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| 1 | A chromosome-level genome assembly of the blackspotted croaker(Protonibea diacanthus)显示文摘The blackspotted croaker(Protonibea diacanthus)is an endangered coastal marine fish.It is also a valuable species that is cultured on the southeast coast of China.While some genetic studies have been conducted to protect this species,genomic resources are lacking.Here,we report a chromosome-scale assembly of P.diacanthus genome by high-depth genome sequencing,assembly,and annotation.The genome scale was 635.69 Mb with contig and scaffold N50 length of 3.33 Mb and 25.60 Mb,respectively.Hi-C scaffolding of the genome resulted in 24 chromosomes of 94.15%total genome.We predicted 23,971 protein-coding genes.In addition,we constructed a phylogenetic tree using 2755 single-copy gene families and identified 462 unique gene families in P.diacanthus genome compared to three other sciaenids.What’s more,from the analysis of gene families,we found that several gene families related to innate immunity were significantly expanded in the blackspotted croaker genome compared to other teleost genomes.The high-quality genome can improve our understanding of the molecular mechanisms behind economically valuable traits and provide insights into characteristics of the immune system. | Tianjun Xu Ye Li Weiwei Zheng Yuena Sun | 2022 | Aquaculture and Fisheries2022，7，6： | 1 |
| 2 | Long noncoding RNA TARL promotes antibacterial activity and prevents bacterial escape in Miichthys miiuy through suppression of TAK1 downregulation显示文摘Noncoding RNA(ncRNA)is an important regulatory factor that plays a major role in innate immunity.However,most studies on ncRNA have focused on mammals,resulting in a knowledge gap on nc RNA in lower vertebrates such as teleost fish.In this study,we identified a new long noncoding RNA(lncRNA),termed TAK1-related lnc RNA(TARL),which can play a positive role in the antibacterial immunity of Miichthys miiuy to Vibrio anguillarum and V.harveyi.We also found a novel micro RNA miR-2188-3p that could target TAK1 and inhibit the host antibacterial response and promote bacterial escape.We further found that the antibacterial effect inhibited by miR-2188-3p could be reversed with TARL.Moreover,V.anguillarum and V.harveyi are the two most susceptible Gram-negative pathogens of aquaculture fish,and the economic losses caused by these two bacteria are immeasurable every year.This study is the first to report on the ability of lnc RNA to prevent the escape of V.anguillarum and V.harveyi in fish through the competing endogenous RNA(ceRNA)mechanism.Our results not only elucidate the ce RNA mechanism of the lncRNA in antibacterial immune responses but also provide new insights into the impact of lnc RNA on host immunity and bacterial escape. | Weiwei Zheng Xing Lv Shiying Xin Yuena Sun Tianjun Xu | 2023 | Science China(Life Sciences)2023，66，6： | 0 |
| 3 | A chromosome-level genome assembly of the miiuy croaker(Miichthys miiuy)using nanopore sequencing and Hi-C显示文摘Miiuy croaker,Miichthys miiuy is an ecologically important teleost species which is widely distributed in southeast coast of China.In this study,we present a chromosomal-scale genome assembly of the miiuy croaker which is an important Sciaenidae fish and economical species.We adopted Oxford Nanopore and Hi-C sequencing techniques to achieve an assembly with high accuracy and completeness.The investigation of genome characteristic and functional features may provide insights into the study of phylogenetic diversity of miiuy croaker.This study can also be beneficial to improve molecular assisted breeding techniques.Moreover,it can be a great resource to better conduct further study of other sciaenids. | Tianjun Xu Ye Li Weiwei Zheng Yuena Sun | 2024 | Aquaculture and Fisheries2024，9，2： | 0 |
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