Jiong-Tang Li

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

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Publications (15)36.46 Total impact

  • Zi-Xia Zhao · Ding-Chen Cao · Jian Xu · Ru Xu · Jiong-Tang Li · Yan Zhang · Peng Xu · Xiao-Wen Sun
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    ABSTRACT: Common carp is a widely cultivated fish with longer than 2,000 years domestication history, due to its strong environmental adaptabilities, especially hypoxia tolerance. The common carp genome has experienced a very recent whole genome duplication (WGD) event. Among a large number of highly similar duplicated genes, a pair of Ras-associated binding-GTPase 1a (Rab1a) genes were found fast diverging. Four analogous Rab1a genes were identified in the common carp genome. Comparisons of gene structures and sequences indicated Rab1a-1 and Rab1a-2 was a pair of fast diverging duplicates, while Rab1a-3 and Rab1a-4 was a pair of less diverged duplicates. All putative Rab1a proteins shared conserved GTPase domain, which enabled the proteins serve as molecular switches for vesicular trafficking. Rab1a-1 and Rab1a-2 proteins varied in their C-terminal sequences, which were generally considered to encode the membrane localization signals. Differential expression patterns were observed between Rab1a-1 and Rab1a-2 genes. In blood, muscle, spleen, and heart, the mRNA level of Rab1a-1 was higher than that of Rab1a-2. In liver and intestine, the mRNA level of Rab1a-2 was higher. Expression of Rab1a-1 and Rab1a-2 showed distinct hypoxia responses. Under severe hypoxia, Rab1a-1 expression was down-regulated in blood, while Rab1a-2 expression was up-regulated in liver. Compared with the less diverged Rab1a-3/4 gene pair, common carp Rab1a-1/2 gene pair exhibited strong characteristics of sub-functionalization, which might contribute to a sophisticated and efficient Ras-dependent regulating network for the hypoxia-tolerant fish. Copyright © 2015. Published by Elsevier Inc.
    Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 06/2015; 188. DOI:10.1016/j.cbpb.2015.06.007 · 1.90 Impact Factor
  • Gui-Bao Xiao · Jiong-Tang Li · Xiao-Min Li · Xiu-Li Wang · Xiao-Wen Sun
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    ABSTRACT: The penguin tetra (Thayeria boehlkei) is one of the most popular aquarium fish and belongs to the family of Characidae. The composition, phylogeny, and classification of this family are uncertain. Here, the complete mitogenome of T. boehlkei was reported to be 16,524 bp in length. It contains 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. Comparing the mitochondrial genome of T. boehlkei with its congener Astyanax mexicanus revealed high-sequence similarity. The mitochondrial genome of T. boehlkei will contribute to conservation studies and evolution analysis of Characidae family.
    Mitochondrial DNA 02/2015; DOI:10.3109/19401736.2015.1007317 · 1.70 Impact Factor
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    ABSTRACT: Whole genome duplication (WGD) results in extensive genetic redundancy. In plants and yeast, WGD is followed by rapid gene deletions and intense expression differentiation with slow functional divergence. However, the early evolution of the gene differentiation processes is poorly understood in vertebrates because almost all studied WGDs are extremely ancient, and the genomes have returned to a diploid status. Common carp had a very recent fourth round of WGD dated to 8 million years ago. It therefore constitutes an ideal model to study early-stage functional divergence and expression differentiation in vertebrates. We identified 1,757 pairs of recently duplicated genes (RDGs) originating from this specific WGD and found that most ancestral genes were retained in duplicate. Most RDGs were conserved and under selective pressure. Gene expression analysis across six tissues revealed that 92.5% of RDG pairs were co-expressed in at least one tissue and that the expression of nearly half pairs ceased to be strongly correlated, indicating slow spatial divergence but rapid expression dissociation. Functional comparison revealed that 25% of pairs had functional divergence, of which neo- and sub-functionalization were the main outcomes. Our analysis revealed slow gene loss but rapid and intense expression and function differentiation after WGD.
    Scientific Reports 02/2015; 5:8199. DOI:10.1038/srep08199 · 5.58 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; 548(2). DOI:10.1016/j.gene.2014.07.034 · 2.08 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 06/2014; 15(6):9386-406. DOI:10.3390/ijms15069386 · 2.86 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; DOI:10.3109/19401736.2014.880902 · 1.70 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; DOI:10.3109/19401736.2013.861451 · 1.70 Impact Factor
  • Chao Li · Lei Cheng · Jiong-Tang Li · Cui-Yun Lu · Yany Wang · Xiao-Wen Sun
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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; 26(2). DOI:10.3109/19401736.2013.823188 · 1.70 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. DOI:10.1186/1471-2164-14-604 · 4.04 Impact Factor
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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; 26(1). DOI:10.3109/19401736.2013.809428 · 1.70 Impact Factor
  • Chao Li · Cui-Yun Lu · Jiong-Tang Li · Lei Cheng · Xian-Hu Zheng · Xiao-Wen Sun
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    ABSTRACT: Abstract The complete mitochondrial genome of Amur sturgeon (Acipenser schrenckii) was determined in this study. The mitogenome is 16,684 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 30.07% for A, 29.36% for C, 16.44% for G and 24.13% for T, with a slight AT bias of 54.20%.
    Mitochondrial DNA 06/2013; 25(4). DOI:10.3109/19401736.2013.800507 · 1.70 Impact Factor
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    ABSTRACT: Chinese sleeper (Perccottus glenii) belongs to the largest vertebrate order, Perciformes. In this study, the complete mitochondrial genome of P. glenii was determined to be 16,487 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. We also analysed the sequence structure of non-coding control region. Comparing the mitochondrial genome of P. glenii with its congener Rhyacichthys aspro showed sequence similarity and the identical gene arrangement. The complete mitochondrial genome of Chinese sleeper provides the basis for the studies in Perciformes evolution and conservation.
    Mitochondrial DNA 01/2013; 24(4). DOI:10.3109/19401736.2012.760081 · 1.70 Impact Factor
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    ABSTRACT: MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRNA regulation as well as to alter miRNA biogenesis. SNPs are often associated with diseases or traits. To date, no studies into the effects of SNPs on miRNA biogenesis and regulation in the common carp have been reported. Using homology-based prediction combined with small RNA sequencing, we have identified 113 common carp mature miRNAs, including 92 conserved miRNAs and 21 common carp specific miRNAs. The conserved miRNAs had significantly higher expression levels than the specific miRNAs. The miRNAs were clustered into three phylogenetic groups. Totally 394 potential miRNA binding sites in 206 target mRNAs were predicted for 83 miRNAs. We identified 13 SNPs in the miRNA precursors. Among them, nine SNPs had the potential to either increase or decrease the energy of the predicted secondary structures of the precursors. Further, two SNPs in the 3' untranslated regions of target genes were predicted to either disturb or create miRNA-target interactions. The common carp miRNAs and their target genes reported here will help further our understanding of the role of miRNAs in gene regulation. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The resource data generated in this study will help advance the study of miRNA function and phenotype-associated miRNA identification.
    BMC Genomics 08/2012; 13:413. DOI:10.1186/1471-2164-13-413 · 4.04 Impact Factor
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    Jin-Tu Wang · Jiong-Tang Li · Xiao-Feng Zhang · Xiao-Wen Sun
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    ABSTRACT: Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event. We have sequenced the transcriptome of common carp using 454 pyrosequencing. After assembling the 454 contigs and the published common carp sequences together, we obtained 49,669 contigs and identified genes using homology searches and an ab initio method. We identified 4,651 orthologous pairs between common carp and zebrafish and found 129,984 paralogous pairs within the common carp. An estimation of the synonymous substitution rate in the orthologous pairs indicated that common carp and zebrafish diverged 120 million years ago (MYA). We identified one round of genome duplication in common carp and estimated that it had occurred 5.6 to 11.3 MYA. In zebrafish, no genome duplication event after speciation was observed, suggesting that, compared to zebrafish, common carp had undergone an additional genome duplication event. We annotated the common carp contigs with Gene Ontology terms and KEGG pathways. Compared with zebrafish gene annotations, we found that a set of biological processes and pathways were enriched in common carp. The assembled contigs helped us to estimate the time of the fourth-round of genome duplication in common carp. The resource that we have built as part of this study will help advance functional genomics and genome annotation studies in the future.
    BMC Genomics 03/2012; 13:96. DOI:10.1186/1471-2164-13-96 · 4.04 Impact Factor
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    ABSTRACT: Common carp is one of the most important aquaculture species in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. Common carp is tetroploid teleost fish with an estimated haploid genome size of about 1700 Mbp and 2n = 100 chromosomes. Although molecular genetics study of common carp had been conducted productively in China for breeding and genetic improvement purpose, genomic resources of the common carp are still relatively underdeveloped until the Common Carp Genome Project (CCGP) was initiated on December 2009. The project aims at building the necessary tools and resources, identifying commercial important genes or traits and boosting the aquaculture industry of common carp. Besides, CCGP will also provide valuable genome data for the study of vertebrate genome evolution and phylogeny as common carp may involve an additional 4th Round of Whole Genome Duplication. CCGP currently includes following tasks: whole genome shotgun deep sequencing and draft assembly employing the next generation sequencing technology, BAC library construction and genome-wide BAC-end sequencing, BAC-based physical mapping, genome-wide marker development and high-density linkage mapping, FISH-based chromosome mapping, transcriptome deep sequencing and genome annotation, functional genomics, bioinformatics and database construction. To date, whole genome sequencing had been completed using multiple platforms including Roche 454, Illumina, SOLiD and traditional Sanger method with various library insertion lengths, generating 175 folds of common carp genome equivalence. The assembled genome has scaffold N50 length of 1.14 Mb and contig N50 length of 31 .1 kb, covering 1710 Mb of common carp. Transcriptome sequences had been collected from both Roche 454 and Illumina HiSeq 2000 platforms. Genome annotation was performed based on transcriptome homology and de novo prediction methods. A total of 31404 genes was annotated in the genome with average length 1917 bp. The fingerprint from over 90,000 BACs of 7x genome equivalence had been collected and the first BAC-based physical map of common carp was constructed, containing 3696 BAC contigs with the N50 length of 688 kb. Over 800,000 SNPs and 13,000 microsatellite loci had been identified from common carp cDNA and BAC-end sequences for high density linkage mapping and map integration. The high-density linkage map of common carp had been constructed with approximate 6000 markers, including around 5000 SNP markers and 1000 SSR markers. The completion of CCGP will lead to better management of breeding selection, disease prevention and transgenic study on the common carp, as well as the other Cyprinidae species.
    International Plant and Animal Genome Conference XX 2012;