A genome-wide analysis of the chloroplast NADH dehydrogenase-like genes in Zostera marina

Journal of Oceanology and Limnology - The chloroplast NADH dehydrogenase-like (NDH) complex, homologous to respiratory complex I, participates in photosystem I cyclic electron flow (PSI-CEF) and...     

Habitat suitability analysis of eelgrass Zostera marina L.in the subtidal zone of Xiaoheishan Island

We present a GIS-based habitat suitability index(HSI) model to identify suitable areas for Zostera marina L. restoration in the subtidal zone of Xiaoheishan Island. The controlling factors in the model,in order of importance,are Secchi depth,sediment composition,water temperature,salinity,current velocity,water depth and nutrient quality. Specific factor piecewise functions have been used to transform parameter values into normalized quality indexes. The weight of each factor was defined using expert knowledge and the analytic hierarchy process(AHP) method. All of the data thus obtained were interpolated using the inverse distance weighted(IDW) interpolation method to create maps for the entire region. In this study,the analysis of habitat suitability in the subtidal zone of Xiaoheishan Island was conducted for four seasons. According to the GIS-based HSI model,the optimal habitat of Z ostera marina L. appears in spring,although habitat remains suitable all year round. On the whole,the optimum site for eelgrass restoration is located in the eastern region,followed by the western and southern regions. We believe that the GIS-based HSI model could be a promising tool to select sites for Z ostera marina L. restoration and could also be applicable in other types of habitat evaluation.     

Biotic and Abiotic Conditions Can Change the Reproductive Allocation of Zostera marina Inhabiting the Coastal Areas of North China

The relationships between reproductive allocation and different factors have been widely recognized for terrestrial plants, but scarcely for marine angiosperms. Focusing on the seagrass Zostera marina, we examined the change in biomass when it was partitioned to growth, vegetative propagation and reproductive allocation of Z. marina. We also evaluated the relationships between reproductive allocation and biotic and abiotic conditions in the coastal areas of north China. The results indicated that the reproductive allocation of Z. marina at the levels of genet, shoot and spathe was positively correlated with shoot characteristics such as height and biomass(P < 0.01), but was negatively correlated with branch number and leaf number per genet(P < 0.01). In addition, the allocation was also affected by other abiotic factors such as water column phosphate concentration(P < 0.05) and sediment total petroleum(P < 0.01). These findings indicated that both biotic and abiotic conditions significantly influenced the reproductive allocation of Z. marina, which may affect further the population dynamics.     

Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance,distribution, and potential for marker development

Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the fi rst genome-wide investigation of microsatellites in the Pacifi c oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacifi c oyster genome is rich in microsatellites. A total of 604 653 repeats were identifi ed, in average of one locus per 815 base pairs(bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of(A)n and(C)n repeats and abundant long(C)n repeats(≥24 bp); 3) large average length of(AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-fl anking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identifi ed. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the fi eld of oyster genetics, particularly for molecular-based selection and breeding.     

Photosynthetic and metabolic responses of eelgrass Zostera marina L. to short-term high-temperature exposure

In recent years, extreme heat events have occurred worldwide and the ocean temperature has been rising, causing stress on the photosynthesis and growth of seagrass. Metabolomics enables detection of metabolic changes under environmental stress. In this study, the photosynthetic physiology and metabolic changes of the eelgrass Zostera marina L. in response to 48 h exposure to 32°C were investigated. The results showed that high temperature induced signi?cant inhibition of photosynthetic effciency(Δ F/F′ m)(23.9%lower than the control), enhanced respiration(58.3% higher), and decreased carbohydrate decomposition products and tricarboxylic acid(TCA) cycle intermediate products, indicating that the energy supply of the eelgrass may be insuffcient at high temperature. In addition, high temperature decreased stearic acid and linoleic acid in eelgrass, suggesting the composition of the membrane system of eelgrass may change at high temperature and implying that high temperature may cause the membrane system to be unstable.     

Influence of temperature and salinity on germination of eelgrass (Zostera marina L.) seeds

Seagrass restoration as part of ocean ecosystem protection has been launched for many years all over the world, but intensive research on this subject in China has just begun in recent years. Seed broadcasting has been widely accepted as the most potentially useful method for seagrass restoration over large areas. We examined the influence of key environmental factors on seed germination to help promote eelgrass bed restoration. Under anoxic conditions, the influence of temperature and salinity on the germination rate of eelgrass (Zostera marina L.) seeds was examined at different combinations of four temperatures (4, 9, 14, and 24°C) and nine salinities (5 to 45, increment of 5). The effect of significant interaction of temperature and salinity on germination rate was observed (ANOVA) (P<0.001). The highest germination rate (83.3 ± 3.5)% was reached in 8 weeks at 14°C and salinity 5. Higher temperature significantly increased the germination rate at salinity 5 (P<0.001) during the whole observation period except for 24°C, while lower salinity significantly increased the germination rate at 14°C (P<0.001). Although significant interaction was found between temperature and salinity (P<0.001), the influence of salinity was stronger than that of temperature for the germination of eelgrass seeds. These results provide useful information for the propagation of artificial seedlings for seagrass restoration in China.     

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.     

Preliminary genome analysis bacterium Pseudoalteromonas potential applications of psychrotolerant marine sp. BSw20308 reveals its

The genus Pseudoalteromonas is ubiquitous in the marine environment and can synthesize a wide range of extracellular compounds. Psychrotolerant Pseudoalteromonas sp. BSw20308 was isolated from the Chukchi Sea, a marginal sea of the Arctic Ocean. It produces a number of extracellular enzymes that can degrade polysaccharides and proteins. The BSw20308 genome was sequenced to 38.1-fold coverage, and the sequences were assembled into 146 contigs （〉~500 bp）. In total, 4 172 open reading frames （ORFs） with an average gene length of 987 bp were detected. At least 86 ORFs were predicted by sequence analysis to encode a variety of catalytic modules involved in the degradation of polysaccharides, proteins, and lipids. In addition, 36 ORFs were predicted to encode catalytic modules involved in the degradation of organic pollutants and halogenated compounds, and in the production of bioactive compounds. The draft genome sequence of BSw20308 provides new information about the ecological function and adaptation of the genus Pseudoalteromonas in Arctic marine environments, and also indicates its potential applica- tions in the biotechnology industries （e.g., enzymology, and pollutant degradation）.     

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.     

Structure Analysis of the Complete Mitochondrial Genome in Cultivation Variety 'Rongfu'

In this report,complete mitochondrial genome sequences of Laminaria cultivation variety 'Rongfu' were obtained.The results showed the length of circular molecule of mtDNA was 37 638 bp(64.7% A+T),encoding three rRNAs(23S,16S and 5S),25 tRNAs,35 known mitochondrial proteins and 3 ORFs.Sequence alignment indicated its mtDNA genome was very similar to that of Laminaria japonica.Phylogenetic trees inferred from concatenated 30 mitochondrial genes showed that 'Rongfu',Laminaria japon-ica,Laminaria longipedalis,L...     

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.     

Cloning,characterization,and expression analysis of the DEAD-box family genes,Fc-vasa and Fc-PL10a,in Chinese shrimp (Fenneropenaeus chinensis)

RNA helicases of the DEAD-box and related families are involved in various cellular processes including DNA replication,DNA repair,and RNA processing.However,the function of DEAD-box proteins in aquaculture species is poorly understood at molecular level.We obtained the full-length cDNA sequences of two genes encoding helicase-related proteins,Fc-vasa and Fc-PL10a,from the testes of Chinese shrimp,Fenneropenaeus chinensis.The two predicted amino acid sequences contain all the conserved motifs characterized ...     

Erratum to: Cloning, characterization, and expression analysis of the DEAD-box family genes, Fc-vasa and Fc-PL10a, in Chinese shrimp (Fenneropenaeus chinensis)

<正>In the original article, the name of the fourth author is incorrect. The correct one is Kyoung Ho Kang, in which "Kang" is the family name. The publishing companies apologize to the author.     

The complete mitochondrial genome of Parachiloglanis hodgarti and its phylogenetic position within Sisoridae

The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized, which is the first mitogenome of the genus Parachiloglanis within Sisoridae. The mitogenome is 16 511-bp long and included 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one control region. The genome composition was A+T biased (58.64%) and exhibited a positive AT-skew (0.095) and a negative GC-skew (?0.283). Compared with other Sisoridae fishes, the characteristics of nucleotide skews, codon usage, and amino acid usage of the P. hodgarti mitogenome are more similar to those of non-Glyptosternoid fishes. Furthermore, the phylogenetic trees show that Sisoridae fishes fall into four major clades and P. hodgarti (Clade I) is basal to the Sisoridae family, forming a sister clade to the Glyptosternoids (Clade IV). The topological structures constructed in this study raised doubts over the traditional classification system. These results will help better understand the features of the P. hodgarti mitogenome and provide a reference for further phylogenetic research on Sisoridae species.

     

Characterization of the Complete Mitochondrial Genome of Arius dispar(Siluriformes: Ariidae) and Phylogenetic Analysis Among Sea Catfishes

The mitochondrial genome(mitogenome) was 16792 bp in length, containing 13 protein coding genes(PCGs), two rRNA genes(12 S rRNA and 16 S rRNA), 22 tRNA genes, and two main non-coding regions. Among these 37 genes, 28 genes were encoded on the heavy strand, while 9 genes were transcribed on the light strand. The non-coding regions of A. dispar included a control region, a light strand replication and another 11 intergenic spacers. The CR of A. dispar contained 8 conserved sequence blocks(CSBs), a termination-associated sequence(TAS) and a pyrimidine tract. Phylogenetic analysis based on 12 PCGs revealed that A. dispar was genetically closest to Arius arius. The families Schilbeidae, Claroteidae, Mochokidae, and Ariidae formed a closely evolved clade. Molecular information from this research introduces mitogenomice data of A. dispar and suggests the phylogenetic relationships among Siluriformes.