it>genome in lacking a large inverted repeat (IR) but differs greatly in gene order. Six of the conserved genes present in <it>Chlorella </it>cpDNA are missing from the <it>Leptosira </it>gene repertoire. The 106 conserved genes, four introns and 11 free standing open reading frames (ORFs) account for 48.3% of the genome sequence. This is the lowest gene density yet observed among chlorophyte cpDNAs. Contrary to the situation in <it>Chlorella </it>but similar to that in the chlorophycean <it>Scenedesmus obliquus</it>, the gene distribution is highly biased over the two DNA strands in <it>Leptosira</it>. Nine genes, compared to only three in <it>Chlorella</it>, have significantly expanded coding regions relative to their homologues in ancestral-type green algal cpDNAs. As observed in chlorophycean genomes, the <it>rpoB </it>gene is fragmented into two ORFs. Short repeats account for 5.1% of the <it>Leptosira </it>genome sequence and are present mainly in intergenic regions.</p> <p>Conclusion</p> <p>Our results highlight the great plasticity of the chloroplast genome in the Trebouxiophyceae and indicate that the IR was lost on at least two separate occasions. The intriguing similarities of the derived features exhibited by <it>Leptosira </it>cpDNA and its chlorophycean counterparts suggest that the same evolutionary forces shaped the IR-lacking chloroplast genomes in these two algal lineages.</p

Nitzschia anatoliensis sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey)

In this article we describe Nitzschia anatoliensis Górecka, Gastineau & Solak sp. nov., an example of a diatom species inhabiting extreme habitats. The new species has been isolated and successfully grown from the highly alkaline Van Lake in East Turkey. The description is based on morphology (light and scanning electron microscopy), the sequencing of its organellar genomes and several molecular phylogenies. This species could easily be overlooked because of its extreme similarity to Nitzschia aurariae but molecular phylogenies indicate that they are only distantly related. Furthermore, molecular data suggest that N. anatoliensis may occur in several alkaline lakes of Asia Minor and Siberia, but was previously misidentified as Nitzschia communis. It also revealed the very close genetic proximity between N. anatoliensis and the endosymbiont of the dinotom Kryptoperidinium foliaceum, providing additional clues on what might have been the original species of diatoms to enter symbiosis.info:eu-repo/semantics/publishedVersio

The Chloroplast Genome of the Green Alga Schizomeris leibleinii (Chlorophyceae) Provides Evidence for Bidirectional DNA Replication from a Single Origin in the Chaetophorales

In the Chlorophyceae, the chloroplast genome is extraordinarily fluid in architecture and displays unique features relative to other groups of green algae. For the Chaetophorales, 1 of the 5 major lineages of the Chlorophyceae, it has been shown that the distinctive architecture of the 223,902-bp genome of Stigeoclonium helveticum is consistent with bidirectional DNA replication from a single origin. Here, we report the 182,759-bp chloroplast genome sequence of Schizomeris leibleinii, a member of the earliest diverging lineage of the Chaetophorales. Like its Stigeoclonium homolog, the Schizomeris genome lacks a large inverted repeat encoding the rRNA operon and displays a striking bias in coding regions that is associated with a bias in base composition along each strand. Our results support the notion that these two chaetophoralean genomes replicate bidirectionally from a putative origin located in the vicinity of the small subunit ribosomal RNA gene. Their shared structural characteristics were most probably inherited from the common ancestor of all chaetophoralean algae. Short dispersed repeats account for most of the 41-kb size variation between the Schizomeris and Stigeoclonium genomes, and there is no indication that homologous recombination between these repeated elements led to the observed gene rearrangements. A comparison of the extent of variation sustained by the Stigeoclonium and Schizomeris chloroplast DNAs (cpDNAs) with that observed for the cpDNAs of the chlamydomonadalean Chlamydomonas and Volvox suggests that gene rearrangements as well as changes in the abundance of intergenic and intron sequences occurred at a slower pace in the Chaetophorales than in the Chlamydomonadales

Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov