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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao key laboratory of Evolution & marine Biodiversity (Ministry of Education) and Institute of Evolution & marine Biodiversity Ocean University of China marine College Shandong University Zoology Department College of ScienceKing Saud University Department of Biology Bradley University laboratory for marine Biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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developmental quantitative genetic analysis of body weights and morphological traits in the turbot, Scophthalmus maximus

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Acta Oceanologica Sinica 2015年第2期34卷 55-62页

作者： WANG Xin'an MA Aijun MA Deyou Yellow Sea fisheries Research Institute Chinese Academy of Fisheries Sciences/Key Laboratory of Sustainable Development of Marine Fisheries Ministry of Agriculture/Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology

In order to elucidate the genetic mechanism of growth traits in turbot during ontogeny, developmental genetic analysis of the body weights, total lengths, standard lengths and body heights of turbots was conducted by mixed genetic models with additive-dominance effects, based on complete diallel crosses with four different strains of Scophthalmus maximus from Denmark, Norway, Britain, and France. Unconditional genetic analysis revealed that the unconditional additive effects for the four traits were more significant than unconditional dominance effects, meanwhile, the alternative expressions were also observed between the additive and dominant effects for body weights, total lengths and standard lengths. Conditional analysis showed that the developmental periods with active gene expression for body weights, total lengths, standard lengths and body heights were 15–18, 15 and 21–24, 15 and 24, and 21 and 27 months of age, respectively. The proportions of unconditional/conditional variances indicated that the narrow-sense heritabilities of body weights, total lengths and standard lengths were all increased systematically. The accumulative effects of genes controlling the four quantitative traits were mainly additive effects, suggesting that the selection is more efficient for the genetic improvement of turbots. The conditional genetic procedure is a useful tool to understand the expression of genes controlling developmental quantitative traits at a specific developmental period（t-1→t） during ontogeny. It is also important to determine the appropriate developmental period（t-1→t） for trait measurement in developmental quantitative genetic analysis in fish.

关键词： Turbot(Scophthalmus maximus L.) growth developmental genetics genetic effect

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Identification of SNP markers correlated with the tolerance of low-salinity challenge in swimming crab(Portunus trituberculatus)

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Acta Oceanologica Sinica 2019年第8期38卷 41-47页

作者： Yanyan Feng Dening Zhang Jianjian Lv Baoquan Gao Jian Li Ping Liu key laboratory of sustainable development of marine fisheries of Ministry of Agriculture Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences

Water salinity condition is an important factor for artificial propagation of the swimming crab(Portunus trituberculatus). Low salinity(LS)-resistant strains are preferred by crab industries. Single nucleotide polymorphism(SNP), the third generation of molecular markers, can be utilized in the breeding of LS-resistant species of P. trituberculatus. Our earlier study identified 615 genes differentially expressed in low-salinity stress compared to the controls. Although thousands of SNP loci have been found, it is hard to identify a SNP marker in correlation with a desired trait. In this study, time-of-flight mass spectrometry(TOF-MS), as an efficient method to select SNPs for the tolerance of LS challenge, was utilized for SNP typing. Fifty gene segments were amplified based on comparative transcriptomics in our earlier study, a total of 18 511 bp DNA fragments were amplified,and eighty-five SNP markers were found. The frequency of the SNPs was estimated to be 0.46 per 100 base pairs of DNA sequences. The rate of the conversion mutation was 81%, while the transversion mutation was 19%. The mutation rate of the G/T(C/A), A/T and G/C was 26%, 12% and 7%, respectively. Eight SNP markers were found to significantly correlate with the adaption of low salinity. Of the eight SNP markers, three linked-SNPs were found in the cuticle proportion gene, and another three SNPs were found in three new genes, and the rest two were found in aquaporin gene and chloride channel gene. The development of these SNP markers found in our study could be primarily used for breeding LS-resistant strains of P. trituberculatus.

关键词： Portunus trituberculatus low salinity time-of-flight mass spectrometry single nucleotide polymorphism SNP

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Response of Yesso scallop Patinopecten yessoensis to acute temperature challenge: physiological and biochemical parameters

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Journal of Oceanology and Limnology 2019年第1期37卷 321-329页

作者： JIANG Weiwei DU Meirong FANG Jianguang GAO Yaping MAO Yuze CHEN Qionglin LIN Fan JIANG Zengjie key laboratory of sustainable development of marine fisheries Ministry of Agriculture Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences laboratory for marine fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology

Water temperature is generally considered to be a major factor af fecting the physiological and biochemical activities of marine bivalves. Here, the physiological and biochemical responses of Yesso scallop, Patinopecten yessoensis, to acute water temperature changes in summer were studied. Scallops were transferred directly to a lower temperature( T dec treatment)(from 23°C to 15°C) or to a higher temperature( Ti nc treatment)(from 15°C to 23°C) for 72 h, respectively. Results showed that the oxygen consumption and ammonia-N excretion rates of P. yessoensis decreased signi?cantly in the T dec treatment but increased dramatically at 6 h in the Ti nc treatment( P <0.05). In the T dec treatment, hepatopancreas antioxidant enzyme activities, superoxide dismutase(SOD) and catalase(CAT) activities, increased substantially within 72 h( P <0.05). However, a signi?cant decrease in CAT activity was found at 12 h in the Ti nc treatment( P <0.01).A signi?cant enhancement of acid phosphatase(ACP) activity and malondialdehyde(MDA) content was detected when scallops were acutely exposed to a temperature of 15°C. The levels of Cu/Zn-SOD gene expression in their gills up-regulated signi?cantly in response to acute temperature changes( P <0.01). These data suggest that acute temperature change af fects physiological and biochemical functions, and improve our knowledge of P. yessoensis under conditions of thermal stress.

关键词： Patinopecten yessoensis acute water temperature changes physiology biochemical activities

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Comparison of the morphometric dynamics of fast-growing and slow-growing strains of turbot Scophthalmus maximus

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Chinese Journal of Oceanology and Limnology 2015年第4期33卷 890-894页

作者：王新安马爱军 Yellow Sea fisheries Research Institute Chinese Academy of Fishery Sciences key laboratory of sustainable development of marine fisheries Ministry of Agriculture Qingdao key laboratory for marine Fish Breeding and Biotechnology

The dynamics of changes in body shape of fast-growing and slow-growing strains of turbot Scophthalmus maximus, and of the differences in body shape between the two strains, were evaluated from 3 to 27 months of age. The ratios of total length/body length, body width/body length and total length/body width were used as morphometric indices. The two strains exhibited different temporal trends in total length/body length but similar trends in body width/body length and total length/body width. Generally, body width/body length of the two strains increased with time and total length/body width decreased. Thus, the bodies of both fast-growing and slow-growing strains of turbot changed from a narrow to a more rounded shape. However, the ratio total length/body length was generally lower, body width/body length was mostly higher and total length/body width was consistently lower in the fast-growing strain than in the slowgrowing strain. Correlation analysis of the three shape ratios with body weight showed that total length/body length and total length/body width were unsuitable, and that width/body length was suitable, for use as a phenotypic marker for selective breeding of turbot for growth in weight.

关键词： Scophthalmus maximus slow-growing strain fast-growing strain morphometric comparison

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Comparison of White Spot Syndrome Virus Infection Resistance Between Exopalaemon carinicauda and Litopenaeus vannamei Under Different Salinity Stresses

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Journal of Ocean University of China 2017年第6期16卷 1195-1205页

作者： GE Qianqian YU Ge SUN Ming LI Jitao LI Jian key laboratory of sustainable development of marine fisheries Ministry of AgricultureYellow Sea Fisheries Research InstituteChinese Academy of Fishery Sciences Function laboratory for marine fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology

Exopalaemon carinicauda is one of the important economic shrimp species in China, and can tolerate a wide range of salinities. However, its disease resistance remains to be unclear in comparison with other shrimp species under salinity stress. In this study, the resistance to white spot syndrome virus(WSSV) of E. carinicauda and Litopenaeus vannamei was determined by comparing their hemocyanin(Hc) and phenoloxidase(PO) activities under different salinity stresses. In E. carinicauda, the PO activity and Hc gene transcript abundance showed a coherent pattern of increase and decrease while Hc content showed a slightly decrease with Vibrio anguillarum and WSSV infections. For both E. carinicauda and L. vannamei under salinity stress, the PO activity showed a positive correlation with the salinity while the Hc content and expression level of its gene increased significantly in salinities of 5, 15 and 25 g L^(-1). The survival rate of E. carinicauda with WSSV infection was higher than that of L. vannamei in the first 24 h under different salinity stresses. Drastic mortality of *** and L. vannamei appeared at 48 h and 3 h post-injection, respectively. Furthermore, compared with L. vannamei, E. carinicauda displayed higher PO activity, Hc content and abundance of Hc gene m RNA. The results collectively indicated that Hc and PO have obviously functional connection in resisting pathogens and tolerating salinity stress, and PO activity and Hc gene m RNA abundance may reflect the resistance of shrimp to disease. E. carinicauda has higher level of immune potential than L. vannamei, suggesting its greater capacity in resisting pathogens under salinity stresses.

关键词： Exopalaemon carinicauda Litopenaeus vannamei hemocyanin phenoloxidase activity WSSV salinity stress

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The Roles of Heat Shock Proteins 70 and 90 in Exopalaemon carinicauda After WSSV and Vibrio anguillarum Challenges

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Journal of Ocean University of China 2018年第2期17卷 399-406页

作者： LI Jitao LI Jian DUAN Yafei CHEN Ping LIU Ping key laboratory of sustainable development of marine fisheries of Ministry of Agriculture Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Function laboratory for marine fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology key laboratory of South China Sea Fishery Resources Exploitation and Utilization Sustainable Development of Marine Fisheries of Ministry of Agriculture South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences

Heat shock proteins(HSPs), such as HSP70 and HSP90, are a suite of highly conserved proteins produced in all cellular organisms when they are exposed to stresses. In aquatic animals, they have been proved to play important roles in response to environmental pollutants and particularly in the non-specific immune responses to pathogen infections. In the present study, the expression profiles of HSP70 and HSP90 genes in hemocytes and hepatopancreas from the ridgetail white prawn Exopalaemon carinicauda infected with WSSV and Vibrio anguillarum were detected using reverse transcription polymerase chain reaction(RT-PCR). After WSSV challenge, the expression level of HSP 70 gene transcripts in the hemocytes and hepatopancreas increased to peak level at 6 h and 48 h, respectively. HSP90 gene transcripts in hemocytes and hepatopancreas were up-regulated significantly at 12 h and 6 h, respectively. During V. anguillarum challenge, the m RNA content of HSP70 gene in hemocytes and hepatopancreas increased significantly at 12 h and 6 h post-infection, respectively. The expression level of HSP90 gene both in hemocytes and hepatopancreas were up-regulated in the first 3 h. The expression patterns of HSP70 and HSP90 genes in hemocytes and hepatopancreas showed temporal and spatial differences after challenged with WSSV and V. anguillarum. The results suggested that HSPs might be involved in immune responses to pathogens challenge in E. carinicauda.

关键词： Exopalaemon carinicauda HSP70 HSP90 expression

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Numerical simulation of the hydrodynamics within octagonal tanks in recirculating aquaculture systems

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Chinese Journal of Oceanology and Limnology 2017年第4期35卷 912-920页

作者：柳瑶刘宝良雷霁霖关长涛黄滨 key laboratory for sustainable development of marine fisheries Ministry of AgricultureYellow Sea Fisheries Research InstituteChinese Academy of Fishery Sciences Shandong Univercity WeihaiMarine College

A three-dimensional numerical model was established to simulate the hydrodynamics within an octagonal tank of a recirculating aquaculture system. The realizable k-e turbulence model was applied to describe the flow, the discrete phase model （DPM） was applied to generate particle trajectories, and the governing equations are solved using the finite volume method. To validate this model, the numerical results were compared with data obtained from a full-scale physical model. The results show that：（1） the realizable k-e model applied for turbulence modeling describes well the flow pattern in octagonal tanks, giving an average relative error of velocities between simulated and measured values of 18% from contour maps of velocity magnitudes; （2） the DPM was applied to obtain particle trajectories and to simulate the rate of particle removal from the tank. The average relative error of the removal rates between simulated and measured values was 11%. The DPM can be used to assess the self-cleaning capability of an octagonal tank; （3） a comprehensive account of the hydrodynamics within an octagonal tank can be assessed from simulations. The velocity distribution was uniform with an average velocity of 15 cm/s; the velocity reached 0.8 m/s near the inlet pipe, which can result in energy losses and cause wall abrasion; the velocity in tank corners was more than 15 cm/s, which suggests good water mixing, and there was no particle sedimentation. The percentage of particle removal for octagonal tanks was 90% with the exception of a little accumulation of 〈5 mm particle in the area between the inlet pipe and the wall. This study demonstrated a consistent numerical model of the hydrodynamics within octagonal tanks that can be further used in their design and optimization as well as promote the wide use of computational fluid dynamics in aquaculture engineering.

关键词： recirculating aquaculture systems octagonal tanks hydrodynamic simulation rate of particle removal

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Karyological analysis of the sea cicada Blepharipoda liberate Shen from the Rizhao intertidal zone, China

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Journal of Oceanology and Limnology 2019年第1期37卷 169-175页

作者： ZHOU Liqing WANG Xuemei WU Biao SUN Xiujun ZHAO Qing ZHANG Gaowei LIU Zhihong YANG Aiguo key laboratory of sustainable development of marine fisheries Ministry of Agriculture Yellow Sea Fisheries Institute Chinese Academy of Fishery Sciences laboratory for marine fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Rizhao Ocean & fisheries Research Institute

Blepharipoda liberate Shen is a commercially valuable seafood species that has important ecological signi?cance in Shandong Province, China. Although B. liberate is crustacean, its external characteristics are not entirely those of shrimps or crabs. The question of whether B. liberate is a shrimp or a crab has been debated in recent years. We studied the karyotype of B. liberate by light microscopy using air-drying and spreading methods. We obtained mitotic chromosomal plates from B. liberate larvae, and from adult B. liberate females subsequent to egg-laying. The results revealed that B. liberate has 53 pairs of chromosomes(i.e., n =53 and 2 n =106), a characteristic shared with four species of crab. The karyogram of B. liberate consists of 25 metacentric, 14 submetacentric, 11 subtelocentric and 3 telocentric pairs. We did not ?nd any heteromorphosis sex chromosomes. Tissue from larvae, gills and ovaries can be used for chromosomal investigations, and we found similar lampbrush chromosomes in ovary cells. Comparatively speaking, larvae tissue is more practical, and ovary tissue is more suitable for the preparation of lampbrush chromosomes. B. liberate is more closely related to crabs than to shrimps, based on the numbers of chromosomes. The B. liberate karyotype reported here provides a basis for further comparative cytogenetic studies of species populations.

关键词： Blepharipoda liberate chromosome karyotype lampbrush chromosome

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Effect of an escape vent in accordion-shaped traps on the catch and size of Asian paddle crabs Charybdis japonica in an artificial reef area

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Chinese Journal of Oceanology and Limnology 2016年第6期34卷 1238-1246页

作者：张鹏李超李文涛张秀梅 College of fisheries Ocean University of China key laboratory of sustainable development of marine fisheries Ministry of Agriculture Shandong Provincial key laboratory of Fishery Resources and Eco- Environment Yellow Sea Fisheries Research InstituteChinese Academy of Fishery Sciences laboratory for marine fisheries and Aquaculture Qingdao National Laboratory for Marine Science and Technology

Accordion-shaped traps are widely used in China to catch the Asian paddle crab C harybdis japonica but traps of conventional design often catch juvenile crabs. A new type of accordion-shaped trap with an escape vent(L×W=4.3 cm×3.0 cm) was designed and a comparative study between the newly designed and conventional traps was performed in the artifi cial reef area of Zhuwang, Laizhou Bay, China from June to August 2012. The mean catch per unit effort(CPUE) of undersized crabs was signifi cantly lower in the vented traps than in the conventional traps(paired t-test, n =30, P development of more sustainable and effi cient crab fi shing methods using accordion-shaped traps.

关键词： Charybdis japonica accordion-shaped trap escape vent selectivity artificial reef area

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