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.

FIG. 1.—

Gene maps of the Schizomeris and Stigeoclonium chloroplast genomes. Coding sequences on the outside of the map are transcribed in a clockwise direction. Genes included in the nine blocks of colinear sequences (numbered 1 to 9) shared between Schizomeris and Stigeoclonium are shown in blue, whereas rearranged or unique genes are shown in red. Group I and group II introns are shown in yellow and orange, respectively; intron ORFs are distinguished from exons by narrower boxes. Arrows mark the putative origin (ori) and terminus (ter) of replication. The duplicated Schizomeris trnS(gcu) is indicated by an asterisk. The rpoB gene consists of two separate ORFs (rpoBa and rpoBb) that are not associated with sequences typical of group I or group II introns. Two free-standing ORFs containing more than 130 codons (orf589 and orf1432) were identified. These ORFs, which are found upstream of the partially duplicated psaA gene and the duplicated trnS(gcu) copy, show no homology with any known DNA sequences. tRNA genes are indicated by the one-letter amino acid code followed by the anticodon in parentheses (Me, elongator methionine; Mf, initiator methionine).

FIG. 2.—

Identification of the putative origin and terminus of replication in Schizomeris cpDNA. (A) Plot of cumulative GC skew over the entire genome sequence. The cumulative GC skew was calculated as indicated in the Materials and Methods; base at position 150,000 was arbitrarily selected to represent the starting point. Above the plot is a representation of the coding strand, either the strand whose sequence has been deposited in GenBank (the top strand) or the alternate strand (bottom strand). The numbers of conserved genes encoded in the filled boxes are indicated. (B) Positions of three highly conserved noncoding sequences (S1, S2, and S3) in the Schizomeris, Stigeoclonium, and Uronema cpDNA regions containing a putative origin of replication. (C) Alignments of the Schizomeris (Sl), Stigeoclonium (Sh), and Uronema (Ub) S1 and S2 sequences.

FIG. 3.—

Sequence divergence, gene rearrangements, and variation in the abundance of diverse categories of sequences in the Schizomeris/Stigeoclonium and Chlamydomonas/Volvox chloroplast genomes. The tree on the left shows the evolutionary distances as inferred from 61 concatenated protein-coding genes as well as the number of inversions for each pair of compared genomes. The numbers of nonsynonymous (upper numbers) and synonymous (lower numbers) nucleotide substitutions estimated by CODEML are shown along each branch. The histograms on the right illustrate the lengths of coding sequences, introns, repeats, and intergenic spacers excluding the repeats. Note that the sequences within the IR were counted only once. Abbreviations: Oc, Oedogonium cardiacum; Ft, Floydiella terrestris; Sh, Stigeoclonium helveticum; Sl, Schizomeris leibleinii; Cr, Chlamydomonas reinhardtii; Vc, Volvox carteri; Ds, Dunaliella salina; So, Scenedesmus obliquus.