Ge Ding

Isolation and characterization of 10 microsatellite markers in Helice tientsinensis (Brachyura: Varunidae)

Ten microsatellite loci of Helice tientsinensis (Brachyura: Varunidae) were isolated and characterized. Those loci were proved polymorphic by 21 individuals from coastal wetland along West-Pacific. The number of observed alleles ranged from 5 to 17. Observed and expected heterozygosity was in the range of 0.324–0.907 and 0.461–0.926 separately. In addition, those markers were tested polymorphic and suitable for further assessing genetic diversity and population structure of Helice tientsinensis.

Transcriptome Analysis of Hepatopancreas from the Cr (VI)-Stimulated Mantis Shrimp (Oratosquilla oratoria) by Illumina Paired-End Sequencing: Assembly, Annotation, and Expression Analysis

Cr (VI), the pathogenicity factor, is widely known to cause toxic effects in living organisms. Given the economic importance of the mantis shrimp ( Oratosquilla oratoria), the understanding of impacts by Cr (VI) is considered important. In this study, transcriptome of mantis shrimp was characterized by a comparison between control and Cr (VI)-treated samples using RNA-seq approach. Totally, 88 234 826 bp and 13.24G clean reads were obtained. The total length and number of unigenes were 68 411 206 bp and 100 918, respectively. The maximal and average length of unigenes was 24 906 bp and 678 bp, respectively (N50, 798 bp). 7115 of these unigenes accounted for 7.05% of the total that were annotated in all databases. After annotation of assembled unigenes, 35 619 of them were assigned into 3 functional categories and 56 subcategories using Gene Ontology; 18 580 of them were assigned into 26 functional categories using Clusters of Orthologous Groups of proteins; 16 864 of them were assigned into 5 major categories and 32 subclasses using KEGG. Finally, 1730 genes were differentially expressed (DGEs), 9 up-regulated pathways (protein digestion and absorption, neuroactive ligand-receptor interaction, pancreatic secretion, tyrosine metabolism, amoebiasis, ECM-receptor interaction, riboflavin metabolism, amino sugar and nucleotide sugar metabolism and AGE-RAGE signaling pathway in diabetic complications) were significantly enriched ( q < 0.05), and one down-regulated pathway ( Staphylococcus aureus infection) was significantly enriched ( q < 0.05). Up-regulation of genes in pathways of protein digestion/absorption ( PepT1/SLC15A and ATP1B) and environment information processing ( COL1AS, COL4A; LAMA3_5, LAMB3; FN1 and TN) may imply the potentially positive toxicity resistance mechanisms.

Development and characterization of microsatellite loci of Oratosquilla oratoria (Crustacea: Squillidae)

Oratosquilla oratoria (Crustacea: Squillidae) is the most dominant species in the indo-pacific ocean, which has been regarded as the marine lives for its good taste and rich nutrition in fishery. In the current study, eleven polymorphic microsatellite loci were isolated from total genome of O. oratoria, and tested their polymorphism in 30 individuals collected from the sea areas of the indo-pacific ocean in Huludao, Qingdao and Yantai. The numbers of observed alleles were from two to eleven. Moreover, the observed heterozygosity from 0.278 to 0.734 was comparable to the expected heterozygosity from 0.555 to 0.776. The microsatellite markers obtained in this study were suitable for further assessing the genetic diversity and population structure of O. oratoria.

Comparative transcriptome analysis of Eriocheir japonica sinensis response to environmental salinity

Chinese mitten crabs (Eriocheir japonica sinensis) are catadromous, spending most of their lives in fresh water, but moving to a mixed salt-fresh water environment for reproduction. The characteristics of this life history might imply a rapidly evolutionary transition model for adaptation to marine from freshwater habitats. In this study, transcriptome-wide identification and differential expression on Chinese mitten crab groups were analysed. Results showed: clean reads that were obtained totalled 93,833,096 (47,440,998 in Group EF, the reference, and 46,392,098 in Group ES, the experimental) and 14.08G (7.12G in Group EF 6.96G in Group ES); there were 11,667 unigenes (15.29%) annotated, and they were located to 230 known KEGG pathways in five major categories; in differential expression analysis, most of the top 20 up-regulated pathways were connected to the immune system, disease, and signal transduction, while most of the top 20 down-regulated pathways were related to the metabolism system; meanwhile, 8 representative osmoregulation-related genes (14-3-3 epsilon, Cu2+ transport ATPase, Na+/K+ ATPase, Ca2+ transporting ATPase, V-ATPase subunit A, Putative arsenite-translocating ATPase, and Cation transport ATPase, Na+/K+ symporter) showed up-regulation, and 1 osmoregulation-related gene (V-ATPase subunit H) showed down-regulation. V-ATPase subunit H was very sensitive to the transition of habitats. These results were consistent with the tests of qRT-PCR. The present study has provided a foundation to further understand the molecular mechanism in response to salinity changing in water.

Adaptively differential expression analysis in gill of Chinese mitten crabs (Eriocheir japonica sinensis) associated with salinity changes

Desalination of marine species has become an important development direction for aquaculture in China and other countries. However, that how to regulate the salt balance to adapt to new freshwater habitats is a serious challenge for marine species in desalination of aquaculture. In the study, Chinese mitten crabs (Eriocheir japonica sinensis) was selected to analyse the adaptively differential expression in salinity changes for their novel characteristics of life history. The results showed that gill was the most relevant tissue in osmoregulation that was validated by biomarkers (Na+/K+-ATP, V-type H+-ATPase) with qPCR. Na+/K+-ATPase is a primary transporter and maintains the body fluid osmolality by actively pumping Na+ to the hemolymph, and V-type H+-ATPase is responsible for acid-base balance and nitrogen excretion. So both transcriptome data and qPCR results showed the significantly differential expression of Na+/K+-ATPase and V-type H+-ATPase in gills. Moreover, NAK-α had the most significantly differential expression level in salinity change, and other genes such as GST, HSP90, S27, UBE, VATB also revealed significantly up-regulation. They are considered the key enzymes during the transition from a marine environment to land. Present results have provided a foundation to further understand the molecular adaptive mechanism in desalination of marine species.

Molecular evolution of mitochondrial coding genes in the oxidative phosphorylation pathway in malacostraca: purifying selection or accelerated evolution?

Abstract The mitochondrion is the energy-producing factory of eukaryotic cells, in which oxidative phosphorylation (OXPHOS) is the main pathway for the production of adenosine triphosphate (ATP) by cellular respiration. Because of their vital role in metabolism, mitochondrial proteins are predicted to evolve primarily under constant purifying selection. However, all mitochondrial coding genes of malacostraca had a significantly higher synonymous nt divergence (Ks) in this study. Complex I (NADH dehydrogenase) and complex V (ATP synthase) had a much higher ratio of non-synonymous to synonymous nt divergence (Ka/Ks) and non-synonymous diversity (πNS), whereas complex III (cytochrome bc1 complex) and complex IV (cytochrome c oxidase) had a significantly lower Ka/Ks and non-synonymous diversity (πNS). The Ka/Ks, πNS, πS, and Ka results revealed that two types of mitochondrial genes, NADH dehydrogenase and ATP synthase, in malacostraca were consistent with accelerated evolution. Furthermore, two other types of mitochondrial genes, cytochrome bc1 complex and cytochrome c oxidase, were consistent with purifying selection. Generally, the evolutionary pattern of all mitochondrial proteins of the OXPHOS pathway in malacostraca was not entirely consistent with purifying selection.

The complete mitochondrial genome of Numenius phaeopus (Charadriiformes, Scolopacidae)

Abstract The complete sequence of the mitochondrial DNA genome of Numenius phaeopus was determined using the polymerase chain reaction method. The whole genome (17,091 bp in length) contained 37 genes (13 protein-coding genes [PCGs], 2 rRNA genes and 22 tRNA genes) and a control region (D-loop), which was similar to the typical mtDNA of vertebrates. Almost all the PCGs in N. phaeopus were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes, which were encoded on the L-strand.