Rubisco spacer sequence divergence in the rhodophyte alga Gracilaria verrucosa and closely related species

Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers

Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase – a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.

AN EXAMINATION OF PACHYMENIA AND AEODES (HALYMENIACEAE, RHODOPHYTA) IN NEW ZEALAND AND THE TRANSFER OF TWO SPECIES OF AEODES IN SOUTH AFRICA TO PACHYMENIA(1)

A phylogenetic study was conducted of species of Halymeniaceae from New Zealand presently placed in Aeodes or Pachymenia, based on maximum-likelihood (ML), maximum-parsimony (MP), and Bayesian analyses of rbcL and nuclear internal transcribed spacer (ITS) rDNA sequences. We used molecular and morphological data in combination with exhaustive sampling of herbarium collections to clarify the taxonomy and distributions of New Zealand members of Pachymenia and Aeodes. Our study confirms the presence of three erect species of Pachymenia on the New Zealand mainland, and we resurrect the name Pachymenia dichotoma J. Agardh for the widely distributed, southernmost species. Species of Aeodes from South Africa are shown to be closely related to Pachymenia carnosa (J. Agardh) J. Agardh, the type species of Pachymenia, and are accordingly transferred to Pachymenia.

Phylogeographic analyses of the 30 degrees S south-east Pacific biogeographic transition zone establish the occurrence of a sharp genetic discontinuity in the kelp Lessonia nigrescens: vicariance or parapatry?

Phylogeographic studies are lacking in the Southern Hemisphere, and in particular in the south-eastern Pacific. To infer the possible scenario for the debated biogeographic transition zone located at 30-33 degrees S along the Chilean coast, we investigated whether there is a concordance between the phylogeographic pattern and the biogeographic transition in the intertidal kelp Lessonia nigrescens whose distribution is continuous across this transition zone. Using a combination of four makers located in the three genomic compartments (chloroplast, mitochondria and nucleus), we showed the presence of two main divergent lineages, possibly cryptic species. There was an exact match of the phylogeographic break with the 30 degrees S biogeographic transition zone, suggesting a common origin. The combined information given by the multilocus approach and by the population analysis suggested the occurrence of a budding speciation, with a northward range expansion.

GRACILARIA HUMMII SP. NOV. (GRACILARIALES, RHODOPHYTA), A NEW NAME FOR THE AGAROPHYTE "GRACILARIA CONFERVOIDES" HARVESTED IN NORTH CAROLINA DURING WORLD WAR II(1)

Gracilaria hummii Hommers. et Freshwater is proposed as a new name for the inshore cylindrical species found in North Carolina that was treated as Gracilaria confervoides (L.) Grev. during World War II, and more recently as G. verrucosa (Huds.) Papenf. Molecular evidence places G. hummii in the Gracilis-group in Gracilaria together with G. gracilis (Stackh.) Steentoft, L. M. Irvine et Farnham, the name currently applied to specimens formerly identified as G. confervoides and G. verrucosa. G. hummii differs from G. gracilis in possessing shallower male conceptacles in which the spermatangial filament originates from a surface cortical cell rather than from a subcortical cell. The cystocarps are similar, except that the gonimoblasts of G. hummii are attached to the base of the pericarp by numerous, prominent thickened terminal tubular cells and because terminal tubular cells are absent above the midregion of the cystocarp or in the vicinity of the ostiole. The gonimoblasts are subtended by a bundle of longitudinally oriented, thick-walled secondary filaments of a type that has not been described before in Gracilaria but that may be characteristic of some other species. G. hummii occupies a basal position in the Gracilis-group and is distinct from all other cylindrical North Carolina Gracilaria species, according to the molecular and morphological evidence.

Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America

Background

Group I introns are found in the nuclear small subunit ribosomal RNA gene (SSU rDNA) of some species of the genus Porphyra (Bangiales, Rhodophyta). Size polymorphisms in group I introns has been interpreted as the result of the degeneration of homing endonuclease genes (HEG) inserted in peripheral loops of intron paired elements. In this study, intron size polymorphisms were characterized for different Porphyra spiralis var. amplifolia (PSA) populations on the Southern Brazilian coast, and were used to infer genetic relationships and genetic structure of these PSA populations, in addition to cox2-3 and rbcL-S regions. Introns of different sizes were tested qualitatively for in vitro self-splicing.

Results

Five intron size polymorphisms within 17 haplotypes were obtained from 80 individuals representing eight localities along the distribution of PSA in the Eastern coast of South America. In order to infer genetic structure and genetic relationships of PSA, these polymorphisms and haplotypes were used as markers for pairwise Fst analyses, Mantel's test and median joining network. The five cox2-3 haplotypes and the unique rbcL-S haplotype were used as markers for summary statistics, neutrality tests Tajima's D and Fu's Fs and for median joining network analyses. An event of demographic expansion from a population with low effective number, followed by a pattern of isolation by distance was obtained for PSA populations with the three analyses. In vitro experiments have shown that introns of different lengths were able to self-splice from pre-RNA transcripts.

Conclusion

The findings indicated that degenerated HEGs are reminiscent of the presence of a full-length and functional HEG, once fixed for PSA populations. The cline of HEG degeneration determined the pattern of isolation by distance. Analyses with the other markers indicated an event of demographic expansion from a population with low effective number. The different degrees of degeneration of the HEG do not refrain intron self-splicing. To our knowledge, this was the first study to address intraspecific evolutionary history of a nuclear group I intron; to use nuclear, mitochondrial and chloroplast DNA for population level analyses of Porphyra; and intron size polymorphism as a marker for population genetics.

PHYLOGENETIC RELATIONSHIPS WITHIN THE STYLONEMATALES (STYLONEMATOPHYCEAE, RHODOPHYTA): BIOGEOGRAPHIC PATTERNS DO NOT APPLY TO STYLONEMA ALSIDII(1)

The Stylonematales is the sole order of the Stylonematophyceae. The order consists of a mixture of filamentous or unicellular taxa that are small, grow on various surfaces, and are described from many floras, indicating that they may be cosmopolitan. Such ubiquity has been proposed to be due to properties of microorganisms, such as large population sizes, rather than human-derived phenomena. While their small nature makes most records fortuitous, we targeted these red algae to get a better understanding of their global distribution, genetic variation, and phylogeographic relationships. Our results indicated that the genera are mostly well supported, except for the position of Stylonema cornu-cervi with Goniotrichopsis reniformis, while intergeneric relationships are mostly unsupported. The most commonly isolated species was Stylonema alsidii. Within this species, several well-supported clades were present. The phylogeographic relationships in S. alsidii showed no obvious biogeographic pattern, with supported clades containing samples from disparate locations, and multiple samples from the same area not grouping together. Some clades showed little genetic variation and wide distributions, possibly indicating human-derived dispersal. Other clades, also with wide distribution, showed more genetic structure and could be candidates for groups formed by natural long-distance dispersal. While all issues on ubiquity cannot be answered with this data set, it would appear that at least S. alsidii is a true ubiquitous taxon. The sister relationship of Rufusia pilicola to the remaining Stylonematophyceae, the presence of the carbohydrate floridoside, and this species' unusual habitat indicate that it belongs to a new order, Rufusiales.

Speciation and biogeography of the Caloglossa leprieurii complex (Delesseriaceae, Rhodophyta)

Studies on the morphology, reproductive compatibility, life cycle and molecular phylogeny of the euryhaline red alga Caloglossa provide insights into the speciation events and biogeographic patterns. The C. leprieurii complex is separated into three morphotypes based on the number of cell rows at nodes and the blade width. The three morphotypes are reproductively incompatible with each other, and furthermore many mating groups are recognized within the morphotypes. Incomplete reproductive isolation is occasionally seen between geographically distant mating groups, whereas no sexual compatibility occurs between sympatrically or parapatrically distributed mating groups. In the molecular phylogenetic analyses, the C. leprieurii complex is resolved as two clusters that phenotypically correspond to the single and multiple cell row types, respectively. The strains belonging to the same mating group are closely related to each other, without exception, while the mating groups showing incomplete reproductive reactions do not always make a clade. The genetic distance is generally not correlative to the geographic distance, and this is also suggested by the morphological data and crossability. These results indicate that allopatric speciation has frequently occurred in this species complex, although there is some evidence of long-distance dispersal.

A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL

A phylogeny for the Rhodophyta has been inferred by parsimony analysis of plastid rbcL sequences representing 81 species, 68 genera, 38 families, and 17 orders of red algae; rbcL encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Levels of sequence divergence among species, genera, and families are high in red algae, typically much greater than those reported for flowering plants. The Rhodophyta traditionally consists of one class, Rhodophyceae, and two subclasses, Bangiophycidae and Florideophycidae. The Bangiophycidae with three orders (Porphyridiales, Compsopogonales, and Bangiales) appears to be polyphyletic, and the Florideophycidae with 17 orders is monophyletic in this study. The current classification of the Florideophycidae based on ultrastructure of pit connections is supported. With the exception of the Rhodogorgonales, which appears to be misplaced, orders with one or two pit-plug cap layers (Hildenbrandiales, Corallinales, Acrochaetiales, Palmanales, Batrachospermales, and Nemaliales) terminate long branches of basal position within Florideophycidae in the most parsimonious rbcL tree. Orders that lack typical cap layers but possess a cap membrane are resolved as a monophyletic clade sister to the Ahnfeltiales. The large order Gigartinales, which is distributed among five rbcL clades, is polyphyletic. Families that possess typical carrageenan in their cell walls are resolved as a terminal clade containing two family complexes centered around the Solieriaceae and Gigartinaceae.

Large ATP synthase operon of the red alga Antithamnion sp. resembles the corresponding operon in cyanobacteria

The large plastid ATP synthase operon of the multicellular red alga Antithamnion sp. was cloned and the sequence of six ATPase genes determined. The operon resembles more the one from cyanobacteria than the ATP synthase operon of the chloroplast genome. The gene order is atpI, H, G, F, D and A, coding for the ATPase subunits a, c, b', b, delta and alpha, respectively. In green plants, the genes atpG and atpD are located in the nucleus. Unlike the situation in three published cyanobacterial ATP synthase operons, atpC, coding for the gamma subunit, is not a part of the rhodoplast operon. A single 4.5 kb transcript was detected with atpG, F, D and A gene probes that could span the whole operon, but no transcript could be detected with atpI and atpH probes. The end of an open reading frame preceding the atp genes shows remarkable homology to elongation factor TS from Escherichia coli. Behind the ATPase cluster, two open reading frames were detected that are not homologous to any known chloroplast gene. One of them may code for a transport protein of unknown specificity. Gene arrangement and sequence comparisons support the hypothesis of a polyphyletic origin of rhodoplasts and chloroplasts.