Mitochondrial Genome of Prasinophyte Alga Pyramimonas parkeae

Prasinophytes are a paraphyletic assemblage of nine heterogeneous lineages in the Chlorophyta clade of Archaeplastida. Until now, seven complete mitochondrial genomes have been sequenced from four prasinophyte lineages. Here, we report the mitochondrial genome of Pyramimonas parkeae, the first representative of the prasinophyte clade I. The circular‐mapping molecule is 43,294 bp long, AT rich (68.8%), very compact and it comprises two 6,671 bp long inverted repeat regions. The gene content is slightly smaller than the gene‐richest prasinophyte mitochondrial genomes. The single identified intron is located in the cytochrome c oxidase subunit 1 gene (cox1). Interestingly, two exons of cox1 are encoded on the same strand of DNA in the reverse order and the mature mRNA is formed by trans‐splicing. The phylogenetic analysis using the data set of 6,037 positions assembled from 34 mtDNA‐encoded proteins of 48 green algae and plants is not in compliance with the branching order of prasinophyte clades revealed on the basis of 18S rRNA genes and cpDNA‐encoded proteins. However, the phylogenetic analyses based on all three genomic elements support the sister position of prasinophyte clades Pyramimonadales and Mamiellales.     

The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region

Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. The complete mitochondrial genome of Solen grandis (Bivalvia: Solenidae) was determined using long-PCR and genome walking techniques. The entire mitochondrial genome sequence of S. grandis is 16,784 bp in length, and contains 36 genes including 12 protein-coding genes (atp8 is absent), 2 ribosomal RNAs, and 22 tRNAs. All genes are encoded on the same strand. Compared with other species, it bears a novel gene order. Besides these, we find a peculiar non-coding region of 435 bp with a microsatellite-like (TA)₁₂ element, poly-structures and many hairpin structures. In contrast to the available heterodont mitochondrial genomes from GenBank, the complete mtDNA of S. grandis has the shortest cox3 gene, and the longest atp6, nad4, nad5 genes.     

Habitat selection and host location by symbiotic shrimps associated with Sargassum communities: The role of chemical and visual cues

One of the most fundamental aspects of symbioses is how the symbionts establish the association. The Sargassum community is comprised of a unique and diverse assemblage of symbiotic organisms, most of which are likely seeking refuge. Host location of the Sargassum habitat by two of the most common invertebrate symbionts, Latreutes fucorum and Leander tenuicornis, was investigated. Based on our trials, neither shrimp species used chemical cues, in the absence of visual cues. Habitat selection of both shrimp species was also examined under a variety of conditions. Our results show that L. fucorum and L. tenuicornis can distinguish visually between different structures and habitats. Specifically, they selected live Sargassum over artificial Sargassum. Moreover, L. fucorum selected Sargassum natans over Sargassum fluitans when only visual cues were available, whereas large-sized L. tenuicornis selected S. fluitans under the same conditions. Conversely, habitat selection trials combining both chemical and visual cues resulted in no preference between the two Sargassum species by either shrimp species. Additional ecological factors that might influence habitat location and selection are discussed, and the importance of Sargassum in terms of pelagic fisheries management.     

A MORPHOLOGICAL AND MOLECULAR STUDY OF AUSTRAL SARGASSUM (FUCALES,PHAEOPHYCEAE) SUPPORTS THE RECOGNITION OF PHYLLOTRICHA AT GENUS LEVEL,WITH FURTHER ADDITIONS TO THE GENUS SARGASSOPSIS1

Sargassum subgenus Phyllotricha currently includes seven species restricted to Australian and New Zealand coasts. A recent study of Cystoseira and other Sargassaceae genera based on mitochondrial 23S DNA and chloroplast‐encoded psbA sequences resulted in the most widely distributed species of subgenus Phyllotricha, Sargassum decurrens, being transferred to the reinstated monospecific Sargassopsis Trevisan. The fate of the residual six Phyllotricha species, however, was not considered. The present study examines these Phyllotricha species, alongside other Sargassum subgenera, Sargassopsis, Sirophysalis trinodis (formerly Cystoseira trinodis) and the New Zealand endemic Carpophyllum Greville, using morphological evidence and the molecular phylogenetic markers cox3, ITS‐2 and the rbcL–S spacer. Our results suggest both the genus Sargassum and Sargassum subgenus Phyllotricha are polyphyletic as currently circumscribed. Four S. subgen. Phyllotricha species, i.e. S. sonderi, S. decipiens, S. varians and S. verruculosum, form a monophyletic group sister to the genus Carpophyllum, and S. peronii is genetically identical to S. decurrens with regard to all three loci. We propose the resurrection of the genus Phyllotricha Areschoug, with type species Phyllotricha sonderi, and include the new combinations Phyllotricha decipiens, Phyllotricha varians and Phyllotricha verruculosum. Sargassum peronii, S. heteromorphum and S. kendrickii are transferred to Sargassopsis and Sargassum peronii is considered a synonym of Sargassopsis decurrens.     

Evidence for extreme sequence divergence between the male‐ and female‐transmitted mitochondrial genomes in the bivalve mollusc,Modiolus modiolus (Mytilidae)

Marine mussels of the family Mytilidae, as well as a number of other bivalves, have a unique system of mitochondrial DNA inheritance called doubly uniparental inheritance (DUI). DUI is characterized by the presence of an ‘F’ mitochondrial genome that is transmitted through mothers to daughters and sons, and an ‘M’ mitochondrial genome that is transmitted only from fathers to sons. In this paper, we demonstrate that DUI exists in the horse mussel, Modiolus modiolus (Linnaeus, 1758) and compare the pattern of molecular evolution of the M and F types in this species. Total DNA was isolated from M. modiolus male and female gonad tissues, as well as from spawned sperm cells. From these DNA samples, partial mitochondrial DNA fragments were amplified from both cytochrome c oxidase subunit I (cox1), and 16S ribosomal RNA (rrnL) genes. Based on cox1 and rrnL sequences, heteroplasmy was observed in M. modiolus and characterized by the resolution of two mitotypes: an F mitotype present in tissues of both males and females, and an M mitotype present in spawned sperm. Using standardized p‐distance and Tamura‐Nei values, M. modiolus is found to display the highest M/F conspecific sequence divergence for any member of the family Mytilidae (i.e. 38% M/F sequence divergence, which is 9% higher than any other intraspecific M/F comparison for the family Mytilidae when standardized using p‐distances across all taxa observed). Sequence analysis also indicated that the M. modiolus M mitotype evolves significantly faster than its conspecific F type. The findings discussed herein broaden the range of mytilid species known to exhibit DUI and they also establish a new threshold for the genetic divergence of male mytilid mitochondrial genomes.     

Use of RAPD in differentiation of selected species of <Emphasis Type="Italic">Sargassum</Emphasis> (Sargassaceae,Phaeophyta)

Sargassum C. Agardh is one of the most common but little understood genera of Phaeophyta in Malaysia. The difficulty in species delineation is due to morphological plasticity. A combination of morphology and random amplified polymorphic DNA (RAPD) studies of selected Sargassum species was carried out to have a better understanding of the taxonomy. Primer OPA13 was found to be good for discriminating between Sargassum species. Sargassum binderi was shown to be different from S. oligocystum (S_D>0.5 = 14.11%), indicating the importance of the vesicle and receptacle in species differentiation. S. baccularia was clearly separated out from S. polycystum and S. stolonifolium using primer OPA13. RAPD analysis showed that the presence of the stolon is an important character for separating S. baccularia (no stolon) from S. polycystum (stolon) and S. stolonifolium (stolon). Presented at the 6th Meeting of the Asian Pacific Society of Applied Phycology, Manila, Philippines.     

Tetrahymena australis (Protozoa,Ciliophora): A Well‐Known But “Non‐Existing” Taxon – Consideration of Its Identification,Definition and Systematic Position

A cryptic species of the Tetrahymena pyriformis complex, Tetrahymena australis, has been known for a long time but never properly diagnosed based on taxonomic methods. The species name is thus invalid according to the International Code of Zoological Nomenclature. Recently, a population isolated from a freshwater lake in Wuhan, China was investigated using live observations, silver staining methods and gene sequence data. This organism can be separated from other described species of the T. pyriformis complex by its relatively small body size, the number of somatic kineties and differences in sequences of two genes, namely the small subunit ribosomal RNA (SSU rRNA) and the mitochondrial cytochrome c oxidase subunit I (cox1). We compared the SSU rRNA gene sequences of all available Tetrahymena species to reveal the nucleotide differences within this genus. The sequence of the Wuhan population is identical to two sequences of a previously isolated strain of T. australis (ATCC #30831). Phylogenetic analyses indicate that these three sequences (X56167, M98015, KT334373) cluster with Tetrahymena shanghaiensis (EF070256) in a polytomy. However, sequence divergence of the cox1 gene between the Wuhan population and another strain of T. australis (ATCC #30271) is 1.4%, suggesting that these may represent different subspecies.     

苦草对砷的富集作用

为了探求合适的水体砷污染修复植物及砷在食物链中传递、累积的特点,以常见的沉水植物-苦草为研究对象,对受砷污染的水体进行修复,结果表明:苦草对水环境中砷的富集能在较短的时间内(3 d)达到一个较大值,到第14天,不同砷水平(2 mg/L)处理下的苦草对砷富集系数均超过200;苦草中砷浓度随处理时间及外源砷浓度的增加而增加,且与外源砷浓度之间存在极显著地正相关;苦草在不同浓度砷处理下都生长良好,对砷胁迫表现出较强的耐受性。因此,苦草对于水体的砷污染有着很好的去除效果,同时也能很好地反映出一个地区的砷污染水平。     

Historical biogeography of the widespread macroalga Sargassum (Fucales,Phaeophyceae)

Sargassum is a cosmopolitan brown algal genus spanning the three ocean basins of the Atlantic, Pacific and Indian Oceans, inhabiting temperate, subtropical and tropical habitats. Sargassum has been postulated to have originated in the Oligocene epoch approximately 30 mya according to a broad phylogenetic analysis of brown macroalgae, but its diversification to become one of the most widespread and speciose macroalgal genera remains unclear. Here, we present a Bayesian molecular clock study, which analyzed data from the order Fucales of the brown algal crown radiation (BACR) group to reconstruct a time-calibrated phylogeny of the Sargassum clade. Our phylogeny included a total of 120 taxa with 99 Sargassum species sampled for three molecular markers – ITS-2, cox3 and rbcLS – calibrated with an unambiguous Sargassaceae fossil from between the lower and middle Miocene. The analysis revealed a much later origin of Sargassum than expected at about 6.7 mya, with the genus diversifying since approximately 4.3 mya. Current geographic distributions of Sargassum species were then analyzed in conjunction with the time-calibrated phylogeny using the dispersal-extinction-cladogenesis (DEC) model to estimate ancestral ranges of clades in the genus. Results strongly support origination of Sargassum in the Central Indo-Pacific (CIP) region with subsequent independent dispersal events into other marine realms. The longer history of diversification in the ancestral CIP range could explain the much greater diversity there relative to other marine areas today. Analyses of these dynamic processes, when fine-tuned to a higher spatial resolution, enable the identification of evolutionary hotspots and provide insights into long-term dispersal patterns.     

Genetic delineation between and within the widespread coccolithophore morpho‐species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta)

Emiliania huxleyi and Gephyrocapsa oceanica are abundant coccolithophore morpho‐species that play key roles in ocean carbon cycling due to their importance as both primary producers and cal‐cifiers. Global change processes such as ocean acidification impact these key calcifying species. The physiology of E. huxleyi, a developing model species, has been widely studied, but its genetic delineation from G. oceanica remains unclear due to a lack of resolution in classical genetic markers. Using nuclear (18S rDNA and 28S rDNA), mitochondrial (cox1, cox2, cox3, rpl16, and dam), and plastidial (16S rDNA, rbcL, tufA, and petA) DNA markers from 99 E. huxleyi and 44 G. oceanica strains, we conducted a multigene/multistrain survey to compare the suitability of different markers for resolving phylogenetic patterns within and between these two morpho‐species. The nuclear genes tested did not provide sufficient resolution to discriminate between the two morpho‐species that diverged only 291Kya. Typical patterns of incomplete lineage sorting were generated in phylogenetic analyses using plastidial genes. In contrast, full morpho‐species delineation was achieved with mitochondrial markers and common intra‐morpho‐species phylogenetic patterns were observed despite differing rates of DNA substitution. Mitochondrial genes are thus promising barcodes for distinguishing these coccolithophore morpho‐species, in particular in the context of environmental monitoring.     

Functional Ecology of Two Contrasting Freshwater Ciliated Protists in Relation to Temperature

We conducted microcosm experiments with two contrasting freshwater ciliates on functional traits (FTs) related to their growth rate (numerical response, NR) and ingestion rate (functional response, FR) over a range of ecologically relevant temperatures. Histiobalantium bodamicum and Vorticella natans are common planktonic ciliates but their abundance, swimming behavior, and temperature tolerance are different. In contrast to most sessile peritrich species, the motile V. natans is not strictly bacterivorous but also voraciously feeds upon small algae. We observed three main alterations in the shape of NR of both species with temperature, that is, change in the maximum growth rate, in the initial slope and in the threshold food level needed to sustain the population. Similarly, maximum ingestion rate, gross growth efficiency (GGE), and cell size varied with temperature and species. These findings caution against generalizing ciliate performance in relation to the ongoing global warming. Our results suggest that V. natans is the superior competitor to H. bodamicum in terms of temperature tolerance and bottom-up control. However, the abundance of V. natans is usually low compared to H. bodamicum and other common freshwater ciliates, suggesting that V. natans is more strongly top-down controlled via predation than H. bodamicum. The taxonomic position of V. natans has been debated. Therefore, to confirm species and genus affiliation of our study objects, we sequenced their small subunit ribosomal RNA (SSU rDNA) gene.     

Species‐specific mitochondrial gene rearrangements in biting midges and vector species identification

Abstract Partial mitochondrial gene sequences of 16 Culicoides species were determined to elucidate phylogenetic relations among species and to develop a molecular identification method for important virus vector species. In addition, the analysis found mitochondrial gene rearrangement in several species. Sequences of the mitochondrial genome region, cox1–trnL2–cox2 (1940–3785 bp) of 16 Culicoides and additional sequences were determined in some species, including whole mitochondrial genome sequences of Culicoides arakawae. Nine species showed common organization in this region, with three genes cox1–trnL2–cox2 and a small or no intergenic region (0–30 bp) between them. The other seven species showed translocation of tRNA and protein‐coding genes and/or insertion of AT‐rich non‐coding sequences (65–1846 bp) between the genes. The varied gene rearrangements among species within a genus is very rare for mitochondrial genome organization. Phylogenetic analyses based on the sequences of cox1+cox2 suggest a few clades among Japanese Culicoides species. No relationships between phylogenetic closeness and mitochondrial gene rearrangements were observed. Sequence data were used to establish a polymerase chain reaction tool to distinguish three important vector species from other Culicoides species, for which classification during larval stages is not advanced and identification is difficult.     

Effects of NaCl salinity on growth, morphology, photosynthesis and proline accumulation of Salvinia natans

The effects of NaCl salinity on growth, morphology and photosynthesis of Salvinia natans (L.) All. were investigated by growing plants in a growth chamber at NaCl concentrations of 0, 50, 100 and 150 mM. The relative growth rates were high (ca. 0.3 d⁻¹) at salinities up to 50 mM and decreased to less than 0.2 d⁻¹ at higher salinities, but plants produced smaller and thicker leaves and had shorter stems and roots, probably imposed by the osmotic stress and lowered turgor pressure restricting cell expansion. Na⁺ concentrations in the plant tissue only increased three-fold, but uptake of K⁺ was reduced, resulting in very high Na⁺/K⁺ ratios at high salinities, indicating that S. natans lacks mechanisms to maintain ionic homeostasis in the cells. The contents of proline in the plant tissue increased at high salinity, but concentrations were very low (<0.1 μmol g⁻¹ FW), indicating a limited capacity of S. natans to synthesize proline as a compatible compound. The potential photochemical efficiency of PSII (F_v/F_m) of S. natans remained unchanged at 50 mM NaCl but was reduced at higher salinities, and the photosynthetic capacity (ETR_max) was significantly reduced at 50 mM NaCl and higher. It is concluded that S. natans is a salt-sensitive species lacking physiological measures to cope with exposure to high NaCl salinity. At low salinities salts are taken up and accumulate in old leaves, and high growth rates are maintained because new leaves are produced at a higher rate than for plants not exposed to salt.     

两种沉水植物对间隙水磷浓度的影响

为研究两种根系特征的沉水植物在生长过程中对间隙水中磷浓度的影响,选取根系较多的沉水植物苦草和根系相对较少的沉水植物黑藻作为实验材料,监测底泥中间隙水各形态磷含量及环境因子的变化,探讨不同根系特征沉水植物对间隙水中磷的影响。结果表明:黑藻和苦草实验组沉积物间隙水中各形态磷的浓度均呈不同程度的降低,黑藻和苦草对于稳定水质,减少底泥中磷向水中转移具有明显的效果;沉水植物不同,底泥间隙水中溶解性总磷(DTP)和溶解性活性磷(SRP)存在明显差异。实验结束时黑藻组和苦草组间隙水中DTP的浓度分别为0.24,0.01 mg/L,SRP的浓度分别为0.22 mg/L,0.004 mg/L。间隙水中磷的形态主要以DTP和SRP为主,溶解性有机磷(DOP)的含量相对较低。沉水植物对间隙水中磷的吸收是降低间隙水中磷含量的重要原因,苦草的吸收能力大于黑藻。沉水植物根系通过降低底泥p H值,提高氧化还原电位(Eh)的方式抑制了底泥中磷的释放。     

Density and height of Sargassum influence rabbitfish (f. Siganidae) settlement on inshore reef flats of the Great Barrier Reef

Macroalgal beds have been suggested to be an important settlement habitat for a diversity of reef fishes, yet few studies have considered how the composition or structure of macroalgal beds may influence fish settlement. The aim of this study was to investigate how the physical characteristics of Sargassum beds, a common macroalga on inshore coral reefs, influence the abundance of recently-settled rabbitfishes (Siganidae) on Orpheus Island, Great Barrier Reef. The abundance of recently-settled rabbitfish (< 3 cm total length), the density and height of Sargassum thalli, and benthic composition were quantified within replicate 1-m² quadrats across 15 mid-reef flat sites. A total of 419 recently-settled rabbitfish from three species (Siganus doliatus, S. lineatus and S. canaliculatus) were recorded across 150 quadrats (range 0–16 individuals m⁻²), with S. doliatus accounting for the majority (85.2%) of individuals recorded. The abundance of S. doliatus and S. lineatus was greatest at moderate Sargassum densities (ca. 20–30 holdfasts m⁻²) and generally increased with Sargassum height and the cover of ‘other’ macroalgae. These findings demonstrate the potential importance of the physical characteristics of macroalgal beds to the settlement of rabbitfishes on inshore reef flats.

     

SYMBIODINIUM NATANS SP. NOV.: A “FREE‐LIVING” DINOFLAGELLATE FROM TENERIFE (NORTHEAST‐ATLANTIC OCEAN)1

We examined a free‐living Symbiodinium species by light and electron microscopy and nuclear‐encoded partial LSU rDNA sequence data. The strain was isolated from a net plankton sample collected in near‐shore waters at Tenerife, the Canary Islands. Comparing the thecal plate tabulation of the free‐living Symbiodinium to that of S. microadriaticum Freud., it became clear that a few but significant differences could be noted. The isolate possessed two rather than three antapical plates, six rather than seven to eight postcingular plates, and finally four rather than five apical plates. The electron microscopic study also revealed the presence of an eyespot with brick‐shaped contents in the sulcal region and a narrow anterior plate with small knob‐like structures. Bayesian analysis revealed the free‐living Symbiodinium to be a member of the earliest diverging clade A. However, it did not group within subclade A_I (=temperate A) or any other subclades within clade A. Rather, it occupied an isolated position, and this was also supported by sequence divergence estimates. On the basis of comparative analysis of the thecal plate tabulation and the inferred phylogeny, we propose that the Symbiodinium isolate from Tenerife is a new species (viz. S. natans). To elucidate further the species diversity of Symbiodinium, particularly those inhabiting coral reefs, we suggest combining morphological features of the thecal plate pattern with gene sequence data. Indeed, future examination of motile stages originating from symbiont isolates will demonstrate if this proves a feasible way to identify and characterize additional species of Symbiodinium and thus match ribotypes or clusters of ribotypes to species.     

Complete mitochondrial genomes of two green lacewings, <Emphasis Type="Italic">Chrysoperla nipponensis</Emphasis> (Okamoto, 1914) and <Emphasis Type="Italic">Apochrysa matsumurae</Emphasis> Okamoto, 1912 (Neuroptera: Chrysopidae)

We describe the complete mitochondrial genomes of the green lacewing species Chrysoperla nipponensis (Okamoto, 1914) and Apochrysa matsumurae Okamoto 1912 (Neuroptera: Chrysopidae). The genomes were 16,057 and 16,214 bp in size, respectively, and comprised 37 genes (13 protein coding genes, 22 tRNA genes and two rRNA genes). A major noncoding (control) region was 1,244 bp in C. nipponensis and 1,407 in A. matsumurae, and the structure was simpler than that reported in other Neuroptera, lacking conserved blocks or long tandem repeats. The overall arrangement of genes was almost the same as that found in most arthropod mitochondrial genomes, with the one exception of a tRNA rearrangement to tRNA-Cys–tRNA-Trp–tRNA-Tyr, rather than the plesiomorphic tRNA-Trp–tRNA-Cys–tRNA-Tyr. A high A + T content (78.89 and 79.02%, respectively), A + T-rich codon bias, and a mismatch between the most-used codon and its corresponding tRNA anticodon were observed as a typical feature of the insect mitochondrial genome.     

Synthesis,antioxidant and photoprotection activities of hybrid derivatives useful to prevent skin cancer

Chronic ultraviolet (UV) radiation exposure is a major cause of skin cancer. A novel series of hybrid derivatives (I–VIII) for use in sunscreen formulations were synthesized by molecular hybridization of t-resveratrol, avobenzone, and octyl methoxycinnamate, and were characterized. The antioxidant activity values for VIII were comparable than to those of t-resveratrol. Compounds I–III and VI demonstrated Sun Protector Factor superior to that of t-resveratrol. Compounds I and IV–VIII were identified as new, broad-spectrum UVA filters while II–III were UVB filters. In conclusion, novel hybrid derivatives with antioxidant effects have emerged as novel photoprotective agents for the prevention of skin cancer.