Browsing by Author "Li, Lisen"
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- Chromosome-level genome assembly of largemouth bass (Micropterus salmoides) using PacBio and Hi-C technologiesPublication . He, Kuo; Zhao, Liulan; Yuan, Zihao; Canario, Adelino; Liu, Qiao; Chen, Siyi; Guo, Jiazhong; Luo, Wei; Yan, Haoxiao; Zhang, Dongmei; Li, Lisen; Yang, SongThe largemouth bass (Micropterus salmoides) has become a cosmopolitan species due to its widespread introduction as game or domesticated fish. Here a high-quality chromosome-level reference genome of M. salmoides was produced by combining Illumina paired-end sequencing, PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. Ultimately, the genome was assembled into 844.88 Mb with a contig N50 of 15.68 Mb and scaffold N50 length of 35.77 Mb. About 99.9% assembly genome sequences (844.00 Mb) could be anchored to 23 chromosomes, and 98.03% assembly genome sequences could be ordered and directed. The genome contained 38.19% repeat sequences and 2693 noncoding RNAs. A total of 26,370 protein-coding genes from 3415 gene families were predicted, of which 97.69% were functionally annotated. The high-quality genome assembly will be a fundamental resource to study and understand how M. salmoides adapt to novel and changing environments around the world, and also be expected to contribute to the genetic breeding and other research.
- Fish lysozyme gene family evolution and divergent function in early developmentPublication . Li, Lisen; Cardoso, João C. R.; Félix, Rute; Mateus, Ana Patricia; Canario, Adelino; Power, Deborah M.Lysozymes are an ancient group of antimicrobial enzymes of the innate immune system. Here we provide a comparative analysis of the evolution and function of lysozymes during early development in fish, the most speciose vertebrate group. In fishes, lineage and species-specific evolution of both C-type (chicken or conventional) and G-type (goose type) genes occurred. Phylogenetic analysis revealed that the teleost lysozyme G-type members group with the tetrapod homologues but the teleost C-type form three different clusters with the tetrapods. Most of the teleost C-type cluster with tetrapod Lyz but there are some that group with the mammalian Lyzl1/2 and LALBA. This suggests that early in gnathostome evolution these genes already existed and that lyzl1/2 and lalba genes are present in fish and tetrapods. Gene synteny analysis to confirm sequence orthologies failed to identify conserved genome regions between teleosts and other vertebrates lysozyme gene regions suggesting that in the ancestral bony fish genome lyz, lyzl1/2, lalba and lyg precursor genes were transposed to different chromosome regions. The homologue of the mammalian lactalbumin (LALBA) gene was identified for the first time in teleosts and was expressed in skin and during egg and larval development. Lysozyme activity was detected in teleost eggs and varied between species and in the gilthead sea bream lyg and lalba transcript abundance differed in eggs and larvae from different brood stock suggesting differences exist in maternal innate immune protection.
- Functional miR-142a-3p induces apoptosis and macrophage polarization by targeting tnfaip2 and glut3 in grass carp (Ctenopharyngodon idella)Publication . Tao, Lizhu; Pang, Yifan; Wang, Anqi; Li, Lisen; Shen, Yubang; Xu, Xiaoyan; Li, JialeIn the process of microbial invasion, the inflammation reaction is induced to eliminate the pathogen. However, un-controlled or un-resolved inflammation can lead to tissue damage and death of the host. MicroRNAs (miRNAs) are the signaling regulators that prevent the uncontrolled progress of an inflammatory response. Our previous work strongly indicated that miR-142a-3p is related to the immune regulation in grass carp. In the present study, we found that the expression of miR-142a-3p was down-regulated after infection by Aeromonas hydrophila. tnfaip2 and glut3 were confirmed as be the target genes of miR-142a-3p, which were confirmed by expression correlation analysis, gene overexpression, and dual luciferase reporter assay. The miR-142a-3p can reduce cell viability and stimulate cell apoptosis by targeting tnfaip2 and glut3. In addition, miR-142a-3p also regulates macrophage polarization induced by A. hydrophila. Our results suggest that miR-142a-3p has multiple functions in host antibacterial immune response. Our research provides further understanding of the molecular mechanisms between miRNAs and their target genes, and provides a new insights for the development of pro-resolution strategies for the treatment of complex inflammatory diseases in fish.
- The immunome and embryo quality in sea bream and sea bassPublication . Li, Lisen; Power, Deborah; Guerreiro, Liliana I.T. dos AnjosGilthead sea bream (Sparus aurata) and European sea bass (Dicentrarchus labrax) are teleosts belonging to Eupercaria and are the most important aquaculture fish species in the Mediterranean region. These two species are ranked second after the Atlantic salmon (Salmo salar) in production volume and value in the European Union (EU) aquaculture sector. Unpredictable fertilized egg/embryo quality and performance remain a bottleneck that threatens sustainability of sea bream and sea bass aquaculture, impeding the increased productivity of aquaculture that entirely depends on hatchery production. To address this issue, criteria and molecular markers linked to embryo quality that could be used to monitor and manage hatchery production were procured. Comparative molecular approaches using molecular biology, proteomics and transcriptomics were performed to analyze embryo performance and immunity in samples from several European commercial hatcheries. The core achievements were the: a) identification and characterization of lysozyme and complement 5 (C5) gene families and embryo and larval gene expression and enzyme activity from a diversity of hatcheries, b) characterization of the embryo proteome from three Mediterranean fish species [white sea bream (Diplodus sargus), meagre (Argyrosomus regius) and sea bream] 24h before hatch and at hatch and identification of common and species specific molecular patterns linked to biological function and putative quality-related proteins, c) comparative transcriptomics of good and poor quality sea bream embryos from several Mediterranean hatcheries. Qualitylinked transcripts and some elements of the regulatory epitranscriptome (non-coding RNA) were identified as well as the contribution of maternal proteins to embryos. Taken together, the results provide a comprehensive description of the molecular basis of sea bream and sea bass embryo development and reveal that immune-related molecules in fertilized eggs are low abundance. The development (quality)-related candidate markers identified will be of value for management of fish embryos in aquaculture hatcheries.
- Using GFP as a biomarker to visualize the process of bacterial infection in black carp (Mylopharyngodon piceus)Publication . Zhang, Xueshu; Xu, Xiaoyan; Shen, Yubang; Li, Lisen; Wang, Rongquan; Li, JialeAs one of the most critical pathogens, Aeromonas hydrophila (AH) can cause motile aeromonad septicemia (MAS) in freshwater fish. In recent decades, a myriad of studies had been done for bacterial infect fish. However, the mechanism of bacterial infects fish especially freshwater fish was scanty. This study was conducted for investigating the invasion pathway of A. hydrophila in vivo of black carp. We have performed A. hydrophila 4332 transformed with a plasmid encoding the green fluorescent protein (pGFPuv) (AH4332GFPuv) in black carp. The AH4332GFPuv had similar growth properties and virulence as the wild-type strains under the simulated natural condition. In this study, black carp were divided into five groups: IM (challenged via immersion), IBD (increased stocking density), SAW (skin artificially wounded by scalpel), MR (mucus removed from the body surface), and C0 (control group). The number of AH4332GFPuv in gill, liver, spleen, intestine, mid kidney, head kidney, muscle, eye, brain, heart, and blood were examined after 72 h post-infection from all groups. Significantly high bacterial numbers were observed in the gills and intestine. The number of bacteria was significantly higher in IBD group than IM group. In conclusion, the gill, intestines, and injured skin are likely to be the primary infection routes.