Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta)

Resolving the taxonomy of the Polysiphonia scopulorum complex and the Bryocladia lineage (Rhodomelaceae, Rhodophyta)

Cryptic diversity is common among marine macroalgae, with molecular tools leading to the discovery of many new species. To assign names to these morphologically similar species, the type and synonyms have to be examined, and if appropriate, new species must be described. The turf-forming red alga Polysiphonia scopulorum was originally described from Rottnest Island, Australia, and subsequently widely reported in tropical and temperate coasts based on morphological identifications. A recent study of molecular species delineation revealed a complex of 12 species in Australia, South Africa, and Europe. These species are placed in a taxonomically unresolved lineage of the tribe Polysiphonieae. The aim of this study was to resolve the genus- and species-level taxonomy of this complex and related species using molecular and morphological information. Three morphologically indistinguishable species of the complex were found at the type locality of P. scopulorum, preventing a straightforward assignment of the name to any of the molecular lineages. Therefore, we propose a molecularly characterized epitype. Polysiphonia caespitosa is reinstated for the only species found in its type locality in South Africa. We describe seven new species. Only one species of the complex can be morphologically recognized, with the other eight species indistinguishable based on morphometric analysis. The studied complex, together with another seven species currently placed in Polysiphonia and two Bryocladia species, formed a clade distinct from Polysiphonia sensu stricto. Based on observations of Bryocladia cervicornis (the generitype), we describe our seven new species in the genus Bryocladia and transfer another nine species from Polysiphonia to Bryocladia.

Gene-rich plastid genomes of two parasitic red algal species, Laurencia australis and L. verruciformis (Rhodomelaceae, Ceramiales), and a taxonomic revision of Janczewskia

Parasitic red algae are an interesting system for investigating the genetic changes that occur in parasites. These parasites have evolved independently multiple times within the red algae. The functional loss of plastid genomes can be investigated in these multiple independent examples, and fine-scale patterns may be discerned. The only plastid genomes from red algal parasites known so far are highly reduced and missing almost all photosynthetic genes. Our study assembled and annotated plastid genomes from the parasites Janczewskia tasmanica and its two Laurencia host species (Laurencia elata and one unidentified Laurencia sp. A25) from Australia and Janczewskia verruciformis, its host species (Laurencia catarinensis), and the closest known free-living relative (Laurencia obtusa) from the Canary Islands (Spain). For the first time we show parasitic red algal plastid genomes that are similar in size and gene content to free-living host species without any gene loss or genome reduction. The only exception was two pseudogenes (moeB and ycf46) found in the plastid genome of both isolates of J. tasmanica, indicating potential for future loss of these genes. Further comparative analyses with the three highly reduced plastid genomes showed possible gene loss patterns, in which photosynthetic gene categories were lost followed by other gene categories. Phylogenetic analyses did not confirm monophyly of Janczewskia, and the genus was subsumed into Laurencia. Further investigations will determine if any convergent small-scale patterns of gene loss exist in parasitic red algae and how these are applicable to other parasitic systems.

Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta)

Cystocloniacae is a highly diverse family of Rhodophyta, including species of ecological and economic importance, whose phylogeny remains largely unresolved. Species delimitation is unclear, particularly in the most speciose genus, Hypnea, and cryptic diversity has been revealed by recent molecular assessments, especially in the tropics. Here, we carried out the first phylogenomic investigation of Cystocloniaceae, focused on the genus Hypnea, inferred from chloroplast and mitochondrial genomes including taxa sampled from new and historical collections. In this work, molecular synapomorphies (gene losses, InDels and gene inversions) were identified to better characterize clades in our congruent organellar phylogenies. We also present taxon-rich phylogenies based on plastid and mitochondrial markers. Molecular and morphological comparisons of historic collections with contemporary specimens revealed the need for taxonomic updates in Hypnea, the synonymization of H. marchantae to a later heterotypic synonym of H. cervicornis and the description of three new species: H. davisiana sp. nov., H. djamilae sp. nov. and H. evaristoae sp. nov.

Phylogenomic analysis of pseudocryptic diversity reveals the new genus Deltalsia (Rhodomelaceae, Rhodophyta)

Molecular analyses, in combination with morphological studies, provide invaluable tools for delineating red algal taxa. However, molecular datasets are incomplete and taxonomic revisions are often required once additional species or populations are sequenced. The small red alga Conferva parasitica was described from the British Isles in 1762 and then reported from other parts of Europe. Conferva parasitica was traditionally included in the genus Pterosiphonia (type species P. cloiophylla in Schmitz and Falkenberg 1897), based on its morphological characters, and later transferred to Symphyocladia and finally to Symphyocladiella using molecular data from an Iberian specimen. However, although morphological differences have been observed between specimens of Symphyocladiella parasitica from northern and southern Europe they have yet to be investigated in a phylogenetic context. In this study, we collected specimens from both regions, studied their morphology and analyzed rbcL and cox1 DNA sequences. We determined the phylogenetic position of a British specimen using a phylogenomic approach based on mitochondrial and plastid genomes. Northern and southern European populations attributed to S. parasitica represent different species. Symphyocladiella arecina sp. nov. is proposed for specimens from southern Europe, but British specimens were resolved as a distant sister lineage to the morphologically distinctive Amplisiphonia, so we propose the new genus Deltalsia for this species. Our study highlights the relevance of using materials collected close to the type localities for taxonomic reassessments, and showcases the utility of genome-based phylogenies for resolving classification issues in the red algae.

Complete chloroplast genome of Chondria tumulosa (Ceramiales, Rhodophyta), a recently described cryptogenic species with invasive traits from Papahānaumokuākea Marine National Monument, Hawai'i

The complete chloroplast genome of Chondria tumulosa, a red alga from Manawai (Pearl and Hermes Atoll), Hawai‘i, was determined and analyzed using next-generation sequencing and de novo assembly approaches. The chloroplast genome sequence of C. tumulosa was 172,617 bp and contained 231 genes, consisting of 197 protein-coding genes, 29 transfer RNA genes, three ribosomal RNA genes, one transfer-messenger RNA gene, one non-coding RNA gene, and one intron inserted into the trnM gene. The number of genes and genome structure was largely similar to other members of the family Rhodomelaceae. The phylogenomic analysis of 32 complete cpDNA from the red algal order Ceramiales showed that C. tumulosa is a distinct species within the Chondrieae tribe, and is a diverging early relative to the other three available Chondria chloroplast genomes.

Complete plastid genome of Cumathamnion serrulatum (Ceramiales, Rhodophyta)

We report the complete plastid genome of Cumathamnion serrulatum, also known as Delesseria serrulata. The plastid genome was 174,192 bp in size. Annotation showed there were 193 protein coding genes, three ribosomal RNAs, and 29 transfer RNAs. One intron was found, and the GC content was 27.2%. The maximum likelihood tree with the concatenated 177 plastid coding genes showed a strong monophyletic relationship to Membranoptera spp. within the Ceramiales.

Divergence times and plastid phylogenomics within the intron-rich order Erythropeltales (Compsopogonophyceae, Rhodophyta)

The advent of high-throughput sequencing (HTS) has allowed for the use of large numbers of coding regions to produce robust phylogenies. These phylogenies have been used to highlight relationships at ancient diversifications (subphyla, class) and highlight the evolution of plastid genome structure. The Erythropeltales are an order in the Compsopogonophyceae, a group with unusual plastid genomes but with low taxon sampling. We use HTS to produce near complete plastid genomes of all genera, and multiple species within some genera, to produce robust phylogenies to investigate character evolution, dating of divergence in the group, and plastid organization, including intron patterns. Our results produce a fully supported phylogeny of the genera in the Erythropeltales and suggest that morphologies (upright versus crustose) have evolved multiple times. Our dated phylogeny also indicates that the order is very old (~800 Ma), with diversification occurring after the ice ages of the Cryogenian period (750-635 Ma). Plastid gene order is congruent with phylogenetic relationships and suggests that genome architecture does not change often. Our data also highlight the abundance of introns in the plastid genomes of this order. We also produce a nearly complete plastid genome of Tsunamia transpacifica (Stylonematophyceae) to add to the taxon sampling of genomes of this class. The use of plastid genomes clearly produces robust phylogenetic relationships that can be used to infer evolutionary events, and increased taxon sampling, especially in less well-known red algal groups, will provide additional insights into their evolution.

Molecular and morphological analyses reveal new taxa additions to the tribe Streblocladieae (Rhodomelaceae, Rhodophyta)

The recent segregation of 12 genera in the tribe Streblocladieae suggests that the taxonomy of some species belonging to Polysiphonia sensu lato is updated with the transfer and the proposal of new combinations. Accordingly, six new additions to the tribe Streblocladieae on the basis of morphological and molecular analyses are presented as a consequence of this new segregation. These additions include the description of the new species Carradoriella platensis sp. nov., the proposal of the following new combinations Eutrichosiphonia paniculata comb. nov., E. tapinocarpa comb. nov., and the reinstatement of Vertebrata curta, V. decipiens, and V. patersonis. Additionally, our morphological observations identified additional diagnostic features for two genera of the Streblocladieae. Carradoriella has branches with sexual reproductive structures arranged adaxially on branchlets, and the recently described Eutrichosiphonia has rhizoids with multicellular digitate haptera. Our study gives insights in regards to the distribution, the diagnostic features for delimiting genera morphologically, and the molecular evolutionary relationships in the Streblocladieae.

Extensive cryptic diversity in the widely distributed Polysiphonia scopulorum (Rhodomelaceae, Rhodophyta): Molecular species delimitation and morphometric analyses

Our knowledge of seaweed diversity and biogeography still largely relies on information derived from morphological identifications, but the use of molecular tools is revealing that cryptic diversity is common among algae. Polysiphonia scopulorum is a turf-forming red alga widely reported in tropical and temperate coasts worldwide. The only study based on material collected from its Australian type locality and the Iberian Peninsula indicates that it is a species complex, but the extent of cryptic diversity across its geographical range is not known. To investigate the species diversity in P. scopulorum, the geographical distribution of species-level lineages and their morphological characterization, we collected 135 specimens from Australia, South Africa and southern Europe. Two gene datasets (cox1 and rbcL) were used to delimit species using three methods (GMYC, PTP, ABGD), leading to a consensus result that our collections of the P. scopulorum complex comprise 12 species. Five of these species were resolved in a highly supported clade, while the other seven species were related to other taxonomically accepted species or in unresolved parts of the tree. Morphometric and statistical analysis of a set of ten quantitative characters showed that there are no clear morphological correlates of species boundaries, demonstrating true cryptic diversity in the P. scopulorum complex. Distribution patterns of the 12 species were variable, ranging from species only known from a single site to species with a wide distribution spanning three continents. Our study indicates that a significant level of undiscovered cryptic diversity is likely to be found in algal turfs, a type of seaweed community formed by small entangled species.

Taxonomic determination of the cryptogenic red alga, Chondria tumulosa sp. nov., (Rhodomelaceae, Rhodophyta) from Papahānaumokuākea Marine National Monument, Hawai'i, USA: A new species displaying invasive characteristics

Survey cruises by the National Oceanic and Atmospheric Administration (NOAA) in 2016 and 2019 yielded specimens of an undetermined red alga that rapidly attained alarming levels of benthic coverage at Pearl and Hermes Atoll, Papahānaumokuākea Marine National Monument, Hawai'i. By 2019 the seaweed had covered large expanses on the northeast side of the atoll with mat-like, extensive growth of entangled thalli. Specimens were analyzed using light microscopy and molecular analysis, and were compared to morphological descriptions in the literature for closely related taxa. Light microscopy demonstrated that the specimens likely belonged to the rhodomelacean genus Chondria, yet comparisons to taxonomic literature revealed no morphological match. DNA sequence analyses of the mitochondrial COI barcode marker, the plastidial rbcL gene, and the nuclear SSU gene confirmed its genus-level placement and demonstrated that this alga was unique compared to all other available sequences. Based on these data, this cryptogenic seaweed is here proposed as a new species: Chondria tumulosa A.R.Sherwood & J.M.Huisman sp. nov. Chondria tumulosa is distinct from all other species of Chondria based on its large, robust thalli, a mat-forming tendency, large axial diameter in mature branches (which decreases in diameter with subsequent orders of branching), terete axes, and bluntly rounded apices. Although C. tumulosa does not meet the criteria for the definition of an invasive species given that it has not been confirmed as introduced to Pearl and Hermes Atoll, this seaweed is not closely related to any known Hawaiian native species and is of particular concern given its sudden appearance and rapid increase in abundance in the Papahānaumokuākea Marine National Monument; an uninhabited, remote, and pristine island chain to the northwest of the Main Hawaiian Islands.

Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era

Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof-of-concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae.

Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics

The order Ceramiales contains about one third of red algal diversity and it was classically classified into four families according to morphology. The first phylogenies based on one or two molecular markers were poorly supported and failed to resolve these families as monophyletic. Nine families are currently recognized, but relationships within and among them are poorly understood. We produced a well-resolved phylogeny for the Ceramiales using plastid genomes for 80 (28 newly sequenced) representative species of the major lineages. Three of the previously recognized families were resolved as independent monophyletic lineages: Ceramiaceae, Wrangeliaceae and Rhodomelaceae. By contrast, our results indicated that the other six families require reclassification. We propose the new order Inkyuleeales, a new circumscription of the Callithamniaceae to include the Spyridiaceae, and a new concept of the Delesseriaceae that includes the Sarcomeniaceae and the Dasyaceae. We also investigated the evolution of the thallus structure, which has been important in the classical delineation of families. The ancestor of the Ceramiales was a monosiphonous filament that evolved into more complex morphologies several times independently during the evolutionary history of this hyperdiverse lineage.

Molecular phylogenetics supports a clade of red algal parasites retaining native plastids: taxonomy and terminology revised

Parasitism is a life strategy that has repeatedly evolved within the Florideophyceae. Historically, the terms adelphoparasite and alloparasite have been used to distinguish parasites based on the relative phylogenetic relationship of host and parasite. However, analyses using molecular phylogenetics indicate that nearly all red algal parasites infect within their taxonomic family, and a range of relationships exist between host and parasite. To date, all investigated adelphoparasites have lost their plastid, and instead, incorporate a host-derived plastid when packaging spores. In contrast, a highly reduced plastid lacking photosynthesis genes was sequenced from the alloparasite Choreocolax polysiphoniae. Here we present the complete Harveyella mirabilis plastid genome, which has also lost genes involved in photosynthesis, and a partial plastid genome from Leachiella pacifica. The H. mirabilis plastid shares more synteny with free-living red algal plastids than that of C. polysiphoniae. Phylogenetic analysis demonstrates that C. polysiphoniae, H. mirabilis, and L. pacifica form a robustly supported clade of parasites, which retain their own plastid genomes, within the Rhodomelaceae. We therefore transfer all three genera from the exclusively parasitic family, Choreocolacaceae, to the Rhodomelaceae. Additionally, we recommend applying the terms archaeplastic parasites (formerly alloparasites), and neoplastic parasites (formerly adelphoparasites) to distinguish red algal parasites using a biological framework rather than taxonomic affiliation with their hosts.

Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta)

Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from 10 species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny, Melanthalia intermedia is sister to a monophyletic clade including Gracilaria and Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes cob and trnL, and trnA and trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between psdD and rrs genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial leuC/leuD operon was found in chloroplast genomes of Gracilaria tenuistipitata, G. chilensis, and M. intermedia, and in extrachromosomal plasmid of G. vermiculophylla. Phylogenetic trees show two different origins of leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.

Widely distributed red algae often represent hidden introductions, complexes of cryptic species or species with strong phylogeographic structure

Despite studies suggesting that most seaweeds are poor dispersers, many red algal species are reported to have circumglobal distributions. Such distributions have mostly been based on morphological identifications, but molecular data have revealed a range of issues with morphologically defined species boundaries. Consequently, the real distribution of such reportedly circumglobal species must be questioned. In this study, we analyzed molecular data sets (rbcL gene) of nine species in the Rhodomelaceae for which samples were available from widely spaced geographical locations. Three overall patterns were identified: (i) species showing strong phylogeographic structure (i.e., phylogenetic similarity correlates with geographical provenance), often to the point that populations from different locations could be considered as different species (Lophosiphonia obscura, Ophidocladus simpliciusculus, Polysiphonia villum, and Xiphosiphonia pinnulata); (ii) species with a broad distribution that is explained, in part, by putative human-mediated transport (Symphyocladia dendroidea and Polysiphonia devoniensis); and (iii) non-monophyletic complexes of cryptic species, most with a more restricted distribution than previously thought (Herposiphonia tenella, Symphyocladia dendroidea, and the Xiphosiphonia pennata complex that includes the species Xiphosiphonia pinnulata and Symphyocladia spinifera). This study shows that widely distributed species are the exception in marine red algae, unless they have been spread by humans.

Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses

The Bryopsidales is a morphologically diverse group of mainly marine green macroalgae characterized by a siphonous structure. The order is composed of three suborders - Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed several inconsistent phylogenetic positions of macroscopic taxa, and several entirely new lineages of microscopic species. A new classification scheme is proposed, which includes the merger of the families Pseudocodiaceae, Rhipiliaceae and Udoteaceae into a more broadly circumscribed Halimedaceae, and the establishment of tribes for the different lineages found therein. In addition, the deep-water genus Johnson-sea-linkia, currently placed in Rhipiliopsis, was reinstated based on our phylogeny.

Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats

The red algal subclass Nemaliophycidae includes both marine and freshwater taxa that contribute to more than half of the freshwater species in Rhodophyta. Given that these taxa inhabit diverse habitats, the Nemaliophycidae is a suitable model for studying environmental adaptation. For this purpose, we characterized plastid genomes of two freshwater species, Kumanoa americana (Batrachospermales) and Thorea hispida (Thoreales), and one marine species Palmaria palmata (Palmariales). Comparative genome analysis identified seven genes (ycf34, ycf35, ycf37, ycf46, ycf91, grx, and pbsA) that were different among marine and freshwater species. Among currently available red algal plastid genomes (127), four genes (pbsA, ycf34, ycf35, ycf37) were retained in most of the marine species. Among these, the pbsA gene, known for encoding heme oxygenase, had two additional copies (HMOX1 and HMOX2) that were newly discovered and were reported from previously red algal nuclear genomes. Each type of heme oxygenase had a different evolutionary history and special modifications (e.g., plastid targeting signal peptide). Based on this observation, we suggest that the plastid-encoded pbsA contributes to the iron controlling system in iron-deprived conditions. Thus, we highlight that this functional requirement may have prevented gene loss during the long evolutionary history of red algal plastid genomes.

Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta)

Little is known about genome organization in members of the order Batrachospermales, and the infra-ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups; (ii) to infer the phylogenetic relationships among these members to better understand the infra-ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene-dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae; differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales); and members of Batrachospermales have the lowest number of protein-coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon sampling.