Dataset Information

The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales.

ABSTRACT: 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.

SUBMITTER: Brouard JS

PROVIDER: S-EPMC3138424 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales.

Brouard Jean-Simon JS Otis Christian C Lemieux Claude C Turmel Monique M

Genome biology and evolution 20110505

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 o ...[more]

PMID: 21546564

Similar Datasets

Project description:BackgroundTo 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 Chlamydomonas (Chlamydomonadales), Scenedesmus (Sphaeropleales), and Stigeoclonium (Chaetophorales) revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by Chlamydomonas and Scenedesmus. 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 Oedogonium cardiacum (Oedogoniales).ResultsLike its three chlorophycean homologues, the 196,547-bp Oedogonium 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 (int and dpoB) revealed high similarities to genes not usually found in cpDNA. At the gene content and gene order levels, the Oedogonium genome most closely resembles its Stigeoclonium counterpart. Characters shared by these chlorophyceans but missing in members of the CS clade include the retention of psaM, rpl32 and trnL(caa), the loss of petA, the disruption of three ancestral clusters and the presence of five derived gene clusters.ConclusionThe Oedogonium chloroplast genome disclosed additional characters that bolster the evidence for a close alliance between the Oedogoniales and Chaetophorales. Our unprecedented finding of int and dpoB 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.

Project description:BackgroundThe chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum.MethodsThe Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed.ResultsThe 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site.DiscussionOur results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites.

Dataset Information

The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales.

Publications

The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets