The first complete organellar genomes of an Antarctic red alga,Pyropia endiviifolia:insights into its genome architecture and phylogenetic position within genus Pyropia(Bangiales,Rhodophyta)

Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes(ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic red alga Pyropia endiviifolia using the Illumina platform. The plastid genome(195 784 bp, 33.28% GC content) contains 210 protein-coding genes, 37 tRNA genes and 6 rRNA genes. The mitochondrial genome(34 603 bp, 30.5% GC content) contains 26 protein-coding genes, 25 tRNA genes and 2 rRNA genes. Our results suggest that the organellar genomes of Py. endiviifolia have a compact organization. Although the collinearity of these genomes is conserved compared with other Pyropia species, the genome sizes show significant differences, mainly because of the different copy numbers of rDNA operons in the pt DNA and group II introns in the mtDNA. The other Pyropia species have 2–3 distinct intronic ORFs in their cox 1 genes, but Py. endiviifolia has no introns in its cox 1 gene. This has led to a smaller mtDNA than in other Pyropia species. The phylogenetic relationships within Pyropia were examined using concatenated gene sets from most of the available organellar genomes with both the maximum likelihood and Bayesian methods. The analysis revealed a sister taxa affiliation between the Antarctic species Py. endiviifolia and the North American species Py. kanakaensis.     

Identification of Cytochrome P450 (CYP) genes in Zhikong scallop (Chlamys farreri)

Cytochrome P450 (CYP) superfamily is one of the membership largest and function most diverse protein superfamily recogniozed among living beings. Members of this superfamily were further assigned to different families and subfamilies based on their amino acid similarities. According to their phylogenetic relationships, the CYP genes which likely diverged from common ancestor gene and may share common functions were grouped into one clan. Widely distributing scallops are a group of the most conspicuous bivalve; however the studies on their CYP is acarce. In this study, we searched the genome and expressed sequence tags of Zhikong scallop (Chlamys farreri) for CYP genes. In total, 88 non-redundant CYP were identified, which were homed in 13 CYPs gene families. Phylogenetic analysis divided these genes into 4 CYP clans. As in deuterostomes, Clan 2 was the largest, which contained 33 genes belonging to CYP1, CYP2, CYP17 and CYP356 families. Clan 3 contgained 19 genes belonging to CYP3, CYP5 and CYP30 families. Clan 4 contained 23 genes, all belonging to CYP4 family. The mitochondrial CYP clan contained 9 genes belonging to CYP10 and CYP24 families. In comparison, protostomes (C. farreri, D. pluex, D. melanogaster) contained more CYP genes than deuterostomes (S. purpuratus and vertebrates) in Clan 2 but less genes in Clan 3 and Clan 4. Our findings will aid to deciphering CYP function and evolution in scallops and bivalves.     

Predicting the reproduction strategies of several microalgae through their genome sequences

Documenting the sex and sexual reproduction of the microalgae is very difficult, as most of the results are based on the microscopic observation that can be heavily influenced by genetic, physiological and environmental conditions. Understanding the reproduction strategy of some microalgae is required to breed them in large scale culture industry. Instead of direct observation of sex and sexual reproduction under microscope, the whole set or the majority of core meiosis genes may evidence the sex and sexual reproduction in the unicellular algae, as the meiosis is necessary for maintaining the genomic stability and the advantages of genetic recombination. So far, the available genome sequences and bioinformatic tools(in this study, homolog searching and phylogenetic analysis) allow us to propose that at least 20 core meiosis genes(among them ≥6 must be meiosis specific) are enough for an alga to maintain its sexual reproduction. According to this assumption and the genome sequences, it is possible that sexual reproduction was carried out by Micromonas pusilla and Cyanidioschyzon merolae, while asexual reproduction was adopted by Bigelowiella natans, Guillardia theta, Nannochloropsis gaditana, N. oceanica, Chlorella variablis, Phaeodactylum tricornutum and Thalassiosira pseudonana. This understanding will facilitate the breeding trials of some economic microalgae(e.g., N. gaditana, N. oceanica, C. variablis and P. tricornutum). However, the reproduction strategies of these microalgae need to be proved by further biological experiments.     

Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the wellknown genus Zoothamnium(Ciliophora,Peritrichia)

In this paper,we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence,for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless,Z oothamnium exhibits higher genetic diversity than the gross morphology of its species. Here,we used all available genetic information for the small subunit of ribosomal RNA(SSU r RNA) and internal transcribed spacer region(ITS1-5.8S-ITS2) for this genus to reconstruct phylogenies for four datasets(SSU rRNA,ITS1,ITS2,and ITS1-5.8S-ITS2) and a combined dataset(SSU rRNA+ITS1-5.8SITS2) using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic,and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly,as with some other groups of ciliates,to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies,covering additional Zoothamnium spp. and members of closely related genera(e.g. Zoothamnopsis,Myoschiston,and Epistylis).     

The Complete Sequence of Mitochondrial COII Gene of Fenneropenaeus chinensis and Its Applicability as a Marker for Phylogenetic Analysis

The complete mitochondrial cytochrome oxidase subunit II (COII) gene of Penaeinae shrimp Fenneropenaeus chinen- sis was cloned and sequenced. The gene is 688 bp in length and codes for 229 amino acids. It shows 83.2%, 87.0% and 83.8% sequence similarity to Marsupenaeus japonicus, Penaeus monodon and Farfantepenaeus notialis, respectively. The A T content of the whole gene and that at the third position of codons are 64.7% and 78.2%, respectively. The phylogenetic relationship between F. chinensis and three other species representing genera Farfanatepenaeus, Marsupenaeus and Penaeus was analyzed. Results showed that the genetic distances among the four taxa ranged from 0.144 0 to 0.200 5, exceeding those estimated with COI and partial 16S rRNA gene sequences among Marsupenaeus, Litopenaeus and Melicertus, and being therefore larger than the value among subgenera. It has been suggested that the COII gene has a faster evolutionary rate than that of the COI gene and partial 16S rRNA gene and could be used for phylogenetic analysis at genus or species level. The results of the present study indicated that Farfantepenaeus, Fenneropenaeus, Marsupenaeus and Penaeus are at a higher phylogenetic level than subgenus, which supports the opinion of the elevation of phylogenetic status of the four subgenera to genus level.     

The Complete Sequence of Mitochondrial COⅡ Gene of Fenneropenaeus chinensis and Its Applicability as a Marker for Phylogenetic Analysis

The complete mitochondrial cytochrome oxidase subunit Ⅱ （COⅡ） gene of Penaeinae shrimp Fenneropenaeus chinensis was cloned and sequenced. The gene is 688 bp in length and codes for 229 amino acids. It shows 83.2%, 87.0% and 83.8% sequence similarity to Marsupenaeus Japonicus, Penaeus monodon and Farfantepenaeus notialis, respectively. The A＋T content of the whole gene and that at the third position of codons are 64.7% and 78.2%, respectively. The phylogenetic relationship between F. chinensis and three other species representing genera Farfanatepenaeus, Marsupenaeus and Penaeus was analyzed. Results showed that the genetic distances among the four taxa ranged from 0.144 0 to 0.200 5, exceeding those estimated with COⅠ and partial 16S rRNA gene sequences among Marsupenaeus, Litopenaeus and Melicertus, and being therefore larger than the value among subgenera. It has been suggested that the COⅡ gene has a faster evolutionary rate than that of the COⅠ gene and partial 16S rRNA gene and could be used for phylogenetic analysis at genus or species level. The results of the present study indicated that Farfantepenaeus, Fenneropenaeus, Marsupenaeus and Penaeus are at a higher phylogenetic level than subgenus, which supports the opinion of the elevation of phylogenetic status of the four subgenera to genus level.     

MiR-430 Can Affect the Mesoderm Formation and Metamorphosis of Paralichthys olivaceus by Targeting lefty Gene

MiR-430 is a non-coding small RNA that participates in early embryonic development by acting on the Nodal signaling pathway.Its functions in Paralichthys olivaceus(P.olivaceus),however,remain unclear.In this study,through biological information technology,we hypothesized lefty was the target gene of miR-430.Lefty is a divergent member of the transforming growth factor-β(TGF-β)superfamily,and is involved in regulating left-right patterning as an antagonist of the Nodal signaling pathway.To study the relationship between miR-430 and lefty gene,miR-430 and fluorescent expression vector were transfected into embryo cells.Our results showed that miR-430 has important effects on early embryonic development.It can inhibit the expressions of lefty and other genes related to Nodal signaling pathway.Additionally,the expression of miR-430 was involved in the metamorphosis of P.olivaceus.This study clarifies the function of miR-430 in P.olivaceus,which will be helpful for further research on the interactions between miR-430 and the Nodal signaling pathway.     

The Optimal Cross-section Design of the “Trapezoid-V” Shaped Drainage Canal of Viscous Debris Flow

Debris flow drainage canal is one of the most widely used engineering measures to prevent and manage debris flow hazards.The shape and the sizes of the cross-section are important parameters when design debris flow drainage canal.Therefore,how to design the appropriate shape and sizes of the cross-section so that the drainage canal can have the optimal drainage capacity is very important and few researched at home and abroad.This study was conducted to analyze the hydraulic condition of a Trapezoid-V shaped drainage canal and optimize its cross-section.By assuming characteristic sizes of the cross-section,the paper deduced the configuration parameter of the cross-section of a Trapezoid-V shaped debris flow drainage canal.By theory analysis,it indicates that the optimal configuration parameter is only related to the side slope coefficient and the bottom transverse slope coefficient.For this study,the Heishui Gully,a first-order tributary of the lower Jinsha River,was used as an example to design the optimal cross-section of the drainage canal of debris flow.     

Transcriptome Analysis of Crassostrea sikamea (♀) × Crassostrea gigas (♂) Hybrids Under and After Thermal Stress

Crossbreeding is an effective approach to manage the genetic decline in aquaculture.One-way hybrids of Crassostrea sikamea(♀)and Crassostrea gigas(♂)have advantages in growth traits and adaptation to high temperature.Here,we used high-throughput sequencing to analyze the molecular processes in the hybrids under and after thermal stress.The hybrids were cultured in the seawater with an increasing temperature from 25℃to 40℃during 10 hours,which is regarded as the thermal stress stage.Then the temperature decreased from 40℃to 25℃within 2 h,which is regarded as the recovery stage.In this study,1293 significant diffe-rentially expressed genes(DEGs)were obtained under thermal stress,of which 576 were upregulated and 717 were downregulated,and 740 significant differentially expressed genes(DEGs)were obtained in the recovery stage,of which the number of upregulated and downregulated genes was 409 and 331,respectively.The antigen processing and presentation,NOD-like,and NF-kappa B path-ways were significantly enriched during the thermal stress stage.The MAPK and PPAR signaling pathways were significantly enrich-ed during the recovery stage.The HSP70,HSP90,and CANX genes were strongly and rapidly upregulated in the control/thermal stress groups but were slightly less upregulated in the thermal stress/recovery group.These results indicate that the innate immune system or nonspecific immunity was deployed to protect interior tissues from thermal stress.In addition,85%of the mutual DEGs were involved in bidirectional regulation(up/down or down/up)when the oysters were removed from the thermal stress to recover.This study provides preliminary insight into the molecular response of C.sikamea(♀)and C.gigas(♂)hybrids to thermal stress and provides a basis for future studies on temperature-adaptation and the possible expansion of hybrid breeding.     

Reconstruction of the Ice Age Glaciation in the Southern Slopes of Mt. Everest, Cho Oyu, Lhotse and Makalu （Himalaya） （Part 1）

1 Introduction, Methods of Evidence and Characteristics of the Investigation Areas The aim of this study was to find geomorph- ological and sedimentological indicators of a past glaciation. In addition to the reconstruction of the maximum extent of Ice Age glacier cover, field investigations combined with panorama photo- graphs and laboratory analyses of samples werefocused on the evidence of glacier trim-lines and -thicknesses. This is the regional continuation of a detailed and spatially …     

Modeling scenic quality of wetland landscape resources in South Dongting Lake, China

This study introduces a method to quantify the scenic value of wetland landscapes and provides the guidance on the allocation of efforts for the purpose of preserving the most important environments.Dongting Lake,a traditional tourist location,is one of the five largest freshwater lakes in China and a Grade 5A National Scenic Region. This study objectively analyzes the scenic resources of South Dongting Lake,and presents a model based on Quantification TheoryⅠto assess wetland scenic landscapes.Employing a multilinear regression relationship between land-scape factors and their associated scenic value,we built up the Wetland Landscape Quantification Model(WLQM), which was used to classify 221 landscapes into five grades.Finally,some suggestions are proposed regarding quantitative assessment and its use for the sustainable development of wetland environments.     

Virescentia guangxiensis(Batrachospermales,Rhodophyta):a new freshwater red algal species from South China

Virescentia guangxiensis,a new species of Virescentia from Guangxi,South China,is described and illustrated based on morphological observations and phylogenetic analysis.This species was distinguished morphologically from other species by the presence of special expansion cells with a variable shape,obovoid,spherical,pear-shaped,located in the penultimate cells of primary or secondary fascicles,rarely terminal on primary fascicles,as well as by small whorls(250-350-μm wide) and short primary fascicles(5-7 cell stories).Phylogenetic analysis of molecular data from the rbcL and COI-5 P loci supported the separation of the proposed new species from other species in the genus Virescentia.This is the first species of the order Batrachospermales reported in Guangxi and the second species of the genus Virescentia reported in China.This study expands the known species diversity and geographical distribution of fre shwater Rhodophyta in China.     

Characterization and analysis of ribosomal proteins in two marine calanoid copepods

Copepods are among the most abundant and successful metazoans in the marine ecosystem. However, genomic resources related to fundamental cellular processes are still limited in this particular group of crustaceans. Ribosomal proteins are the building blocks of ribosomes, the primary site for protein synthesis. In this study, we characterized and analyzed the c DNAs of cytoplasmic ribosomal proteins(c RPs) of two calanoid copepods, P seudodiaptomus poplesia and A cartia pacifi ca. We obtained 79 c RP c DNAs from P. poplesia and 67 from A. pacifi ca by c DNA library construction/sequencing and rapid amplifi cation of c DNA ends. Analysis of the nucleic acid composition showed that the copepod c RP-encoding genes had higher GC content in the protein-coding regions(CDSs) than in the untranslated regions(UTRs), and single nucleotide repeats(3 repeats) were common, with "A" repeats being the most frequent, especially in the CDSs. The 3′-UTRs of the c RP genes were signifi cantly longer than the 5′-UTRs. Codon usage analysis showed that the third positions of the codons were dominated by C or G. The deduced amino acid sequences of the c RPs contained high proportions of positively charged residues and had high p I values. This is the fi rst report of a complete set of c RP-encoding genes from copepods. Our results shed light on the characteristics of c RPs in copepods, and provide fundamental data for further studies of protein synthesis in copepods. The copepod c RP information revealed in this study indicates that additional comparisons and analysis should be performed on different taxonomic categories such as orders and families.     

Genome Sequence of a Marine Carotenoid Producing Yeast Rhodotorula mucilaginosa CYJ03

Carotenoids are valuable pigments that have been widely used in food,pharmaceutical,animal breeding and cosmetics industries.Due to the increasing demand for carotenoids of natural origin,the trend for production of carotenoids by red yeast has become popular.Strain Rhodotorula mucilaginosa CYJ03 was isolated from northern Yellow Sea of China for its carotenoid producing potential.It was found that the whole genome of CYJ03 was 19.03 Mb in size and contained 6301 protein-coding genes including a gene cluster for the carotenoids biosynthesis.The genome sequence would be valuable for exploring the potential biological properties of CYJ03,as well as for facilitating the molecular genetic analysis and the manipulation of carotenoids accumulation in this strain,and for the development of it as an engineered host for carotenoid production.     

Relict glacial landscape in the Sierra Baguales Mountain Range(50°-51° S): evidence of glaciation dynamics and types in the eastern foothills of the southern Patagonian Andes

The glacial morphology of southern South American presents invaluable evidence to reconstruct former glacier behaviour and its relation to climate and environmental changes. However, there are still spatial and temporal gaps in the reconstruction of the Holocene Patagonian glacial landscape. Here we present the first geomorphological record for the Sierra Baguales Mountain Range(SBMR), forming the eastern foothills of the Southern Patagonian Andes 200 km from the Pacific coast. This area is topographically isolated from the Southern Patagonian Ice Field(SPIF), and is affected by the Westerly Winds. The study area shows evidence of ice sheet and alpine glaciations related to Andean uplift,which caused a marked climatic contrast between its western and eastern flanks since the Last Glacial Maximum(LGM). The regional rock mass strength and precipitation gradient acted as a controlling factor in the glacial cirque distribution and sizes, as well as in the development of glaciation types. We report new radiocarbon dates associated with warm/dry to cold/wet climatic changes during the middle Holocene, when former small alpine glaciers were located in the uppermost section of the SBMR basins, and eventually converged to form a small ice field or a composite valley glacier at lower elevations.This can be explained by an estimated regional temperature drop of 3.8°C±0.8°C, based on a 585±26m Equilibrium Line Altitude(ELA) descent, inferred by geomorphological evidence and the Accumulation Area Ratio(AAR), in addition to a free-air adiabatic lapse rate. Subsequently, the glaciers receded due to climatic factors including a rise in temperature, as well as non-climatic factors, mainly the glacier bedrock topography.     

A Preliminary Study on the Relation Between the Thermal and Geometric Surface Centroids of the Western Pacific Warm Pool

Numerous published results have showr the importance of the Wcstern Pacific Warm Pool （WPWP）surface centroid movement in ENSO-（EI Nino/Southcrn Oscillation）rclated studies .Howcver,some rccent research conclusions make it necessary to clarify the differenccs of the currently exicing two types of WPWP surface centroid：the geometric centroid and the thermal （heat）centrold.This study analyzes the physical backgrounds of the two typcs of centroid and points out their differenccs.which suggest that different types of ccntroid may scrve different study purposes.This study also shows that the ‘geometric center’of WPWP.actually a close approximation to the mass ccntroid,is more related to the Nino-3 region sca surfacc temperaturc（SST）ancmaly and can also be regarded as an important indicator of ENSO events.