Mitochondrial phylogenomics reveal the origin and adaptive evolution of the deep-sea caridean shrimps(Decapoda:Caridea)

The deep-sea is considered as the most extensive ecosystem on the Earth.It is meaningful for elucidating the life origins by exploring the origin and adaptive genetic mechanisms of the large deepsea organisms.Caridean shrimps have colonized and successfully adapted to deep-sea environments.They provide an ideal model to analyze the origin and adaptive evolution of modern deep-sea fauna.Here,we conducted the phylogenetic analyses of mitocho ndrial genomes(mitogenomes) from carideans,including 11 newly sequences reported in this investigation to explore the habitat origins,divergence times,and adaptive evolution of deep-sea(seamounts and hydrothermal vents) caridean shrimps.The results showed that the species of deep-sea Caridea formed a monophyletic group.Phylogenetic analysis supported that the deepsea caridean shrimps may originated from shallow sea.The hydrothermal vents alvinocaridid shrimps and Lebbeus shinkaiae from Thoridae underwent a second range expansion from seamounts to vent ecosystems.Estimates of divergence time showed that the caridean shrimps invaded into deep-sea at 147.75 Ma.The divergence of most of the modern seamount and hydrothermal vent species are in the late Cretaceous/early Tertiary.This may associate with the geological events of the Western Pacific,the climate change,and the global deep-water anoxic/dysoxic events during this period.Twenty-two potentially important adaptive residues were detected in the deep-sea shrimp lineage,which were located in atp6,atp8,cox1,cox3,cytb,nad2,nad4 l,and nad5.This investigation adds our understanding of the evolutionary history of deep-sea caridean shrimps,and provides insights into the mitochondrial genetic basis of deep-sea adaptation in this group.     

Comparative analysis of mitochondrial genome of a deepsea crab Chaceon granulates reveals positive selection and novel genetic features

Deep-sea organisms survive in an extremely harsh environment.There must be some genetic adaptation mechanisms for them.We systematically characterized and compared the complete mitochondrial genome(mitogenome) of a deep-sea crab(Chaceon granulates) with those of shallow crabs.The mitogenome of the crab was 16 126 bp in length,and encoded 37 genes as most of a metazoan mitogenome,including 13 protein-coding genes(PCGs),22 transfer RNA(tRNA) genes,and 2 ribosomal RNA(rRNA) genes.The gene arrangement and orientation was conserved in the crabs.However,a unique mitogenome element regulator,the origin of light-strand replication(O L),was firstly predicted in the present crab mitogenome.In addition,further positive selection analysis showed that two residues(33 S in ND3 and 502 I in ND5) in C.granulates mitogenome were positively selected,indicated the selective evolution of the deep-sea crab.Therefore,the mitogenome of deep-sea C.granulates showed a unique O_L element and positive selection.These special features would influence the mitochondrial energy metabolism,and be involved in the adaptation of deepsea environment,such as oxygen deficits and low temperatures.     

中国南沙群岛的双壳纲贝类

报道了中国南沙群岛的双壳纲贝类141种,分隶于5亚纲8目36科77属.从种类的组成中,帘蛤科有18种,蚶科15种,扇贝科11种,鸟蛤科10种,锉蛤科8种,贻贝科、海菊蛤科和樱蛤科各7种,砗磲科6种,其他各科的种类均在5种以内.按种的性质而论,大多数属于和珊瑚礁有密切联系的热带种或亚热带种,区系性质为印度-西太平洋区的印尼-马来亚区.     

越南沿海的双壳纲软体动物

报道了越南沿海的双壳纲软体动物 32 0种 ,隶属 3亚纲、6目、2 6总科、4 1科、1 4 8属。从种类的组成中 ,帘蛤科有 5 7种 ,蚶科 32种 ,樱蛤科 2 9种 ,贻贝科 2 5种 ,鸟蛤科 1 6种 ,牡蛎科 1 4种 ,蛤蜊科 1 3种 ,珍珠贝科和扇贝科各 1 2种 ,紫云蛤科 1 1种 ,竹蛏科 1 0种 ,其他各科的种类均在 7种以内。按种的性质而论 ,越南沿海主要是由热带种和亚热带种类组成 ,还有与珊瑚礁紧密联系的热带种。就越南沿海双壳纲软体动物分类区系而论 ,应属印度—西太平洋区的印尼—马来亚区。     

Are Acila divaricata and Acila mirabilis One Species or Two Distinct Species?Evidence from COI Mitochondrial DNA

Acila divaricata (Hinds, 1843) and A. mirabilis (Adams and Reeve, 1850) are common benthic bivalves in China. A number of researchers have proposed that the latter species is a junior synonym of the former species. Because of morphological similarities, it is difficult to distinguish these two species based on visual examination only. For better understanding of their taxonomy, the mitochondrial COI gene fragments of five individuals of A. divaricata from the East China Sea and six individuals of A. mirabilis from the Yellow Sea were sequenced in this study. The phylogenetic relationships of the obtained COI sequences, together with nineteen sequences of three species of the genus Nucula, were analyzed. The pairwise intra- and inter-specific distances for the COI sequences ranged from 0.002 to 0.017 and from 0.128 to 0.134, respectively, and no overlap was found. Phylogenetically, A. divaricata and A. mirabilis form distinct clades and cluster into a sister to all other Nucula species. The results indicated that A. divaricata and A. mirabilis are two distinct species. The differences in the morphology and distribution between the two species were briefly discussed.     

Molecular phylogeny of the genus Clibanarius(Decapoda: Anomura: Diogenidae) based on mitochondrial and nuclear DNA sequences

Clibanarius,a genus of hermit crabs,is one of the most diverse genera within Diogenidae.However,studies on the phylogeny within Clibcanarius is very limited.We reconstruct the molecular phylogeny of the genus Clibanarius based on two mitochondrial(16 S rRNA and COI)and two nuclear protein-coding(NaK and PEPCK)genes using a multigene phylogenetic approach.Eleven selected Clibanarius species from the Indo-West Pacific are analyzed and the Bayesian and maximum likelihood analyses produced identical results in topology.Results suggest that C.rutilus and C.infraspinatus are more closely related to each other than to C.snelliusi,and C.striolatus shows a close relationship to C.longitarsus.The close association of C.merguiensis with C.englaucus and C.humilis is strongly supported by the divergence of C.virescens from them.Our phylogenetic results contradict the morphological classification scheme proposed for Clibanarius and indicate that the relative length of dactyls and propodi is not phylogenetically significant in Clibanarius.In addition,we speculate that the morphological characteristic of the median cleft of the telson might be phylogenetically important for Clibanarius.     

Development of organelle single nucleotide polymorphism(SNP) markers and their application for the identification of cytoplasmic inheritance patterns in Pyropia yezoensis(Bangiales,Rhodophyta)

The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitocho ndria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria) inheritance in P yezoensis,the wild type RZ(maternal strain) was cro ssed with the red mutant HT(paternal strain) and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT) were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP) loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.     

Effects of ocean acidification on the metabolic rates of three species of bivalve from southern coast of China

Oceanic uptake of anthropogenic carbon dioxide results in a decrease in seawater pH, a process known as "ocean acidification". The pearl oyster Pinctada fucata, the noble scallop Chlamys nobilis, and the green-lipped mussel Perna viridis are species of economic and ecological importance along the southern coast of China. We evaluated the effects of seawater acidification on clearance, respiration, and excretion rates in these three species. The animals were reared in seawater at pH 8.1 (control), 7.7, or 7.4. The clearance rate was highest at pH 7.7 for P. fucata and at pH 8.1 for C. nobilis and P. viridis. The pH had little effecton the respiration rate of P. fucata and P. viridis. In contrast, the respiration rate was significantly lower atpH 7.4 in C. nobilis. The excretion rate was significantly lower at pH 7.4 than pH 8.1 for all species. Theresults indicate that the reduction in seawater pH likely affected the metabolic process (food intake, oxygenconsumption, and ammonia excretion) of these bivalves. Different species respond differently to seawateracidification. Further studies are needed to demonstrate the exact mechanisms for this effect and evaluateadaptability of these bivalves to future acidified oceans.     

Aquatic molluscs in high mountain lakes of the Eastern Alps (Austria): Species-environment relationships and specific colonization behaviour

Mountain lakes represent essential stages for aquatic species on their way colonizing habitats of more elevated regions. Despite extensive biological and chemical study, only little has been reported about the species number and density of freshwater molluscs in these waters. The article presented here elucidates the dispersal of aquatic gastropods and bivalves in 12 mountain lakes that are commonly situated in the Eastern Alps, Austria. Molluscs were recorded at 120 sample points, where a total of 13 species (8 gastropods and 5 bivalves) could be determined. Species distribution data as well as results from contemporarily conducted physico-chemical factor recording were subject to weighted average analysis. In addition, a global marginality coefficient indicating the particularity of a habitat inhabited by a focal species as well as a global tolerance coefficient expressing the width of a niche occupied by this species were computed. Species-environment relationships exhibited that species number and specific density decrease with increasing geographic altitude, declining water temperature, and decreasing amount of submerged vegetation. Whilst waters of the montane altitude level are partly charcterized by high number of mollusc species (> 10), lakes of the subalpine altitude level commonly bear 1 or 2 species with <<1 ind./m2. As proposed by the results of statistics, 9 of the 13 mollusc species are characterized by a pronounced behaviour as specialists with respect to most environmental factors. The four remaining species, Pisidium casertanum, Galba truncatula, Radix labiata, and Radix balthica, act as generalists which increases their pioneering role in the long-term occupation of the Central-alpine region.     

Genome-Wide Patterns of Codon Usage in the Pacific Oyster Genome

The use of synonymous codons with varying frequencies has been observed in many species, and the magnitude varies among closely related species and genes within the same genome. Mutational processes or natural selective pressures affect this bias.However, a systematic investigation of codon usage pattern for molluscan species and its association with the two factors hasn't been conducted. In this study, the whole genome codon usage patterns in oyster genome is investigated using the relative synonymous codon usage(RSCU) method, and 17 putative optimal codons were identified, wherein most had either a cytosine(C) or guanine(G)residue at the third position. Results showed that codon bias was positively associated with gene expression levels and breadth. Optimal codons had different mutational bias patterns compared with nonoptimal codons. Moreover, the results show that codon bias is negatively associated with nucleotide diversity. In the oyster genome, the fourfold degenerate codons are affected by different selective pressures, which can be regarded as an evidence that natural selection shapes codon usage patterns. This research will help to understand how natural selection and mutation bias affect codon usage in Mollusca genomes.     

Methods Comparison for Microsatellite Marker Development： Different Isolation Methods, Different Yield Efficiency

Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time- and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop (Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time- and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the mi-crosatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.     

The Ulva prolifera genome reveals the mechanism of green tides

The genome of green microalgae has rarely been reported.Ulva prolifera is a green microalga that has received much attention.Despite research articles about U.prolifera in recent years,we know very little about its genome.Therefore,the 87.9-Mb haploid genome(containing 10 311 protein-coding genes)of U.prolifera was studied,and the genome was compared with that of U.mutabilis,which is the only published Ulva species.Results showed that the two species are closely related.A phylogenetic tree was constructed among U.prolifera and other green algae available in GenBank,revealing the evolutionary status of U.prolifera in Chlorophyta.To understand why U.prolifer a could grow rapidly,we identified some genes related to growth,such as those involved in cell division,phosphorylation,and cell proliferation.In addition,genes related to stress resistance were found,which supports the notion that U.prolifera grows vigorously in nature.These results help to characterize green tides from a new perspective and reveal some important insight into the biology of U.prolifera.     

流沙湾底栖贝类耐污值的研究

于2008年3月～2009年1月在流沙湾设7采样站,对底栖贝进行了6次采样调查。用Lenat耐污值估算方法对流沙湾底栖贝类耐污进行分析,建立16个分类单元(科)贝类的耐污值谱。结果表明,16个分类单元(科)的耐污值均在6.5以上,其中骨螺科、织纹螺科和汇螺科的耐污值为10.0;马蹄螺科、笔螺科和帘蛤科耐污值在9.0~9.9之间;蚶科、贻贝科、牡蛎科、樱蛤科、竹蛏科、绿螂科、牙螺科和钥孔虫戚科在8.0~8.9之间;蟹守螺科与滨螺科在6.0~7.0之间。流沙湾大多数贝类的耐污值集中于耐污值谱的高端(≥8.0),水体的环境梯度值处于较高值,说明流沙湾已处于中度到高度的污染水平。     

右江盆地二叠纪末深水相无脊椎动物凉水分子的发现及其地质意义

对右江盆地二叠纪末腕足类和介形虫的全球古地理分布以及其他海相无脊椎动物的组合特征进行了详细研究,发现该盆地多个门类生物和华南其他地区(尤其是扬子海盆)存在明显差异。腕足类和介形虫有一部分为凉水分子或古冷水圈分子,具有冷水与暖水分子混生的特征;放射虫具有远洋生物组合的特征;双壳类含大量土著种。这些特征表明:二叠纪末,右江盆地水体相当深,为半深海-深海环境,水温较凉,适合于凉水分子生存;右江盆地和扬子西缘的古特提斯洋连通,是古特提斯洋伸向华南盆地的边缘盆地。      

Availability and use of willow species in representative cold desert areas of northwestern himalaya, India

Willow species(Salix fragilis L.and S.alba L.) are important elements of cold desert agroforestry systems in the Lahaul valley,northwestern Himalaya.Their ability to grow through shoot-cuttings plantations under extreme and xeric climatic conditions of cold deserts,makes them ecologically suited and socially accepted for forestry programmes.Willow species in cold deserts may combat desertification and can thrive well in these areas as compared to any other species.Salix fragilis L.and S.alba L.are under cultivation in the Lahaul valley.However,S.fragilis is widely cultivated under the agroforestry and plantation forestry systems.In the Lahaul valley,willow species are used as subsistence resources and for socio-religious purposes.The present study was carried out to examine the vegetation analysis,density,diversity and distribution of willow species,present status and potential willow plantation sites and uses.The results of present study revealed that a higher species density was recorded at middle altitude villages(Jahlma-3,000 m asl and Hinsa-2,700 m asl),except,a higher density of S.fragilis was at Khoksar(3,200 m asl) in plantation forestry on south-facing slopes.In forests,S.fragilis was planted mainly along the water channels,resulted a low density.The shrubby willow species occurred naturally in the entire Lahaul valley up to an altitude of 3,850 m asl.81% of households felt the scarcity of willow trees,whereas,19% of households were satisfied with the willow trees they owned.The majority of willow species were planted in middle altitudes on privately owned irrigated lands.It was rated most potential prospective willow planting site by the farmers.Small size of land-holdings was one of the main constraints for establishing a large number of willow plantations.Commercial aspects of willow species need to be investigated to encourage the farmers to plant more willows further.     

The phylogeny of native and exotic scallops cultured in China based on 16S rDNA sequences

Scallops of the Family Pectinidae are a valuable resource in marine industry of the world. Understanding the phylogeny of the family is important for the development of the industry. In this study, partial 16S mitochondrial rDNA genes were obtained from 8 scallop species that are commonly cultured indigenous and transplanted species in China. Phylogenetic relationships of Pectinidae were analyzed based on the 8 sequences and other 5 published ones in GenBank, representing 9 genera of the family. The molecular phylogeny trees were constructed using 3 methods with software PHYLIP. The results showe that total 13 species of scallops clustered in 4 clades. Pecten maximus joins P. jacobaeus then Amusium pleuronectes in cluster, indicating close relationship of genus Amusium with Pecten in evolution. P. yessoensis is close to Chlamysfarreri and C. islandica. No enough material was available to single out genus Patinopecten as an independent monophyletic subfamily. The position ofAdamussium colbecki indicates that it is far from genus Pecten but near to genus Chlamys in evolution.     

Dinophysis caudata generated lipophilic shellfish toxins in bivalves from the Nanji Islands,East China Sea

A 12-month program of monitoring potentially toxic microalgae(that produce lipophilic shellfi sh toxins; LSTs) and their toxins in bivalves was conducted from April 2006 to March 2007 in the Nanji Islands, East China Sea. Two Dinophysis species, D. caudata and D. acuminata, were identifi ed, and D. caudat a was found to be the dominant species. D. caudata was detected in water samples between April and June 2006, and between February and March 2007. It reached its highest abundances in May, with a mean abundance of 1.38×10 2 cells/L in surface water and 1.25×10 2 cells/L in bottom water(10 m deep). The temporal distribution of D. caudata was associated with the occurrence of LSTs in bivalve samples, which mostly occurred at the same time as D. caudata blooms, between April and July 2006. All of the cultured bivalves sampled between April and June were contaminated with LSTs, with an average toxicity of 85 μg okadaic acid(OA) eq./100 g meat, which was four times higher than the Chinese regulatory limit(20 μg OA eq./100 g meat). Ten out of fi fteen wild samples(66.7%) collected during the same period were positive for LSTs, and contained an average LST toxicity of 45 μg OA eq./100 g meat(more than twice the regulatory value). Cultured Patinopecten yessoensis collected on 15 May 2006 had the highest toxicity, 320 μg OA eq./100 g meat, and relatively high toxicities(80 to 160 μg OA eq./100 g meat) were found in bivalves until the end of July.     

雷州半岛大珠母贝贝壳凿孔贝类的初步研究

对雷州半岛海域大珠母贝贝壳凿孔贝类进行了调查研究。结果显示:雷州半岛海域大珠母贝贝壳凿孔贝均为小型的双壳类,褶白蚶Acarplicata(Dillwyn)、偏顶蛤Modiolussp.、翘鳞蛤Irusspp.(两种)、单韧穴蛤Vulsella sp.、杯石蛏Lithophaga calyculata(Carpenter)、蝶铰蛤Trigonothracia sp.、短壳肠蛤Botula silicula(Lamarck)、楔形开腹蛤Gastrochaena cuneiformis Spengler等共9种,其中短壳肠蛤(Botula silicula(Lamarck))的出现频率最高,达50%左右,为雷州半岛大珠母贝贝壳凿孔贝类的主要种类;大珠母贝年龄越大,寄生凿孔贝类数量越多;凿孔贝类可以在孔穴中生活较长时间,最长为6a,生长过程中分泌腐蚀性物质腐蚀贝壳,在贝壳内侧形成斑痕,或凿穿贝壳。     

Comparative Analysis of Mitochondrial Control Region Sequence from Three Flatfish Species （Pleuronectidae）

The 5‘-end of the mitochondrial control region sequences of three flatfishes (Pleuronectiformes: Pleuronectidae) were amplified and sequenced. These sequences were compared with those of other three Pleuronectids species retrieved from GenBank. A phylogenetic tree was constructed based on the partial control region sequences. The results of phylogenetic analysis are consistent with those of conventional systematics. Compared to previous studies, the structure of the 5‘-end of mitochondrial control region was analyzed. The terminal associated sequence motif and its complementary motif were identified at the 5‘-end of the sequences. A conserved sequence block, named as CM5‘ d, was identified in the 5‘-end of control region sequences in all Pleuronectids. Another central conserved sequence block, named as CSB-F, was detected in the central conserved blocks.