Xiao-Wen Sun

Chinese Academy of Fishery Sciences, 北江, Zhejiang Sheng, China

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Publications (59)69.73 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Abstract Ili marinka (Schizothorax pseudoaksaiensis) belongs to the family Cyprinidae, which is found only in Ili River in the Xinjiang Uygur Autonomous Region. In this study, we reported the complete sequence of mitochondrial genome of S. pseudoaksaiensis. The genome is 16,586 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and the non-coding control regions (D-loop). The complete mitochondrial genome base composition is 29.80% for A, 17.85% for G, 25.31% for T, and 27.04% for C, with a slight A+T bias of 55.11%. The mitochondrial genome can contribute to the studies on genetic diversity and conservation of S. pseudoaksaiensis.
    Mitochondrial DNA 09/2014; · 1.71 Impact Factor
  • Li-Na Peng, Jian-Guo Lu, Xiao-Wen Sun
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    ABSTRACT: Lampetra morri belongs to the Petromyzontidae family. It is one of the most important freshwater aquaculture species in China. In this study, the complete sequence of mitochondrial genome of L. morri was 16,451 base pair, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 repeat regions. The percentage of G + C content was 39.33%. This is the first time of the mitochondrial genome of L. morri being sequenced, and it provides insights into the evolution of Cyclostomata mitochondrial genomes, particular in Lampetra family.
    Mitochondrial DNA 08/2014; · 1.71 Impact Factor
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    ABSTRACT: Two distinct myoglobin (mb) transcripts have been reported in common carp, Cyprinus carpio, which is a hypoxia-tolerant fish living in habitats with greatly fluctuant dissolved oxygen levels. Recombinant protein analysis has shown functional specialization of the two mb transcripts. In this work, analysis for mb-containing bacterial artificial chromosome (BAC) clones indicated different genome loci for common carp myoglobin-1 (mb-1) and myoglobin-2 (mb-2) genes. Fluorescence in situ hybridization (FISH) revealed that mb-1 and mb-2 located on separate chromosomes. In both of the mb-1 and mb-2 containing BAC clones, gene synteny was well conserved with the homologous region on zebrafish chromosome 1, supporting that the common carp specific mb-2 gene originated from the recent whole genome duplication event in cyprinid lineage. Transcription factor binding sites search indicated that both common carp mb genes lacked specificity Protein 1 (Sp1) and myocyte enhancer factor-2 (MEF2) binding sites, which mediated muscle-specific and calcium-dependent expression in the well-studied mb promoters. Potential hypoxia response elements (HRE) were predicted in the regulatory region of common carp mb genes. These characteristics of common carp mb gene regulatory region well interpreted the hypoxia-inducible, non-muscle expression pattern of mb-1. In the case of mb-2, a 10bp insertion to the binding site of upstream stimulatory factor (USF), which was a co-factor of hypoxia inducible factor (HIF), might cause the non-response to hypoxia treatment of mb-2. The case of common carp mb gene duplication and subsequent differentiation in expression pattern and protein function provided an example for adaptive evolution toward aquatic hypoxia tolerance.
    Gene 07/2014; · 2.20 Impact Factor
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    ABSTRACT: Semen was treated with ultraviolet irradiation to genetically inactivate the sperm. Gynogenetic haploidy was induced artificially in the German mirror carp, Cyprinus carpio L. A systematic study of the status of early embryonic development, the number of chromosomes, chromosomal banding patterns and fluorescent in situ hybridization (FISH), and a microsatellite analysis were performed. The fertility, hatchability, and survival rates of the gynogenetic group were significantly lower than those of the normal control fertilization group (P < 0.05). Gynogenetic larval growth was abnormal and the embryos did not survive. The chromosome number of the gynogenetic group was 50, whereas that of the control group was 100. The gynogenetic group had a single silver-staining point, one CMA3/DA/DAPI-positive position, and a single FISH-positive signal, whereas the control group had two silver-staining points, two CMA3/DA/DAPI-staining positions, and two FISH-positive signals. The microsatellite analysis showed that all the genes of the gynogenetic group derived from the female parent and that the females generated a set of haploid (n = 50) gametes during meiosis. Using chromosome manipulation, this study confirms that the German mirror carp has two sets of chromosomes and is an evolutionary tetraploid (2n = 100).
    Aquaculture International 06/2014; · 1.04 Impact Factor
  • Xiang-Fei Kong, Jiong-Tang Li, Xiao-Wen Sun
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    ABSTRACT: Abstract The guppy (Poecilia reticulata), a member of the Poeciliidae family, is one of the most popular aquarium fish. Here, we reported the complete mitochondrial genome of P. reticulata. The genome is 16,570 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The structure of non-coding control region was also analyzed. Comparing the mitochondrial genome of P. reticulata with its congener Xiphophorus maculatus revealed the high sequence similarity and the identical gene structure. The complete mitochondrial genome of the guppy would help study the evolution of Poeciliidae family.
    Mitochondrial DNA 02/2014; · 1.71 Impact Factor
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    ABSTRACT: Abstract The complete mitochondrial genome of Hemiculter leucisculus was determined to be 16,617 bp. It contains the structure of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and non-coding control region (D-loop). The critical central conserved sequences (CSB-D, CSB-E, and CSB-F) were also detected. The determination of H. leucisculus mitogenome would play an important role in genetic diversity and population vitality in Cyprinidae.
    Mitochondrial DNA 01/2014; · 1.71 Impact Factor
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    ABSTRACT: Abstract The mitochondrial genome was amplified in two large overlapping fragments by long PCR and one gap PCR. The complete Northeastern China burbot mitogenome sequence (KC844053) is 16,575 bp in length. Similar to most vertebrata, the mitogenome has a set of 37 genes: including 13 protein-coding, 22 tRNA and 2 rRNA genes. More than 98% nucleotide sequence was simil to the reported individual.
    Mitochondrial DNA 01/2014; · 1.71 Impact Factor
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    ABSTRACT: Abstract The complete mitochondrial genome of Gnathopogon argentatus was determined to be 16,607 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. The complete mitochondrial genome of G. argentatus is 16,607 bp in length with 56.02% AT content, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The complete mitochondrial genome of G. argentatus was obtained for the first time and would play an important role in population structure and conservation genetic studies.
    Mitochondrial DNA 01/2014; · 1.71 Impact Factor
  • Ru Xu, Zi-Xia Zhao, Yan Zhang, Peng Xu, Xiao-Wen Sun
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    ABSTRACT: Abstract In this study, we sequenced and determined the complete mitochondrial genome of rosy barb (Puntius conchonius). The circular mitochondrial genome (17,082 bp) consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. This is the first report on the complete mitogenome sequence of rosy barb (P. conchonius).
    Mitochondrial DNA 01/2014; · 1.71 Impact Factor
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    ABSTRACT: Abstract Amur whitefin gudgeon (Romanogobio tenuicorpus) belongs to the family Cyprinidae, it is freshwater aquaculture species in China. In the report, we determined the complete mitochondrial genome sequence of Romanogobio tenuicorpus, which is 16,600 bp long circular molecule with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, the conserved sequence blocks, CSB1, CSB2 and CSB3 were also detected.
    Mitochondrial DNA 01/2014; · 1.71 Impact Factor
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    ABSTRACT: Abstract The kissing gourami (Helostoma temminkii) belongs to the Labyrinth fishes (Perciformes: Anabantoidei), which exhibits a wide variety of behavioral traits. In this study the complete mitogenome of H. temminkii was determined to be 16,740 bp in length. It contains 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The sequence structure of non-coding control region was also analyzed. Comparing the mitochondrial genome of H. temminkii with its closely related species Colisa lalia showed the similarity of 78%. The complete mitochondrial genome of H. temminkii provides resource for phylogenetic analysis on Anabantoidei.
    Mitochondrial DNA 01/2014; · 1.71 Impact Factor
  • Ru Xu, Zi-Xia Zhao, Peng Xu, Xiao-Wen Sun
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    ABSTRACT: Abstract We first sequenced the complete mitochondrial genome of silvertip tetra (Hasemania nana). The mitogenome was determined to be 16,581 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. All genes were encoded on the heavy strand with the exception of ND6 and eight tRNA genes. Mitochondrial DNA information provided the basis for the studies in species identification and conservation of the species' natural resources.
    Mitochondrial DNA 01/2014; · 1.71 Impact Factor
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    ABSTRACT: The strategies by which freshwater teleosts maintain acid-base homeostasis under alkaline stress are attractive and have been explored for a long time. In this study, a cyprinid fish that tolerates extremely alkaline environments (pH 9.6), Leuciscus waleckii, was used as a model to explore the molecular mechanisms of acid-base regulation. Using a lab-controlled alkaline challenge test and 454 sequencing, the transcriptomes of their gills and kidney were profiled and compared. mRNA profiling produced 1 826 022 reads, generated 30 606 contigs with an average length of 1022 bp, of which 19 196 were annotated successfully. Comparative analysis of the expression profiles between alkaline and freshwater L. waleckii habitats revealed approximately 4647 and 7184 genes that were differentially expressed (p < 0.05) in gills and kidney, respectively, of which 2398 and 5127 had more than twofold changes in expression. Gene ontology analysis and KEGG enrichment analysis were conducted. Comprehensive analysis found that genes involved in ion transportation, ammonia transportation, and arachidonic acid metabolism pathways changed dramatically and played important roles in acid-base homeostasis in fish under alkaline stress. These results support the existing hypotheses about candidate genes involved in acid-base regulation under alkaline stress and prompt several new hypotheses. The large transcriptome dataset collected in this study is a useful resource for the exploration of homeostasis modulation in other fish species.
    Molecular BioSystems 01/2014; · 3.35 Impact Factor
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    ABSTRACT: Twenty-five polymorphic microsatellite markers were developed in Amur sturgeon (Acipenser schrenckii. In a survey population, these markers yielded a total of 168 alleles with the number of alleles per locus ranged from 2 to 18. Average observed heterozygosity of these loci ranged from 0.27 to 1.00. These markers could enrich the available molecular markers for genome mapping and genetic diversity analysis of sturgeons. These loci not only should detect sufficient genetic diversity to allow kinship analysis for broodstock management and stock assessment for delineation of fine-scale population structure, but also will contribute greatly to resource conservation.
    Conservation Genetics Resources 01/2014; · 1.14 Impact Factor
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    ABSTRACT: Yellow catfish (Pelteobagrus fulvidraco) is one of the important economic freshwater fish in Eastern Asia. In recent years, the wild resources were decreased sharply due to overfishing and pollution. It is necessary to conserve the wild stocks for the sustainable use of the species. In this study, 200 microsatellite markers were isolated from yellow catfish genome using Roche 454 pyrosequencing method. Among these markers, 57 exhibited polymorphism in yellow catfish population collected from Songhua River in China. The number of alleles ranged from 2 to 13 and the number of effect alleles ranged from 1.112 to 8.980. The observed heterozygosity (H o) and the expected heterozygosity (H e) varied from 0.106 to 0.957 and from 0.102 to 0.898, respectively. Most loci conformed to Hardy–Weinberg equilibrium with the exclusion of five loci. These polymorphic loci will be valuable for population genetic structure and genetic conservation for the P. fulvidraco.
    Conservation Genetics Resources 01/2014; · 1.14 Impact Factor
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    ABSTRACT: Both sexual reproduction and unisexual reproduction are adaptive strategies for species survival and evolution. Unisexual animals have originated largely by hybridization, which tends to elevate their heterozygosity. However, the extent of genetic diversity resulting from hybridization and the genomic differences that determine the type of reproduction are poorly understood. In Carassius auratus, sexual diploids and unisexual triploids coexist. These two forms are similar morphologically but differ markedly in their modes of reproduction. Investigation of their genomic differences will be useful to study genome diversity and the development of reproductive mode. We generated transcriptomes for the unisexual and sexual populations. Genes were identified using homology searches and an ab initio method. Estimation of the synonymous substitution rate in the orthologous pairs indicated that the hybridization of gibel carp occurred 2.2 million years ago. Microsatellite genotyping in each individual from the gibel carp population indicated that most gibel carp genes were not tri-allelic. Molecular function and pathway comparisons suggested few gene expansions between them, except for the progesterone-mediated oocyte maturation pathway, which is enriched in gibel carp. Differential expression analysis identified highly expressed genes in gibel carp. The transcriptomes provide information on genetic diversity and genomic differences, which should assist future studies in functional genomics.
    International Journal of Molecular Sciences 01/2014; 15(6):9386-406. · 2.46 Impact Factor
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    ABSTRACT: Abstract The complete mitochondrial genome of sterlet (Acipenser ruthenus) was determined in this study. The mitogenome is 16,790 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (the control region and the putative origin of the light strand replication) with a typical vertebrate mitochondrial gene arrangement. The overall base composition of the heavy strand is 30.26% for A, 29.00% for C, 16.23% for G and 24.51% for T, with a slight AT bias of 54.77%.
    Mitochondrial DNA 09/2013; · 1.71 Impact Factor
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    ABSTRACT: Generation of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments. We describe L_RNA_scaffolder, a novel genome scaffolding method that uses long transcriptome reads to order, orient and combine genomic fragments into larger sequences. To demonstrate the accuracy of the method, the zebrafish genome was scaffolded. With expanded human transcriptome data, the N50 of human genome was doubled and L_RNA_scaffolder out-performed most scaffolding results by existing scaffolders which employ mate-pair libraries. In these two examples, the transcript coverage was almost complete, especially for long transcripts. We applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased. The simplicity and high-throughput of RNA-seq data makes this approach suitable for genome scaffolding. L_RNA_scaffolder is available at http://www.fishbrowser.org/software/L_RNA_scaffolder.
    BMC Genomics 09/2013; 14(1):604. · 4.40 Impact Factor
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    ABSTRACT: In this study, 149 polymorphic markers were screened from 200 microsatellite markers. From a family of mirror carp, which included 107 individuals. All samples were analyzed for body correlation, and intermuscular bone number was tested using the General Linear Model (GLM) single marker regression. Determination of the threshold values by 10,000 permutation tests showed that eight markers had significant correlation (P<0.05), in which HLJ3086, HLJ3642 and HLJ3515 had very significant correlation with intermuscular bone number (P<0.01). In addition, the genotypes of the captured correlative loci were determined by Duncan's test using SPSS17.0 software. Markers were used to screen the protein and nucleotide database in the National Center for Biotechnology Information (NCBI). Blasting results showed that HLJ2891 was highly correlated (92%) with latrophilin-2-like and HLJ3515 was highly correlated (81%) with serine/threonine-protein kinase 32B-like of zebrafish. These functional markers and genotypes may provide an efficient basis for marker-assisted selection of intermuscular bone number in mirror carp.
    Zoological Research 08/2013; 34(4):406-10.
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    ABSTRACT: Abstract Pike perch (Sander canadensis) is a member of the largest order of Osteichthyes, Perciformes, and is an important ecological and economic freshwater species, which distributes in Ili River and Ergis River of Xinjiang Province, China. In this study, we sequenced the whole mitochondrial genome of pike perch, and analyzed the similarity with its related species. The mitochondrial genome of S. canadensis is 16,542 bp in length with 55.05% AT content, contained 13 protein coding genes, 22 tRNA genes, 2 ribosomal genes and an 892 bp non-coding region. In control region, 6 CSBs (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E and CSB-F), one potential TAS and one poly-T region were identified. Comparing all protein-coding genes and whole genome sequence with 4 species of Perciformes (three species of Percidae, Perca flavescens. Percina macrolepida. Etheostoma radiosum and one outgroup Oreochromis sp. red tilapia), ND3 gene has the highest mutation rate, and S. canadensis has higher similarity with Perca flavescens than others. The mitochondrial genomic sequence will help us to study the conservation genetic and evolution of Percidae.
    Mitochondrial DNA 07/2013; · 1.71 Impact Factor

Publication Stats

104 Citations
69.73 Total Impact Points

Institutions

  • 2006–2014
    • Chinese Academy of Fishery Sciences
      • Freshwater Fisheries Research Center
      北江, Zhejiang Sheng, China
  • 2013
    • Northeast Forestry University
      Charbin, Heilongjiang Sheng, China
  • 2011–2013
    • Dalian Ocean University
      Lü-ta-shih, Liaoning, China