Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs

Background Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium. Results Analysis of mitogenomes in three closely related species in this genus revealed they were 3–6-fold larger in size (56–132 kbp) than in other red algae, that have genomes of size 21–43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences. Conclusion Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA.

Resurrection of the Family Grateloupiaceae Emend. (Halymeniales, Rhodophyta) Based on a Multigene Phylogeny and Comparative Reproductive Morphology

The marine red algal order Halymeniales currently includes two families, the Halymeniaceae and Tsengiaceae, and consist of 38 genera and about 358 species. Phylogenetic analyses on specific taxa of the order are common, but not comprehensive, leaving the many intra-ordinal relationships within the Halymeniales unresolved. To reassess the phylogeny of the Halymeniales, we conducted extensive phylogenetic analyses based on 207 rbcL sequences and multigene analyses (rbcL, psaA, psbA, cox1, and LSU) using 47 taxa from the order. The combined data set fully supports the monophyly of the Grateloupia sensu lato clade. Phylogenetic assessment of the reproductive structures in the order using the type of auxiliary cell ampullae, pericarp origin, and tetrasporangial development characters, supports a Grateloupia sensu lato clade distinct from the Halymeniaceae exemplified by the generitype Halymenia. As a result, we propose to reinstate the family Grateloupiaceae Schmitz based on the Grateloupia sensu lato clade and including Grateloupia and eight other genera: Dermocorynus, Mariaramirezia, Neorubra, Pachymeniopsis, Kintokiocolax, Phyllymenia, Prionitis, and Yonagunia. The emended Grateloupiaceae is distinguished from the Halymeniaceae by the following three characteristics; (i) simple unbranched and unilateral type of auxiliary cell ampullae, (ii) pericarp formed densely by the fusion of secondary medullary filaments from subcortical cells and lateral ampullary filaments from a fusion cell complex, (iii) tetrasporangia originating laterally from the outer cortex. The Halymeniales comprises the monophyletic Grateloupiaceae, Halymeniaceae sensu lato (which requires further study), and the Tsengiaceae.

Investigating diversity, evolution, development and physiology of red algal parasites from New Zealand

<p>Red algal parasites have evolved independently over a 100 times and grow only on other red algal hosts. Most parasites are closely related to their host based on the similarity of their reproductive structures. Secondary pit connections between red algal parasites and their hosts are used to transfer parasite organelles and nuclei into host cells. Morphological and physiological changes in infected host cells have been observed in some species. Parasite mitochondrial genomes are similar in size and gene content to free-living red algae whereas parasite plastids are highly reduced. Overall, red algal parasites are poorly studied and thus the aim of this study was to increase the general knowledge of parasitic taxa with respect to their diversity, evolutionary origin, development, physiology, and organelle evolution. Investigation of the primary literature showed that most species descriptions of red algal parasites were poor and did not meet the criteria for defining a parasitic relationship. This literature study also revealed a lack of knowledge of many key parasitic processes including early parasite development, host cell “control”, and parasite origin. Many of these poorly studied research areas were addressed in this thesis. Phylogenetic analyses, using a range of markers from all three genomes (cpDNA: rbcL, nDNA: actin, LSU rRNA; mtDNA: cox1), showed different patterns of phylogenetic relationships for the four new red algal parasites and their hosts. The parasites Phycodrys novae-zelandiophila sp. nov. and Vertebrata aterrimophila sp. nov. closest relative is its host species. Cladhymenia oblongifoliophila sp. nov. closest relative is its host species based on nuclear and mitochondrial markers whereas the plastid markers group the parasite with Cladhymenia lyallii, suggesting that the parasite plastid was acquired when previously parasitizing C. lyallii. Judithia parasitica sp. nov. grows on two Blastophyllis species but the parasites’ closest relative is the non-host species Judithia delicatissima. Developmental studies of the parasite Vertebrata aterrimophila, showed a unique developmental structure (“trunk-like” cell) not known in other parasites, plus localised infection vi and few changes in infected host cells. High-throughput-sequencing revealed mitochondrial genomes of similar size, gene content and order in the parasite Pterocladiophila hemisphaerica to its host Pterocladia lucida, and a reduced non-photosynthetic plastid in the parasite. Mitochondrial (mt) and plastid (cp) genome phylogenies placed Pterocladiophila hemisphaerica on long branches, either as sister to Ceramiales (mt) or Gracilariales (cp). Further analyses, filtering non-elevated plastid genes grouped the parasite neither with the Gracilariales (mt) or Gelidiales (cp) on shorter branches but without support. Nuclear phylogeny grouped P. hemisphaerica as sister to the Gelidiales and other red algal orders and was the only phylogenetic relationship with support. Investigations of photosystem II capacity using PAM fluorometry, and quantifying chlorophyll a content in three pigmented parasites, showed different host nutrient dependencies. Rhodophyllis parasitica and Vertebrata aterrimophila are not able to photosynthesize and are fully dependent on host nutrients. Pterocladiophila hemisphaerica is able to photosynthesize independently, even though it has a reduced non-photosynthetic plastid genome, and therefore is only partially dependent on its host. This study advances our current understanding of red algal parasites and highlights many possibilities for future research including genome evolution and understanding parasite diversity.</p>

Investigating diversity, evolution, development and physiology of red algal parasites from New Zealand

<p>Red algal parasites have evolved independently over a 100 times and grow only on other red algal hosts. Most parasites are closely related to their host based on the similarity of their reproductive structures. Secondary pit connections between red algal parasites and their hosts are used to transfer parasite organelles and nuclei into host cells. Morphological and physiological changes in infected host cells have been observed in some species. Parasite mitochondrial genomes are similar in size and gene content to free-living red algae whereas parasite plastids are highly reduced. Overall, red algal parasites are poorly studied and thus the aim of this study was to increase the general knowledge of parasitic taxa with respect to their diversity, evolutionary origin, development, physiology, and organelle evolution. Investigation of the primary literature showed that most species descriptions of red algal parasites were poor and did not meet the criteria for defining a parasitic relationship. This literature study also revealed a lack of knowledge of many key parasitic processes including early parasite development, host cell “control”, and parasite origin. Many of these poorly studied research areas were addressed in this thesis. Phylogenetic analyses, using a range of markers from all three genomes (cpDNA: rbcL, nDNA: actin, LSU rRNA; mtDNA: cox1), showed different patterns of phylogenetic relationships for the four new red algal parasites and their hosts. The parasites Phycodrys novae-zelandiophila sp. nov. and Vertebrata aterrimophila sp. nov. closest relative is its host species. Cladhymenia oblongifoliophila sp. nov. closest relative is its host species based on nuclear and mitochondrial markers whereas the plastid markers group the parasite with Cladhymenia lyallii, suggesting that the parasite plastid was acquired when previously parasitizing C. lyallii. Judithia parasitica sp. nov. grows on two Blastophyllis species but the parasites’ closest relative is the non-host species Judithia delicatissima. Developmental studies of the parasite Vertebrata aterrimophila, showed a unique developmental structure (“trunk-like” cell) not known in other parasites, plus localised infection vi and few changes in infected host cells. High-throughput-sequencing revealed mitochondrial genomes of similar size, gene content and order in the parasite Pterocladiophila hemisphaerica to its host Pterocladia lucida, and a reduced non-photosynthetic plastid in the parasite. Mitochondrial (mt) and plastid (cp) genome phylogenies placed Pterocladiophila hemisphaerica on long branches, either as sister to Ceramiales (mt) or Gracilariales (cp). Further analyses, filtering non-elevated plastid genes grouped the parasite neither with the Gracilariales (mt) or Gelidiales (cp) on shorter branches but without support. Nuclear phylogeny grouped P. hemisphaerica as sister to the Gelidiales and other red algal orders and was the only phylogenetic relationship with support. Investigations of photosystem II capacity using PAM fluorometry, and quantifying chlorophyll a content in three pigmented parasites, showed different host nutrient dependencies. Rhodophyllis parasitica and Vertebrata aterrimophila are not able to photosynthesize and are fully dependent on host nutrients. Pterocladiophila hemisphaerica is able to photosynthesize independently, even though it has a reduced non-photosynthetic plastid genome, and therefore is only partially dependent on its host. This study advances our current understanding of red algal parasites and highlights many possibilities for future research including genome evolution and understanding parasite diversity.</p>

Reorganizing parasitic Delesseriaceae: taxonomic revision of Asterocolax

Red algal parasites are highly host specific organisms that are morphologically reduced with decreased pigmentation. Only found within the Florideophyceae, red algal parasites have evolved within eight orders, with the greatest parasite diversity found in the Ceramiales. A quarter of the ceramialian parasites in the family Delesseriaceae are described in the genus Asterocolax. The initial morphological description of Asterocolax led to the creation of an independent genus devoted to these parasitic species, but molecular data have repeatedly demonstrated that Asterocolax species, and likely many other red algal parasites, resolve within the genera of free-living red algae, often within the same genus as their hosts. Here and in previous studies, phylogenetic analysis of the internal transcribed spacer region of the ribosomal DNA has shown at least six instances of independent evolution of Asterocolax species, mainly interspersed among the free-living macroalgal genera of Phycodrys and Polyneura. As most Asterocolax are sister species to their hosts, they are independently derived from a photosynthetic ancestor, and together, do not form a monophyletic parasitic genus. Here we conduct a long overdue taxonomic revision of the red algal parasitic genus Asterocolax, describe a new species within the genus, and propose nomenclatural changes for four other species to reduce the polyphyletic clades encompassing Asterocolax.

Investigation of the red algal parasites Rhodophyllis parasitica sp. nov. and Pterocladiophila hemisphaerica from New Zealand

<p>Red algal parasites are common within red algae and most parasites are closely related to their host. Red algal parasites can switch hosts and their development is unique. Red algal parasites are poorly known in New Zealand. There are only four parasites described in New Zealand and those are based on morphological characteristics. This thesis focuses on the two red algal parasites Rhodophyllis parasitica sp. nov. and Pterocladiophila hemisphaerica from New Zealand. First, development and phylogeny and distribution of an undescribed red algal parasite growing on Rhodophyllis membranacea was investigated. Microscopy, molecular markers (ITS2, cox1, cox2-3 spacer) and phylogenetic analysis, and herbarium sampling were used to address these questions. The parasite, described as Rhodophyllis parasitica sp. nov. shows a close relationship of all genomes to Rhodophyllis membranacea, which suggests that the parasite evolved from its hosts. The parasite is widely distributed throughout New Zealand. The second parasite, Pterocladiophila hemisphaerica was grouped taxonomically, based on morphology, in the order Gracilariales and parasitizes Pterocladia lucida in the order Gelidiales. Molecular marker were used to reveal the relationship of Pterocladiophila hemisphaerica to its host: if the parasite is grouped in the Gracilariales or the Gelidiales; if host switches might have occurred; and if atp8 is present in the parasite. Nuclear DNA (SSU rRNA, LSU rRNA), mitochondrial (cox1) and plastid regions (rbcL-rbcS spacer) from the parasite were sequenced and phylogenetic analysis performed. New primer were designed to amplify atp8 and genetic analysis performed. Pterocladiophila hemisphaerica evolved in the Florideophytes but neither in the Gracilariales or Gelidiales and the parasite possibly switched hosts at least two times, which was shown by three different origins of chloroplast, mitochondria and nuclear DNA. Atp8 in the parasite is present but probably a pseudogene. Rhodophyllis parasitica sp. nov. is the first described red algal parasite species in New Zealand in 55 years and Pterocladiophila hemisphaerica is the first parasite with organelles and nuclei with different histories of origin.</p>

Investigation of the red algal parasites Rhodophyllis parasitica sp. nov. and Pterocladiophila hemisphaerica from New Zealand

<p>Red algal parasites are common within red algae and most parasites are closely related to their host. Red algal parasites can switch hosts and their development is unique. Red algal parasites are poorly known in New Zealand. There are only four parasites described in New Zealand and those are based on morphological characteristics. This thesis focuses on the two red algal parasites Rhodophyllis parasitica sp. nov. and Pterocladiophila hemisphaerica from New Zealand. First, development and phylogeny and distribution of an undescribed red algal parasite growing on Rhodophyllis membranacea was investigated. Microscopy, molecular markers (ITS2, cox1, cox2-3 spacer) and phylogenetic analysis, and herbarium sampling were used to address these questions. The parasite, described as Rhodophyllis parasitica sp. nov. shows a close relationship of all genomes to Rhodophyllis membranacea, which suggests that the parasite evolved from its hosts. The parasite is widely distributed throughout New Zealand. The second parasite, Pterocladiophila hemisphaerica was grouped taxonomically, based on morphology, in the order Gracilariales and parasitizes Pterocladia lucida in the order Gelidiales. Molecular marker were used to reveal the relationship of Pterocladiophila hemisphaerica to its host: if the parasite is grouped in the Gracilariales or the Gelidiales; if host switches might have occurred; and if atp8 is present in the parasite. Nuclear DNA (SSU rRNA, LSU rRNA), mitochondrial (cox1) and plastid regions (rbcL-rbcS spacer) from the parasite were sequenced and phylogenetic analysis performed. New primer were designed to amplify atp8 and genetic analysis performed. Pterocladiophila hemisphaerica evolved in the Florideophytes but neither in the Gracilariales or Gelidiales and the parasite possibly switched hosts at least two times, which was shown by three different origins of chloroplast, mitochondria and nuclear DNA. Atp8 in the parasite is present but probably a pseudogene. Rhodophyllis parasitica sp. nov. is the first described red algal parasite species in New Zealand in 55 years and Pterocladiophila hemisphaerica is the first parasite with organelles and nuclei with different histories of origin.</p>

The coexistence of cryptic algal species: Temporal and spatial distribution of filamentous members of the red algal order Bangiales in the Wellington region

<p>Current research on marine cryptic species, through the use of molecular tools, is revealing unexpected diversity and relationships [...]. A number of cryptic filamentous Bangiales have been recorded from Wellington, New Zealand; all morphologically indistinguishable and all apparently occupying the same niche within the upper inter-tidal. Researchers have reported finding more than one member of the filamentous Bangiales coexisting at a single location in Wellington’s inner harbour (Farr et al. 2001, Wendy Nelson pers. comm.). This raises the question: to what extent are these cryptic lineages coexisting? Are there differences in their temporal and spatial distribution? Does distribution at a small-scale, within sites in the Wellington region, reflect the physiological differences and ecological adaption reported from the culture studies of Bödeker et al. 2008? This research sought to investigate the small-scale distribution of these cryptic lineages to test for temporal or spatial variation, and draw conclusions about the nature of their coexistence in the Wellington region. To achieve this, samples were taken from six sites in Wellington over a period of nine months. Molecular methods, as described in Chapter 2, were utilised to identify the various taxa. This identification data then provided the basis for the ecological analyses presented in Chapter 3.</p>

The coexistence of cryptic algal species: Temporal and spatial distribution of filamentous members of the red algal order Bangiales in the Wellington region

<p>Current research on marine cryptic species, through the use of molecular tools, is revealing unexpected diversity and relationships [...]. A number of cryptic filamentous Bangiales have been recorded from Wellington, New Zealand; all morphologically indistinguishable and all apparently occupying the same niche within the upper inter-tidal. Researchers have reported finding more than one member of the filamentous Bangiales coexisting at a single location in Wellington’s inner harbour (Farr et al. 2001, Wendy Nelson pers. comm.). This raises the question: to what extent are these cryptic lineages coexisting? Are there differences in their temporal and spatial distribution? Does distribution at a small-scale, within sites in the Wellington region, reflect the physiological differences and ecological adaption reported from the culture studies of Bödeker et al. 2008? This research sought to investigate the small-scale distribution of these cryptic lineages to test for temporal or spatial variation, and draw conclusions about the nature of their coexistence in the Wellington region. To achieve this, samples were taken from six sites in Wellington over a period of nine months. Molecular methods, as described in Chapter 2, were utilised to identify the various taxa. This identification data then provided the basis for the ecological analyses presented in Chapter 3.</p>

The Recent Carbonate Sediments of Palmyra Atoll, Northern Line Islands, Central Pacific Ocean

<p>Palmyra Atoll is an isolated carbonate reef system located approximately 1600 km south of Hawaii in the northern Line Islands, central Pacific Ocean. Sediment samples from the lagoons and tidal zones were analyzed for grainsize and composition, and the results used to compile detailed maps and interpret the environments and lithofacies present. A distinct grainsize distribution was observed forming concentric bands ranging from coarse gravel rubble on the outer reef through to finer material in the interior of the atoll in the deep lagoons, where peloidal muds prevail. Five lithologic facies have been identified and typical sediments are poorly sorted and near-symmetrical in their grainsize distribution. On average, sediments are medium sand. A distinct chlorozoan assemblage was observed with coral and calcareous red algal fragments forming half of the sediment, with varying amounts of molluscs, Halimeda and foraminifera being the lesser major constituents. Lagoonal and tidal sediments showed little variation in composition between locations and lacked clear compositional zonation, characteristic of other larger atolls of the Pacific. Palmyra Atoll is unique in that it has had little human intervention for the last sixty years and as a result uninhibited natural processes are occurring. It is also unique in that it displays relatively deep for its size (<55 m), steep-sided compartmentalized lagoons that have abundant fine material (upward of 70% silt or finer), a feature not commonly observed at other Pacific atolls. This fine material has been identified as a peloidal mud and its mode and rate of deposition may be partly controlled by the abundant zooplankton in the lagoons. Recent sediments of Palmyra Atoll are almost entirely carbonate, originating from reef organisms inhabiting the atoll. The only other material is small amounts of siliceous sponge skeletons.</p>