ABSTRACT Algae require specific acclimation strategies to cope with spectral variability in shallow marine habitats. We investigated how the siphonous green alga Derbesia alters its photosynthetic and metabolic processes under white (WL), blue (BL), green (GL), red (RL), and far-red light (FL) by conducting photobiological and transcriptomic sampling over a 10-day period. Our results show two contrasting photoacclimation strategies: BL and GL promoted metabolic activity associated with growth, whereas FL and RL induced a low-light-like survival strategy characterized by reduced growth and suppression of the core metabolism. Photosynthetic acclimation across all conditions primarily occurs within the light dependent reactions. BL and GL promoted early acclimation marked by the immediate activation of light-harvesting complexes (LHCs) and a key transcriptional regulator MYB , and showed better acclimation marked by the sustained activation of ATPases, ATP transporters, and hormone-signaling components. BL induced a distinct transcriptional shift during the transition to prolonged exposure, including enhanced cyclic electron transport, and key regulators of protein synthesis, DNA replication, and transcriptional regulation. In contrast, FL, and to a lesser extent RL, triggered responses resembling low light acclimation with constrained growth, characterized by inefficient energy utilization, enlarged antenna systems, chloroplast proliferation with aggregations, and reduced growth rates. This study suggests high accumulation of core photopigments and reduction in chlorophyll a / b is an acclimatory response to FL, and consistently higher activation of core metabolic processes under WL likely indicates the evolutionary adaptation of Derbesia to shallow coastal environments where broad-spectrum light predominates. Additionally, our newly sequenced draft genome of the Derbesia strain for this study could serve as a genomic resource for future molecular photobiology research in Bryopsidales algae.

Samples tentatively identified as Bostrychia moritziana were collected in freshwater habitats from two locations in the States of São Paulo (Cananéia) and Rio de Janeiro (Trindade), southeastern Brazil. Culture observations for more than 20 years, combined with analyses of DNA sequences of the mitochondrial (COI-5P) and the plastid (rbcL) genes, supported the proposal of a new species of Bostrychia. The new species is morphologically closely related to B. moritziana and B. radicans, but it is phylogenetically distinguished by DNA sequence data. Reproduction in culture was by abortive tetrasporangia. Phylogenetic analyses showed that the Brazilian samples formed a clade that was sister to B. moritziana sequences in the rbcL tree. Likewise, in the COI tree, these samples were a clade but nested among three B. moritziana sequences. The morphological similarity of the new species with B. moritziana and B. radicans, which have been regarded as species complexes, is intriguing. The sequence divergences found in this study (> 6% for rbcL and COI-5P) suggested that the new species is distant enough to be recognized as a distinct species in comparison to the closest species B. moritziana.

Organelle genomes offer a powerful tool for red algal evolutionary studies. Although the number of Rhodophyta genomes has increased substantially over the past 2 decades, only two mitochondrial genomes have been reported for the red algal order Thoreales. In this study, we generated 10 new complete mitochondrial genomes of Thoreales, representing the order's two genera and eight species, which, combined with additional mitogenomes of related orders of the subclass Nemaliophycidae, resulted in a comprehensive dataset of 20 mitogenomes. Thoreales mitogenomes exhibited little variation, ranging in length from 25,022 bp to 26,369 bp, with GC content from 25.6% to 28.3%, gene numbers from 46 to 54, and protein-coding genes from 21 to 25. Four genes were missing in one or more species (atp4, rpl20, sdh2, and sdh4), and no introns were detected. Synteny among members of Thoreales was highly conserved and similar to other orders of Nemaliophycidae. Phylogenomic analyses strongly supported the monophyly of Thoreales within Nemaliophycidae. Within the order, Nemalionopsis and Thorea as well as the relationship among the species received full support. Nemalionopsis shawii and N. parkeri formed an early-diverging clade that was sister to Thorea, which had species that resolved into two distinct lineages lacking evident geographic or morphological differentiation. By expanding the available dataset from two to 10 mitogenomes, this study provides a broad organellar perspective on Thoreales evolution, contributing to new insights into the systematics and diversification of freshwater red algae and, potentially, for clarifying inter-ordinal relationships within Nemaliophycidae.

SummaryRed seaweeds form part of an ancient lineage of eukaryotes that were one of the first to evolve multicellularity. Although they share a common evolutionary origin with modern-day plants and display complex multicellular development, we still lack comprehensive genome data from the most highly-evolved groups of red algae. Here, we present a chromosome-level genome assembly ofBostrychia moritziana, a species that is classified into the Rhodomelaceae family of the Ceramiales order, both of which constitute the largest and most diverse family and order of red algae, respectively. Contrary to the commonly held view that red algae generally have small genomes, we report significant genome size expansion inBostrychiaand other Ceramiales species, which we posit as one of at least three independent genome expansion events that occurred during red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole genome duplications, but in the case ofBostrychiaappear to be largely driven by the dramatic proliferation of a single lineage of giantPlavakaDNA transposons. Consistent with increased genome size, we identify a substantial increase in gene content inBostrychiathat was shaped both byde novogene emergence and by the amplification of gene families in common with other Ceramiales seaweeds, providing key insight into the genetic adaptations underpinning the evolutionary success of this species-rich order. Finally, our sex-specific assemblies enabled us to resolve the UV sex chromosomes inBostrychia, which feature expanded gene-rich sex-linked regions. Notably, these sex-linked regions each harbour a distinct TALE-HD transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this highly successful group of red seaweeds can provide insight into the evolutionary origins and universal principles of complex multicellular plant life.

Red algae are an ancient eukaryotic lineage that were among the first to evolve multicellularity. Although they share a common origin with modern-day plants and display complex multicellular development, comprehensive genome data from the most highly evolved red algal groups remain scarce. Here, we present a chromosome-level genome assembly of Bostrychia moritziana, a complex red seaweed in the Rhodomelaceae family of the Ceramiales-the largest and most diverse order of red algae. Contrary to the view that red algal genomes are typically small, we report significant genome size expansion in Bostrychia and other Ceramiales, which represents one of at least three independent expansion events in red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole-genome duplications, but in Bostrychia rather stem from the proliferation of a single lineage of giant Plavaka DNA transposons. Consistent with its enlarged genome, Bostrychia has an increased gene content shaped by de novo gene emergence and amplified gene families in common with other Ceramiales, providing insight into the genetic adaptations underpinning this successful and species-rich order. Finally, our sex-specific assemblies resolve the UV sex chromosomes in Bostrychia, which feature expanded gene-rich sex-linked regions. Notably, each sex chromosome harbors a three amino acid loop extension homeodomain (TALE-HD) transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this red seaweed lineage can provide insight into the evolutionary origins and universal principles underpinning complex multicellularity.

Dictyotopsis propagulifera is an enigmatic species of brown algae, first described by Wilhelm Troll in 1931. In the present study, we successfully established a unialgal culture strain of D. propagulifera collected from mangrove sediments in Perak, Malaysia, directly across the Malacca Strait from the type locality in Indonesia. Our observations over 10 years of culture confirm vegetative propagule formation as originally described by Troll. However, sexual reproduction typical of Dictyotales (e.g. flagellate sperm and non-flagellate eggs) was not confirmed. Detailed ultrastructural analysis revealed that D. propagulifera shares many cellular characteristics with Dictyota, including chloroplasts with the three-layered thylakoid lamellae, well-developed plasmodesmata forming pit fields and the presence of a single apical meristematic cell. In addition, biochemical analysis confirmed the presence of the polyol mannitol as main photosynthetic product and organic osmolyte, which is characteristic for brown algae. Phylogenomic analysis using both plastid and mitochondrial genomes, along with multigene analysis, further supports the monophyly of D. propagulifera and Dictyota, following the earlier divergence of Dictyopteris. These findings not only provide an updated description of D. propagulifera based on modern microscopy techniques, but also propose potential evolutionary pathways responsible for its developmental patterns and asexual reproductive strategy.

Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.

Most genera of the freshwater red algal order Batrachospermales have been systematically revised using molecular and morphological data, but Sirodotia Kylin remains to be thoroughly reviewed. In this investigation, DNA sequence data for the rbcL, COI-5P and LSU markers of specimens collected worldwide were combined with morphological observations to assess their specific diversity, infer their relationships and evaluate the morphological characters relevant for species identification. Phylogenetic analyses showed the genus to be a monophyletic lineage with high support. Inter- and intra-specific divergence values were well-delineated with higher interspecific (2.1-7% and 4.4-10.5%) and lower intraspecific (0-2.4% and 0-3.8%) variations for rbcL and COI-5P sequences, respectively. LSU sequences revealed lower interspecific divergence values than the COI-5P sequences (0.7-3.3%) indicating less resolution as a barcode marker. Nine species are recognized based on DNA sequence data, morphological characters and geographic distribution. Five species were previously described (S. assamica Necchi, Rossignolo, Yasmin, J.A.West & Ganesan, S. delicatula Skuja, S. huillensis (Welwitsch ex West & GSWest) Skuja, S. kennedyi A.L.Szinte, J.C.Taylor & M.L.Vis and S. suecica Kylin) and four new species are proposed (S. amazonica Necchi, N.L.Rossignolo & M.O.Paiano, sp. nov., S. aquiloamericana Necchi, N.L.Rossignolo & M.L.Vis, sp. nov., S. cryptica Necchi, N.L.Rossignolo & M.O.Paiano, sp. nov. and S. delicatuliformis Necchi, N.L.Rossignolo & M.O.Paiano, sp. nov.). Diagnostic characters for the genus are confirmed to be carpogonia asymmetric with a basal protuberance and carposporophytes diffuse with indeterminant prostrate filaments producing determinate erect branches terminating in carposporangia. The following morphological characters were applied to distinguish species: primary fascicle cell number, spermatangial arrangement, origin of gonimoblast filament and size of carposporangia. Based on morphology, S. sinica, S. segawae and S. yutakae are proposed as synonyms of S. suecica and S. ateleia Skuja of S. delicatula. The status of three species (S. cirrhosa Skuja ex M.S.Balakr. & B.B.Chaugule, S. gardneri Skuja ex Flint and S. huangshanensis Z.X.Shi & S.L.Xie) could not be confirmed due to lack of type specimens and published information on informative diagnostic characters.

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.

Marine phylogeographic studies have recently shown that historical events, oceanography and ecological factors shape patterns of biodiversity and population connectivity. In southeastern Australia a historical geographic barrier, the Bassian Isthmus, results in deep genetic differentiation between some marine taxa. Using partial mitochondrial cytochrome oxidase subunit I (COI) DNA sequences, we investigated the genetic diversity and phylogeography among 26 populations of the red alga Bostrychia intricata along the southeastern Australian coast. Our genetic data revealed the occurrence of five cryptic B. intricata species (lineages N5, N7, N8, N9 and N10), two of which (N9 and N10) are newly discovered and endemic to Tasmania, while cryptic species N5 and N7 were confined to mainland Australia. Species N8 was more genetically diverse and extensively distributed than the other cryptic species, because it occurred both on mainland Australia and in Tasmania. We also detected a clear east-west phylogeographic break between cryptic species N7 and N5, and between haplotypes of species N8 on either side of Wilsons Promontory (the southernmost tip of mainland Australia). Spatial analysis of molecular variance identified three clusters of populations of species N8 along the south coast of Australia, and the split among these groups corresponded to extensive sandy areas: Coorong dunefield and Ninety Mile Beach. Additionally, our study detected the separation between mainland Australian (species N5 and N7) and Tasmanian species (N9 and N10) across the Bass Strait. We suggest that phylogeographic breaks and genetic differentiation in cryptic B. intricata species likely correlate to the historical Bassian land bridge, present-day habitats and different oceanographic circulation patterns.

This study presents the validation of a high-performance liquid chromatography diode array detector (HPLC-DAD) method for the determination of different mycosporine-like amino acids (MAAs) in the red alga Bostrychia scorpioides. The investigated MAAs, named bostrychines, have only been found in this specific species so far. The developed HPLC-DAD method was successfully applied for the quantification of the major MAAs in Bostrychia scorpioides extracts, collected from four different countries in Europe showing only minor differences between the investigated samples. In the past, several Bostrychia spp. have been reported to include cryptic species, and in some cases such as B. calliptera, B. simpliciuscula, and B. moritziana, the polyphyly was supported by differences in their MAA composition. The uniformity in the MAA composition of the investigated B. scorpioides samples is in agreement with the reported monophyly of this Bostrychia sp.

The recently described red alga Tsunamia transpacifica (Stylonematophyceae) was previously isolated from plastic drift found at the pacific coast, but the natural habitat remains unknown. Here, we investigate ultrastructural details and the low molecular weight soluble carbohydrate composition to get further insight into the adaptation to this uncommon habitat. By means of high pressure freeze fixation, followed by freeze substitution, we could detect an up to 2-µm-thick cell wall surrounded by a distinct layer of extracellular polymeric substances (EPS), likely responsible for the adhering capacities of Tsunamia . The central position of the nucleus and multilobed parietal chloroplast, already observed by light microscopy, could be confirmed. The ultrastructure revealed large electron-dense bodies (EB) in the central cytoplasm, likely resembling degradation products of the chloroplast. Interestingly, these structures contained phosphorous and cobalt, and iron was found in smaller rounded electron-dense bodies by electron energy loss spectroscopy (EELS). Accumulation of these elements suggests a high biosorption activity of Tsunamia . Liquid chromatography-mass spectrometry (LC–MS) data showed the presence of two heterosides (floridoside and digeneaside) together with the polyol sorbitol, which are known as organic osmolytes and compatible solutes. Taken together, these are the first observations on ultrastructural details, element storage and accumulation of protective compounds are contributing to our understanding of the ultrastructural and osmotic solute basis for the ability of Tsunamia to thrive on plastic surfaces.

Red algae (Rhodophyta) are primarily found in marine habitats around the world and they have been a prolific source of structurally diverse natural products. Among them the genus Bostrychia (Ceramiales, Rhodomelaceae) consists of approximately 40 taxonomically accepted species, and some, e. g., B. tenella, B. radicans, B. moritziana, B. simpliciuscula and B. intricate, include cryptic species. DNA sequence data show three genetic lineages within Bostrychia calliptera, another polyphyletic species requiring further taxonomic investigation. In an attempt to examine whether there are differences in the metabolite pattern that support the re-circumscription of the species and to uncover biogeographic patterns, phytochemical profiling of those samples used for DNA sequencing was conducted. This investigation revealed clearly three different chemotypes, corresponding to the lineages of the published molecular analysis results. The first lineage had a distinct and recognizably different phytochemical profile in contrast to the second and the third lineage which shared some similarities. Still, variations in the pattern of their phenolic compounds allowed a clear discrimination between the second and third lineage, too. The most important marker substances were isolated and their structures elucidated resulting in the characterization of four undescribed phenols. The isolated substances from B. calliptera are considered as suitable chemotaxonomic markers within this polyphyletic group.

The Gracilariaceae is a species-rich family, with a number of members having high commercial value as sources of agar. Members of this family are also known for their phenotypic plasticity and convergent morphologies, resulting in considerable taxonomic confusion. Over the past two decades, two species of Agarophyton (previously part of Gracilaria) have been recognised in New Zealand with very similar morphologies and growth habits, and they have been incorrectly grouped as Agarophyton chilense. Agarophyton chilense is distributed in Chile and New Zealand and is genetically distinct from Agarophyton sp. from Australia and New Zealand. We name this new species A. transtasmanicum sp. nov. Morphologically A. transtasmanicum has fewer medullary cell layers and a more abrupt transition in cell size between cortex and medulla than A. chilense. The cox1 and rbcL dataset grouped A. transtasmanicum as sister to A. tenuistipitatum with high support. Clarifying the distinctions between A. chilense and A. transtasmanicum will enable further research, including investigating differences in distribution patterns, physiology, ecology, and chemical composition of these two Agarophyton species.

In India the genus Sirodotia has been documented solely on morphological data. A new species of Sirodotia (Sirodotia assamica sp. nov.) was found in two localities in the State of Assam, India. Phylogenetic relationships of the new species were inferred on the basis of DNA sequence data for the plastid rbcL gene and the barcode region of the mitochondrial COI-5P gene. Taxonomic affinities of the new species were determined by morphological analyses and a distinctive character was found for this species: spermatangia arranged in clusters. Although this character is also observed in S. huillensis, both species are genetically highly divergent (4.5–5.0% for rbcL and 9.6–10.1% for COI-5P). DNA sequences from Indian specimens formed a well-supported clade, sister to S. delicatula from Malaysia. DNA sequence divergence between S. assamica and S. delicatula varied from 2.5–2.7% for rbcL and COI-5P. Intraspecific divergence between the two sequences from India were low (0.4–0.5%). A full description and photographs of the new species are provided, as well as a comparison with morphologically similar and phylogenetically allied species reported from India and other Asian regions.

Ectocarpus is a genus of common marine brown algae. In 1995 a strain of Ectocarpus was isolated from Hopkins River Falls, Victoria, Australia, constituting one of few available freshwater or nearly freshwater brown algae, and the only one belonging to Ectocarpus . It has since been used as a model to study acclimation and adaptation to low salinities and the role of its microbiota in these processes. However, little is known about the distribution of this strain or whether it represents a stable population. Furthermore, its microbiota may have been impacted by the long period of cultivation. Twenty-two years after the original finding we searched for Ectocarpus in the Hopkins River and surrounding areas. We found individuals with ITS and cox 1 sequences identical to the original isolate at three sites upstream of Hopkins River Falls, but none at the original isolation site. The osmolarity of the water at these sites ranged from 74-170 mOsmol, and it was rich in sulfate. The diversity of bacteria associated with the algae in situ was approximately one order of magnitude higher than in previous studies of the original laboratory culture, and 95 alga-associated bacterial strains were isolated from E. subulatus filaments on site. In particular, Planctomycetes were abundant in situ but rare in the laboratory-cultured strain. Our results confirm that E. subulatus has stably colonized the Hopkins River, and the newly isolated algal and bacterial strains offer new possibilities to study the adaptation of Ectocarpus to low salinity and its interactions with its microbiome.

This study presents a chemotaxonomic investigation of the genus Bostrychia through the quantitation of the major mycosporine-like amino acids (MAAs). The presence of some cryptic species had been suggested in the B. moritziana/B. radicans complex and MAA-profiling in respective samples revealed different chemotypes within this species complex. Another possibly polyphyletic species is Bostrychia simpliciuscula; previous molecular phylogenetic analyses showed four genetic lineages within this species, one of which was recently distinguished as a new species. Phytochemical profiling of those samples used for DNA analyses revealed four different chemotypes, corresponding to the above four lineages and it supports the re-circumscription of the other three B. simpliciuscula lineages. Therefore, mycosporine-like amino acids are considered as suitable chemotaxonomic markers for the reassessment of the classification of B. simpliciuscula. The determination of the MAA patterns in these algae was possible after developing and validating a suitable high-performance liquid chromatography–diode array detector (HPLC-DAD) method.

Culture isolates of the genus Hypoglossum (Delesseriaceae, Rhodophyta) were obtained and their development and morphological structure over many years were followed in the laboratory. Molecular data (rbcL, large subunit ribosomal DNA, and cytochrome c oxidase subunit I) were obtained from these strains and evidence presented to recognize the new species: Hypoglossum sabahense from Sabah, Malaysia Because various aspects of morphology in culture specimens differ significantly from types based on field specimens we have to rely mainly on the molecular criteria in ascribing a new taxonomic name here. This also is complicated by the major lack of molecular phylogenetic evidence for Hypoglossum and other Delesseriaceae. The 'Germling Emergence Method' and 'serendipity' are proving valuable in discovering significant new taxa from laboratory cultures which otherwise might never be known.

The taxonomy, classification, and phylogenetic relationships of the brown seaweed genus Iyengaria with other members of the family Scytosiphonaceae remain poorly understood. In this study, we addressed some problems in the systematics (taxonomic and classification status) and phylogenetic position of Iyengaria based on our studies on the generitype Iyengaria stellata from Kuwait and South Africa. We confirm that I. stellata is conspecific with Colpomenia capensis based on molecular and morpho‐anatomical data and that the species has a disjunct distribution within the Indian Ocean. Also, the distinguishing features of two Iyengaria species (I. nizamuddinii and ‘I. lobocylindrica’) described from Karachi, Pakistan, are within the morphological range of I. stellata. Hence, these two taxa are considered here as junior heterotypic synonyms of I. stellata. Our molecular phylogenetic analyses suggested the polyphyly of the genus Iyengaria, with the recently described Iyengaria quadriseriata from India forming close associations with Rosenvingea intricata. As such, we remove I. quadriseriata from the genus Iyengaria and relegate it as a synonym of R. intricata. Consequently, by recognizing only one species, our proposals considerably reduce the species diversity in the genus. Moreover, our culture studies suggested that I. stellata exhibits an alternation of heteromorphic generations, similar to other species in the Scytosiphonaceae. Under culture conditions, I. stellata also produced plurangia on microthalli, confirming its affinity with other phylogenetically close relatives in the ‘Hydroclathrus group’ of the family Scytosiphonaceae such as Colpomenia, Rosenvingea, and Chnoospora.