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  1. Article ; Online: Daphnia sp. (Branchiopoda: Cladocera) Mitochondrial Genome Gene Rearrangement and Phylogenetic Position Within Branchiopoda.

    Zheng, Sixu / Zhang, Chi / Zhou, Jianshe / Zhang, Shufei / Liu, Yifan / Jin, Xun / Wang, Yunpeng / Liu, Bingjian

    Biochemical genetics

    2023  

    Abstract: In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum ... ...

    Abstract In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum Crustacea, which originated in the Cambrian period of the Paleozoic. The complete mitogenome sequence of Daphnia sp. (Branchiopoda: Cladocera) was sequenced and annotated in this study and deposited in GenBank. The sequence structure of this species was studied by comparing the original sequences with BLAST. In addition, we have also researched the mechanisms of their mitochondrial gene rearrangement by establishing a model. We have used the Bayesian inference [BI] and maximum likelihood [ML] methods to proceed with phylogenetic analysis inference, which generates identical phylogenetic topology that reveals the phylogenetic state of Daphnia. The complete mitogenome of Daphnia sp. shows that it was 15,254 bp in length and included two control regions (CRs) and 37 genes (13 protein-coding genes, 22 tRNAs and two ribosomal RNAs [16S and 12S]). In addition to tRNA-Ser (GCT), other tRNAs have a typical cloverleaf secondary structure. Meanwhile, the mitogenome of Daphnia sp. was clearly rearranged when compared to the mitogenome of typical Daphnia. In a word, we report a newly sequenced mitogenome of Daphnia sp. with a unique rearrangement phenomenon. These results will be helpful for further phylogenetic research and provide a foundation for future studies on the characteristics of the mitochondrial gene arrangement process in Daphnia.
    Language English
    Publishing date 2023-12-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2168-4
    ISSN 1573-4927 ; 0006-2928
    ISSN (online) 1573-4927
    ISSN 0006-2928
    DOI 10.1007/s10528-023-10594-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 578: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: New perspectives on the genetic structure of dotted gizzard shad (

    Peng, Ying / Liu, Yifan / Li, Jiasheng / Zhang, Kun / Jin, Xun / Zheng, Sixu / Wang, Yunpeng / Lü, Zhenming / Liu, Liqin / Gong, Li / Liu, Bingjian

    Marine life science & technology

    2024  Volume 6, Issue 1, Page(s) 50–67

    Abstract: To maintain, develop and rationally utilize marine organisms, understanding their genetic structure and habitat adaptation pattern is necessary. : Supplementary information: The online version contains supplementary material available at 10.1007/ ... ...

    Abstract To maintain, develop and rationally utilize marine organisms, understanding their genetic structure and habitat adaptation pattern is necessary.
    Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00216-2.
    Language English
    Publishing date 2024-02-12
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 3006215-9
    ISSN 2662-1746 ; 2096-6490
    ISSN (online) 2662-1746
    ISSN 2096-6490
    DOI 10.1007/s42995-024-00216-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Comparative Analysis of the Complete Mitochondrial Genomes of Three Sisoridae (Osteichthyes, Siluriformes) and the Phylogenetic Relationships of Sisoridae.

    Wang, Yunpeng / Chen, Shiyi / Liu, Yifan / Zhang, Shufei / Jin, Xun / Zheng, Sixu / Li, Jiasheng / Peng, Ying / Zhang, Kun / Zhang, Chi / Liu, Bingjian

    Biochemical genetics

    2024  

    Abstract: The family Sisoridae is one of the largest and most diverse Asiatic catfish families, with most species occurring in the water systems of the Qinhai-Tibetan Plateau and East Himalayas. At present, the phylogenetic relationship of the Sisoridae is ... ...

    Abstract The family Sisoridae is one of the largest and most diverse Asiatic catfish families, with most species occurring in the water systems of the Qinhai-Tibetan Plateau and East Himalayas. At present, the phylogenetic relationship of the Sisoridae is relatively chaotic. In this study, the mitochondrial genomes (mitogenomes) of three species Creteuchiloglanis kamengensis, Glaridoglanis andersonii, and Exostoma sp. were systematically investigated, the phylogenetic relationships of the family were reconstructed and to determine the phylogenetic position of Exostoma sp. within Sisoridae. The lengths of the mitogenomes' sequences of C. kamengensis, G. andersonii, and Exostoma sp. were 16,589 bp, 16,531 bp, and 16,529 bp, respectively. They all contained one identical control region (D-loop), two ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs) and 22 transfer RNA (tRNA) genes. We applied two approaches, Bayesian Inference (BI) and Maximum Likelihood (ML), to construct phylogenetic trees. Our findings revealed that the topological structure of both ML and BI trees exhibited significant congruence. Specifically, the phylogenetic tree strongly supports the monophyly of Sisorinae and Glyptosternoids and provides new molecular biological data to support the reconstruction of phylogenetic relationships with Sisoridae. This study is of great scientific value for phylogenetic and genetic variation studies of the Sisoridae.
    Language English
    Publishing date 2024-04-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2168-4
    ISSN 1573-4927 ; 0006-2928
    ISSN (online) 1573-4927
    ISSN 0006-2928
    DOI 10.1007/s10528-024-10793-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 578: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Chromosome-level genome assembly and population genomic analysis reveal evolution and local adaptation in common hairfin anchovy (Setipinna tenuifilis).

    Liu, Bingjian / Li, Jiasheng / Peng, Ying / Zhang, Kun / Liu, Qi / Jin, Xun / Zheng, Sixu / Wang, Yunpeng / Gong, Li / Liu, Liqin / Lü, Zhenming / Liu, Yifan

    Molecular ecology

    2023  

    Abstract: Understanding the genetic structure and the factors associated with adaptive diversity has significant implications for the effective management of wild populations under threat from overfishing and climate change. The common hairfin anchovy (Setipinna ... ...

    Abstract Understanding the genetic structure and the factors associated with adaptive diversity has significant implications for the effective management of wild populations under threat from overfishing and climate change. The common hairfin anchovy (Setipinna tenuifilis) is an economically and ecologically important pelagic fish species, spanning a broad latitudinal gradient along marginal seas of the Northwest Pacific. In this study, we constructed the first reference genome of S. tenuifilis using PacBio long reads and high-resolution chromosome conformation capture (Hi-C) technology. The assembled genome was 798.38 Mb with a contig N50 of 1.43 Mb and a scaffold N50 of 32.42 Mb, which were anchored onto 24 pseudochromosomes. A total of 22,019 genes were functionally annotated, which accounted for 95.27% of the predicted protein-coding genes. Chromosomal collinearity analysis revealed chromosome fusion or fission events in Clupeiformes species. Three genetic groups of S. tenuifilis were revealed along the Chinese coast using restriction site-associated DNA sequencing (RADseq). We investigated the influence of four bioclimatic variables as potential drivers of adaptive divergence in S. tenuifilis, suggesting that these environmental variables, especially sea surface temperature, may play important roles as drivers of spatially varying selection for S. tenuifilis. We also identified candidate functional genes underlying adaptive mechanisms and ecological tradeoffs using redundancy analysis (RDA) and BayeScan analysis. In summary, this study sheds light on the evolution and spatial patterns of genetic variation of S. tenuifilis, providing a valuable genomic resource for further biological and genetic studies on this species and other closely related Clupeiformes.
    Language English
    Publishing date 2023-07-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.17067
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea.

    Jin, Xun / Guo, Xingle / Chen, Jian / Li, Jiasheng / Zhang, Shufei / Zheng, Sixu / Wang, Yunpeng / Peng, Ying / Zhang, Kun / Liu, Yifan / Liu, Bingjian

    Genes & genomics

    2022  Volume 45, Issue 3, Page(s) 377–391

    Abstract: Background: In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed.: Objective: The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position ... ...

    Abstract Background: In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed.
    Objective: The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea.
    Methods: The sample of Hemigrapsus sinensis was collected and DNA was extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. DnaSP was used to calculate Ka/Ks.
    Results: This mitochondrial genome shows that it was 15,900 bp and encoded 13 PCGs, 22 tRNA genes, two rRNA genes, and one control region. The genome composition tends to A + T (74.34%) and presents a negative GC-skew (- 0.22) and AT-skew (- 0.03). The PCGs initiation codon was the typical ATN and termination codon was the typical TAN, incomplete T or missing. The ML and BI trees showed that H. sinensis was most closely related to Hemigrapsus and clustered together with the Varunidae. And our phylogenetic trees provide proof that Ocypodoidea and Grapsoidea may be of common origin. Meanwhile, in the phylogenetic tree, parallel mixing of Chiromantes and Orisarma raised doubts over the traditional classification system. Besides, Incomplete Lineage sorting (ILS) was observed in Varunidae. In the subsequent analysis of evolution rate, we found that all of the PCGs (NAD4 was not calculated) had undergone negative selections, indicating the conservation of mitochondrial genes of H. sinensis during the evolution.
    Conclusion: Therefore, researching the complete mitogenome of H. sinensis would be contributing to molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.
    MeSH term(s) Animals ; Phylogeny ; Genome, Mitochondrial ; Brachyura/genetics ; Genes, Mitochondrial ; RNA, Transfer/genetics
    Chemical Substances RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2022-11-08
    Publishing country Korea (South)
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2504587-8
    ISSN 2092-9293 ; 1976-9571
    ISSN (online) 2092-9293
    ISSN 1976-9571
    DOI 10.1007/s13258-022-01319-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Experimental Investigation on the Interaction Forces between Clathrate Hydrate Particles in the Presence of a Water Bridge

    Liu, Chenwei / Chen Litao / Han Guangming / Li Mingzhong / Li Yuxing / Zheng Sixu

    Energy & Fuels. 2017 May 18, v. 31, no. 5

    2017  

    Abstract: The agglomeration of hydrate particles is one of the main causes of hydrate accumulation or bedding in oil and gas pipelines. The unconverted water droplets in the system play a crucial role in hydrate particle agglomeration. In this study, a novel ... ...

    Abstract The agglomeration of hydrate particles is one of the main causes of hydrate accumulation or bedding in oil and gas pipelines. The unconverted water droplets in the system play a crucial role in hydrate particle agglomeration. In this study, a novel technique was developed to directly measure the interaction forces between cyclopentane hydrate particles with a water bridge between them using a micromechanical force apparatus. On the basis of the developed method, the interaction forces at different temperatures and water bridge volumes and the effects of mineral oil were experimentally studied. At a low subcooling level of 1.7 °C, the contact areas and adhesion forces between the hydrate particles and water droplets increased with the increase in the water droplet volume. For the case of a higher subcooling level of 6.2 °C, rapid hydrate formation between the bridging water droplets prevented the hydrate particles from being effectively wetted, resulting in a small contact area. There was no clear relationship between the contact area/adhesion force and the water droplet volume. The hydrates formed on the water bridge could dramatically strengthen the adhesion force, while the addition of mineral oil in cyclopentane could retard the water droplets from converting into hydrates, consequently decreasing the adhesion force. The measured adhesion forces between the hydrate particles and water droplets may provide further insight into the hydrate agglomeration process.
    Keywords adhesion ; droplets ; mineral oil ; pipelines ; temperature
    Language English
    Dates of publication 2017-0518
    Size p. 4981-4988.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1483539-3
    ISSN 1520-5029 ; 0887-0624
    ISSN (online) 1520-5029
    ISSN 0887-0624
    DOI 10.1021%2Facs.energyfuels.7b00364
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: Chromosome-level genome assembly of the dotted gizzard shad (

    Liu, Bing-Jian / Zhang, Kun / Zhang, Shu-Fei / Liu, Yi-Fan / Li, Jia-Sheng / Peng, Ying / Jin, Xun / Wang, Yun-Peng / Zheng, Si-Xu / Gong, Li / Liu, Li-Qin / Lü, Zhen-Ming

    Zoological research

    2021  Volume 43, Issue 2, Page(s) 217–220

    MeSH term(s) Animals ; Chromosomes ; Evolution, Molecular ; Fishes/genetics ; Genome
    Language English
    Publishing date 2021-11-28
    Publishing country China
    Document type Letter
    ISSN 2095-8137
    ISSN 2095-8137
    DOI 10.24272/j.issn.2095-8137.2021.351
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Determination of Diffusion Coefficient for Alkane Solvent–CO2 Mixtures in Heavy Oil with Consideration of Swelling Effect

    Zheng, Sixu / Li Huazhou Andy / Sun Huijuan / Yang Daoyong

    Industrial & Engineering Chemistry Research. 2016 Feb. 17, v. 55, no. 6

    2016  

    Abstract: A generalized methodology has been developed and successfully applied to determine diffusion coefficient of alkane solvent–CO₂–heavy oil systems with consideration of swelling effect. Theoretically, a one-dimensional and one-way mass transfer model ...

    Abstract A generalized methodology has been developed and successfully applied to determine diffusion coefficient of alkane solvent–CO₂–heavy oil systems with consideration of swelling effect. Theoretically, a one-dimensional and one-way mass transfer model incorporating the volume translated Peng–Robinson equation of state (PR EOS) has been developed to describe the mass transfer from alkane solvent–CO₂ mixture to heavy oil, which accounts for the oil swelling effect resulted from gas dissolution. The heavy oil sample has been characterized as three pseudocomponents, while the binary interaction parameter (BIP) correlations are tuned with the experimentally measured saturation pressures. Both apparent diffusion coefficients for gas mixtures and individual diffusion coefficient of each component of a mixture are determined once the discrepancy between the measured and calculated dynamic swelling factors of heavy oil has been minimized. The volume translated PR EOS with the three characterized pseudocomponents and the tuned BIP correlations is able to accurately predict the phase behavior of alkane solvent–CO₂–heavy oil systems. Compared to the apparent diffusion coefficient, better agreements between the measured and calculated dynamic swelling factors have been obtained by use of the individual diffusion coefficients. Addition of C₃H₈ into CO₂ stream is found to not only diffuse faster into heavy oil than CO₂ but also contribute to a larger degree of oil swelling, leading to a faster and enhanced swelling effect of C₃H₈–CO₂–heavy oil system in comparison with the CO₂–heavy oil system.
    Keywords alkanes ; carbon dioxide ; diffusivity ; engineering ; equations ; mass transfer ; models ; oils ; streams
    Language English
    Dates of publication 2016-0217
    Size p. 1533-1549.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1484436-9
    ISSN 1520-5045 ; 0888-5885
    ISSN (online) 1520-5045
    ISSN 0888-5885
    DOI 10.1021%2Facs.iecr.5b03929
    Database NAL-Catalogue (AGRICOLA)

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