钙质红藻化石的主要类群特征及演化

钙质红藻是指可以发生生物钙化作用在其细胞壁上沉淀碳酸钙的红藻。钙质红藻可以保存为化石,是红藻古生物研究中的重要类群,具有重要的生态意义,但以往的研究对钙质红藻类群的系统分类及地史分布缺乏清晰认识。本文详细综述了钙质红藻化石的系统分类,归属于红藻门(Rhodophyta)红藻纲(Rhodophyceae)的4个目7个科,分别为珊瑚藻亚纲(Corallinophycidae)珊瑚藻目(Corallinales)的珊瑚藻科(Corallinaceae)、石叶藻科(Lithophyllaceae)、宽珊藻科(Mastophoraceae)和管孔藻科(Solenoporaceae),混石藻目(Hapalidiales)的混石藻科(Hapalidiaceae),孢石藻目(Sporolithales)的孢石藻科(Sporolithaceae)以及真红藻亚纲(Florideophycidae)耳壳藻目(Peyssonneliales)的耳壳藻科(Peyssonneliaceae)。最早的钙质红藻为管孔藻科,出现于中奥陶世,于中新世灭绝。珊瑚藻科最早出现于晚志留世并于白垩纪辐射演化至今,其他科均于白垩纪...     

中国新疆塔里木盆地上奥陶统良里塔格组的钙藻化石

钙藻是可以发生生物钙化作用形成钙质"骨骼"的分属多个门类的藻类的俗称。钙藻最早出现于寒武纪,奥陶纪发生第一次辐射演化。本文系统讨论了绿藻门绒枝藻目(Dasycladales)、羽藻目钙扇藻科(Udoteaceae)的科和属级分类标准和红藻门珊瑚藻科、管孔藻科(Solenoporaceae)属级分类标准及其中各属分类中存在的问题。塔里木盆地晚奥陶世在塔中—巴楚台地和塔北台地发育了一套礁滩相良里塔格组碳酸盐岩,其中含有丰富的钙藻化石。本文系统描述了来自塔里木盆地塔中、巴楚、塔北地区取心井上奥陶统良里塔格组岩层中的钙藻化石11个属15个种。包括绿藻门绒枝藻目西莱特藻科(Seletonellaceae)的Dasyporella,Kazakhstanelia,Vermiporella,Aphroporella,Arthroporella,绿藻门的羽藻目Bryopsidales(siphonales)的钙扇藻科的Dimor phosiphon,Palaeo porella,红藻门珊瑚藻目(Corallinales)的管孔藻科的Solenopora,Parachaetetes及Corallinales incertus familiae的Petro-phyton,以及分类位置不明的Monili porella。其中绒枝藻Ajakmalajsoria被视作Kazakhstanelia的同义名。     

Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages

Cryptomonad algae acquired their plastids by the secondary endosymbiotic uptake of a eukaryotic red alga. Several other algal lineages acquired plastids through such an event [1], but cryptomonads are distinguished by the retention of a relic red algal nucleus, the nucleomorph [2]. The nucleomorph (and its absence in other lineages) can reveal a great deal about the process and history of endosymbiosis, but only if we know the relationship between cryptomonads and other algae, and this has been controversial. Several recent analyses have suggested a relationship between plastids of cryptomonads and some or all other red alga-containing lineages [3-6], but we must also know whether host nuclear genes mirror this relationship to determine the number of endosymbiotic events, and this has not been demonstrated. We have carried out an expressed sequence tag (EST) survey of the cryptomonad Guillardia theta. Phylogenetic analyses of 102 orthologous nucleus-encoded proteins (18,425 amino acid alignment positions) show a robust sister-group relationship between cryptomonads and the haptophyte algae, which also have a red secondary plastid. This relationship demonstrates that loss of nucleomorphs must have taken place in haptophytes independently of any other red alga-containing lineages and that the ancestor of both already contained a red algal endosymbiont.     

Retrospective analysis of the marine flora of Vostok Bay,Sea of Japan

A general list of the flora of Vostok Bay (Sea of Japan) compiled on the basis of original and literature data includes 161 species, among them 25 green algae, 42 brown algae, 90 red algae, and 4 species of seagrass. In the period from 2000 to 2004, 114 species of macrophytes (19 green algae, 29 brown algae, 63 red algae, and 3 species of seagrass) were found in Vostok Bay; 19 species of algae were first records for this bay. On the whole, the flora of Vostok Bay is dominated by warm-water species, among which Asian low-boreal species occupy the leading position. The flora of Vostok Bay is changing under the influence of global climatic and local anthropogenic factors. In recent years, there is a tendency for the proportion of warm-water species to increase. The local anthropogenic influence on the flora of Vostok Bay has caused changes in the species composition of plant communities.     

WHAT DOES COMBINING MOLECULAR DATA SETS TELL US ABOUT DIATOM ORIGINS AND PHYLOGENY?

The past several years have seen an abundance of molecular sequence data gathered on heterokont algae and other stramenopiles with the goal of resolving phylogenetic relationships among major groups. The original focus was on SSU rDNA sequence, but lately a significant number of sequences of plastid and mitochondrial encoded genes (specifically rbcL and coxI) have been made available. Of particular interest to us has been the origin of diatoms and the relationship of diatoms to other stramenopiles. According to most claims based on morphological data, typically viewed from a non-rigorous evolutionary taxonomy standpoint (i.e. not with explicit cladistic or phylogenetic systematic methodology), diatoms are closely related to silica-scaled golden brown algae (chrysophytes or synurophytes). SSU rDNA sequence data, however, often place diatoms at the base of the heterokont alga tree, and chryso/synurophytes at the tip with eustigmatophytes, for example, as the chryso/synurophyte sister group. More recent analysis of rbcL sequences, however, supports the traditional classification. It is not automatically to be assumed that there is incongruence between the sequences, however. Taxon sampling is different in the different analyses, methods of analysis are often different, assumptions used to "filter" data are different, etc. Moreover, the relative strength of signal appears to be different in the data sets. We will present an analysis of combined SSU, rbcL and coxI data, an analysis of taxon-sampling issues, and review underlying assumptions and methodologies in an attempt to a) better understand the results of prior studies and b) reconcile the different hypotheses.     

Microalgal metabolites

The extraordinary chemical diversity seen in the cyanobacteria (blue-green algae) is especially pronounced in the ubiquitous tropical marine species, Lyngbya majuscula. The gene clusters responsible for the production of some of the secondary metabolites have recently been elucidated. The dinoflagellates, which are lower eukaryotic algae, also demonstrate chemical diversity and produce unique polycyclic ethers of polyketide origin. A new mechanism for the formation of the truncated polyketide backbones has recently been proposed. The toxicogenicity of dinoflagellates of the genus Pfiesteria has been the focus of controversy--are they 'killer organisms', as alleged? A recent investigation of Pfiesteria genes seems to rule out the presence of polyketide synthase, which is the gene responsible for the production of most dinoflagellate toxins.     

Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates

Plastids (photosynthetic organelles of plants and algae) are known to have spread between eukaryotic lineages by secondary endosymbiosis, that is, by the uptake of a eukaryotic alga by another eukaryote. But the number of times this has taken place is controversial. This is particularly so in the case of eukaryotes with plastids derived from red algae, which are numerous and diverse. Despite their diversity, it has been suggested that all these eukaryotes share a recent common ancestor and that their plastids originated in a single endosymbiosis, the so-called "chromalveolate hypothesis." Here we describe a novel molecular character that supports the chromalveolate hypothesis. Fructose-1,6-bisphosphate aldolase (FBA) is a glycolytic and Calvin cycle enzyme that exists as two nonhomologous types, class I and class II. Red algal plastid-targeted FBA is a class I enzyme related to homologues from plants and green algae, and it would be predicted that the plastid-targeted FBA from algae with red algal secondary endosymbionts should be related to this class I enzyme. However, we show that plastid-targeted FBA of heterokonts, cryptomonads, haptophytes, and dinoflagellates (all photosynthetic chromalveolates) are class II plastid-targeted enzymes, completely unlike those of red algal plastids. The chromalveolate enzymes form a strongly supported group in FBA phylogeny, and their common possession of this unexpected plastid characteristic provides new evidence for their close relationship and a common origin for their plastids.     

The red algal-higher fungi phylogenetic link: the last ten years

The review of the red algal theory for ancestry of Ascomycetes and Basidiomycetes published 10 years ago by the author is updated. Criticisms are answered and new data are discussed. The production of choline sulfate, lenthionine and lanosol are added to the biochemical similarities between red algae and higher fungi. Distribution of polyols is shown to be in favour of the origin of higher fungi from parasitic red algae. As predicted, NADP-linked glutamate dehydrogenase has been found in red algae, and additional reports of chitin in various algae have been published. New supporting data come from the ultrastructure of red algae: mitosis outside the Ceramiales and ultrastructure of vegetative cells and tetrasporocysts of Corallinaceae. On the other hand, the discovery of proplastids in Holmsella makes it less fungus-like. However, no decisive argument has yet been produced for or against the theory. Further light should be expected from protein and nucleic acid sequences. Promising partial sequences of cytochrome c have indeed been published for red algae but the published 5 S ribosomal RNA sequences have not proven relevant to the problem. Sequences of the slower-evolving large rRNA and cytochrome c of red algae could provide convincing evidence and are urgently needed.     

Phycocolloid chemistry as a taxonomic indicator of phylogeny in the Gigartinales, Rhodophyceae: A review and current developments using Fourier transform infrared diffuse reflectance spectroscopy

The taxonomic significance of the polysaccharide structures of algal cell walls has been underscored several times over the past few decades but has never been pursued systematically. Many changes in red algal systematics and the biochemical analyses of phycocolloids have occured in recent years. The cell-wall composi-tion of representatives of 167 (24.7%) genera and 470 (11.5%) species of red algae has been documented.The method developed by Chopin and Whalen for carrageenan identification by Fourier transform infrared diffuse reflectance spectroscopy is extended to the study of phycocolloids for diverse species in many red algal orders. This paper focuses on the Gigartinales in which representatives of 28 (68.3%) families, 88 (50.6%) genera and 224 (27.9%) species have been analyzed. In light of recent molecular phylogenies, some patterns of distribution of key phycocolloid attributes, corresponding to familial and ordinal level groupings, are emerging; however, more species remain to be analyzed. The well-documented biochemical alternation of generations in the Phyllophoraceae, Petrocelidaceae and Gigartinaceae still holds (with two exceptions), but this pattern was not recorded in other families of Gigartinales.     

Analysis of 1,5-anhydro-D-fructose, microthecin, and 4-deoxy-glycero-hexo-2,3-diulose in algae using gas chromatography-mass spectrometry in selected ion monitoring mode

A sensitive and selective method for detection and quantification of 1,5-anhydro-D-fructose, microthecin, and 4-deoxy-glycero-hexo-2, 3-diulose using GC-MS in selected ion monitoring mode has been developed. These compounds, which occur in many biological systems, have here been quantified in the red alga Gracilariopsis lemaneiformis. A screening of other algae showed the occurrence of 1, 5-anhydro-D-fructose in several other species of red algae as well as in some green and brown algae.     

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

Background  

The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them.     

Further study on polyamines in primitive unicellular eukaryotic algae

The possible usefulness of polyamines as chemotaxonomic markers has been investigated in eukaryotic algae. Polyamines were analyzed in 12 species of primitive unicellular eukaryotic algae including some anomalous species. Norspermidine and norspermine in addition to putrescine and spermidine are widely distributed in most unicellular species of the algae. However, neither norspermidine nor norspermine was found in the taxonomically conflicting algae, Cyanophora and Glaucocystis, which contain cyanellae, or in a primitive red alga, Porphyridium. A thermoacidophilic eukaryotic alga, Cyanidium, is rich in both norspermidine and norspermine. Appreciable amounts of spermine and sym-homospermidine were detected only in the species belonging to the Rhodophyta (red algae).     

To be or not to be a compatible solute: bioversatility of mannosylglycerate and glucosylglycerate

Mannosylglycerate (MG) is an intracellular organic solute found in some red algae, and several thermophilic bacteria and hyperthermophilic archaea. Glucosylglycerate (GG) was identified at the reducing end of a polysaccharide from mycobacteria and in a free form in a very few mesophilic bacteria and halophilic archaea. MG has a genuine role in the osmoadaptation and possibly in thermal protection of many hyper/thermophilic bacteria and archaea, but its role in red algae, where it was identified long before hyperthermophiles were even known to exist, remains to be clarified. The GG-containing polysaccharide was initially detected in Mycobacterium phlei and found to regulate fatty acid synthesis. More recently, GG has been found to be a major compatible solute under salt stress and nitrogen starvation in a few microorganisms. This review summarizes the occurrence and physiology of MG accumulation, as well as the distribution of GG, as a free solute or associated with larger macromolecules. We also focus on the recently identified pathways for the synthesis of both molecules, which were elucidated by studying hyper/thermophilic MG-accumulating organisms. The blooming era of genomics has now allowed the detection of these genes in fungi and mosses, opening a research avenue that spans the three domains of life, into the role of these two sugar derivatives.     

The nucleotide sequences of 5S rRNAs from two red algae, Gracilaria compressa and Porphyra tenera

The nucleotide sequences of 5S rRNA from two red algae, Gracilaria compressa and Porphyra tenera have been determined. The two 5S rRNAs are fairly dissimilar to each other in their sequences (65% identity), although they are both composed of 121 nucleotides. Their secondary structures are generally of the eukaryotic with a prokaryotic characteristic. Judged from the 5S rRNA sequence data, the red algae are phylogenically distinct from green and brown algae, and they, Porphyra in particular, are evolutionally most ancient among the eukaryotes of which 5S rRNA sequence has been determined.     

Isolation of a Unique Marine Bacterium Capable of Growth on a Wide Variety of Polysaccharides from Macroalgae

A unique marine bacterium has been isolated which can be cultured on a variety of polysaccharides and cell wall preparations from red and brown algae.     

ELECTRON MICROSCOPY OF MEMBRANOUS BODIES AND GENOPHORE IN CHLOROPLASTS OF BOTRYOCLADIA BOTRYOIDES (RHODYMENIALES, RHODOPHYTA)1

An ultrastructural study on the chloroplasts of the red alga Botryocladia botryoides( Wulfen) J. Feldmann has been carried out to investigate the morphology of globular membranaous bodies (MBs) located between thylakoids. These membranous bodies show an electron dense lumen, in which a pair of denser cores occasionally occurs. The lumen is electron transparent in the chloroplasts of vacuolized, non-dividing cells. The surface of MBs is in contact with the fibrils representing the plastidial genophore; the fibrils sometimes bridge the surface of MBs with the nearest thylakoid. In some planes of section a membranous stalk connecting a MB with thylakoids has been made evident .
Because the presence of similar bodies in chloroplasts and mitochondria of other red algae, as well as in mitochondria of yeast in which an intense synthesis of DNA occurs, the authors propose that MBs in red algae have a role in the replication of the genophore .     

A molecular timeline for the origin of photosynthetic eukaryotes

The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution.     

When Less is More: Red Algae as Models for Studying Gene Loss and Genome Evolution in Eukaryotes

Genome evolution is usually viewed through the lens of growth in size and complexity over time, exemplified by plants and animals. In contrast, genome reduction is associated with a narrowing of ecological potential, such as in parasites and endosymbionts. But, can nuclear genome reduction also occur in, and potentially underpin a major radiation of free-living eukaryotes? An intriguing example of this phenomenon is provided by the red algae (Rhodophyta) that have lost many conserved pathways such as for flagellar motility, macroautophagy regulation, and phytochrome based light sensing. This anciently diverged, species-rich, and ecologically important algal lineage has undergone at least two rounds of large-scale genome reduction during its >1 billion-year evolutionary history. Here, using recent analyses of genome data, we review knowledge about the evolutionary trajectory of red algal nuclear and organelle gene inventories and plastid encoded autocatalytic introns. We compare and contrast Rhodophyta genome evolution to Viridiplantae (green algae and plants), both of which are members of the Archaeplastida, and highlight their divergent paths. We also discuss evidence for the speculative hypothesis that reduction in red algal plastid genome size through endosymbiotic gene transfer is counteracted by ongoing selection for compact nuclear genomes in red algae. Finally, we describe how the spliceosomal intron splicing apparatus provides an example of “evolution in action” in Rhodophyta and how the overall constraints on genome size in this lineage has left significant imprints on this key step in RNA maturation. Our review reveals the red algae to be an exciting, yet under-studied model that offers numerous novel insights as well as many unanswered questions that remain to be explored using modern genomic, genetic, and biochemical methods. The fact that a speciose lineage of free-living eukaryotes has spread throughout many aquatic habitats after having lost about 25% of its primordial gene inventory challenges us to elucidate the mechanisms underlying this remarkable feat.     

Transient gene expression system established in Porphyra yezoensis is widely applicable in Bangiophycean algae

The establishment of transient gene expression systems in the marine red macroalga Porphyra yezoensis has been useful for the molecular analysis of cellular processes in this species. However, there has been no successful report about the expression of foreign genes in other red macroalgae, which has impeded the broader understanding of the molecular biology of these species. We therefore examined whether the P. yezoensis transient gene expression system was applicable to other red macroalgae. The results indicated that a codon-optimized GUS, designated PyGUS, and plant-adapted sGFP(S65T) were successfully expressed under the control of the P. yezoensis PyAct1 promoter in gametophytic cells of six Porphyra species and also in Bangia fuscopurpurea, all of which are classified as Bangiophyceae. In contrast, there were no reporter-expressing cells in the Florideophycean algae examined. These results indicate the availability of PyGUS and sGFP as reporters and the 5' upstream region of the PyAct1 gene as a heterologous promoter for transient gene expression in Bangiophycean algae, which could provide a clue to the efficient expression of foreign genes and transformation in marine red macroalgae.