Changwei Shao

Chinese Academy of Fishery Sciences

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Songlin Chen

Chinese Academy of Fishery Sciences

Qian Wang

Central China Normal University

Xiaolin Liao

Hunan University of Traditional Chinese Medicine

Wenteng Xu

Qingdao National Laboratory for Marine Science and Technology

Yongsheng Tian

Chinese Academy of Fishery Sciences

Zhongdian Dong

Guangdong Ocean University

Kaiqiang Liu

Chinese Academy of Fishery Sciences

Yangzhen Li

Chinese Academy of Fishery Sciences

Shuo Li

China Pharmaceutical University

Ying Zhu

Southwest Minzu University

Cooperative Institutions

Chinese Academy of Fishery Sciences

208

Ministry of Agriculture and Rural Affairs

126

Chinese Academy of Sciences

126

Qingdao National Laboratory for Marine Science and Technology

118

University of Chinese Academy of Sciences

Shanghai Ocean University

Chinese Academy of Agricultural Sciences

BGI Group (China)

Ocean University of China

Zhejiang University

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The First High-Quality Chromosome-Level Genome of the Lutjanus erythropterus (Bloch, 1790) Using Single-Tube Long Fragment Reads and Hi-C Technologies

Genome Biology and Evolution (2023)

Zhuoxin Lai Gyamfua Afriyie Haitao Cui Lujun Chen Zhenmin Xu

Lutjanus erythropterus (Bloch, 1790), a Perciformes from the Lutjanidae family, is a commercially important species because of its taste and abundance. Despite the increase in genome resources in recent years, few genome assemblies are available within this fish family for comparative and functional studies. In this study, we determined the chromosomal genome of Crimson snapper using high-throughput Single-Tube Long Fragment Reads sequencing technology and Hi-C data. The final assembly size was 973.04 Mb with contig and scaffold N50 values of 1.51 and 40.65 Mb, respectively. We successfully scaffolded 95.84% of the genome sequence onto 24 chromosomes ranging in length from 19.37 to 49.48 Mb. A total of 22,663 genes and 13,877 gene families were identified in the genome, with 29 gene families being L. erythropterus-specific. A phylogenetic analysis using single-copy gene families showed that L. erythropterus and Larimichthys crocea had the closest genetic relationship with a divergence time of ∼47.7 Ma. This new genomic resource will facilitate comparative genomic studies as well as genetic breeding programs for L. erythropterus.

Microchromosome

10.1093/gbe/evad171

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Citations (2)

Draft genomes of female and male turbot (Scophthalmus maximus)

Figshare (2019)

Hao Xu Xiwen Xu Songlin Chen Changwei Shao

Turbot (Scophthalmus maximus) is a commercially important species and is among the most produced flatfish in aquaculture. It has a drastic sexual dimorphism where females are larger. We sequenced and de novo assembled female and male genomes in the present study. Female_evm.gff3 is the annotation gff3 file of the female turbot’s assembled genome. turbot_Orthogroups.tsv is a list of the gene families generated in your analysis. turbot_TE.denovo.gff and turbot_TE.homo.gffare the repeat annotations. turbot_alignment.fasta is the alignment used for the phylogenetic analysis. turbot_phylogenetic.treefile is an output of phylogenetic tree.

Scophthalmus

10.6084/m9.figshare.8943176

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Citations (0)

A patched1 gene homologue participates in female differentiation of Cynoglossus semilaevis

Gene Expression Patterns (2022)

Qi Qian Zhongdian Dong Ning Zhang Changwei Shao Wenteng Xu

Patched

Sexual Differentiation

10.1016/j.gep.2022.119265

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Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection

Fish & Shellfish Immunology (2014)

Xiang Zhang Shaolin Wang Songlin Chen Yadong Chen Yang Liu

Vibrio anguillarum

Candidate gene

10.1016/j.fsi.2014.11.018

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Citations (115)

Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals (Octocorallia: Alcyonacea): Insights into slow evolution and adaptation to extreme deep-sea environments

动物学研究 (2023)

Zhan-Fei Wei Kaiwen Ta Nannan Zhang Shanshan Liu Liang Meng

A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1 633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea (SCS). Based on mitochondrial genomic characteristics, morphological examination, and sclerite scanning electron microscopy, the samples were categorized into four suborders (Calcaxonia, Holaxonia, Scleraxonia, and Stolonifera), and identified as 9 possible new cold-water coral species. Assessments of GC-skew dissimilarity, phylogenetic distance, and average nucleotide identity (ANI) revealed a slow evolutionary rate for the octocoral mitochondrial sequences. The nonsynonymous (

Octocorallia

10.24272/j.issn.2095-8137.2023.039

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Citations (8)

Isolation and characterization of polymorphic microsatellite loci from black snapper Sebastodes fuscescens (Houttuyn)

Conservation Genetics (2009)

Jing-Feng Yang Lili Zhao Changwei Shao Xiang Shan Ji Xiaolin Liao

Linkage Disequilibrium

10.1007/s10592-008-9788-6

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Citations (1)

Temporal Transcriptome Analysis Reveals Dynamic Expression Profiles of Gametes and Embryonic Development in Japanese Flounder (Paralichthys olivaceus)

Genes (2021)

Xiancai Hao Qian Wang Jilun Hou Kaiqiang Liu Bo Feng

The maternal-to-zygotic transition (MZT) is a crucial event in embryo development. While the features of the MZT across species are shared, the stage of this transition is different among species. We characterized MZT in a flatfish species, Japanese flounder (Paralichthys olivaceus). In this study, we analyzed the 551.57 GB transcriptome data of two types of gametes (sperms and eggs) and 10 embryo developmental stages in Japanese flounder. We identified 2512 maternal factor-related genes and found that most of those maternal factor-related genes expression decreased at the low blastula (LB) stage and remained silent in the subsequent embryonic development period. Meanwhile, we verified that the zygotic genome transcription might occur at the 128-cell stage and large-scale transcription began at the LB stage, which indicates the LB stage is the major wave zygotic genome activation (ZGA) occurs. In addition, we indicated that the Wnt signaling pathway, playing a diverse role in embryonic development, was involved in the ZGA and the axis formation. The results reported the list of the maternal genes in Japanese flounder and defined the stage of MZT, contributing to the understanding of the details of MZT during Japanese flounder embryonic development.

Paralichthys

Olive flounder

Blastula

10.3390/genes12101561

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Citations (4)

Isolation and characterization of polymorphic microsatellite DNA markers in the rock bream (Oplegnathus fasciatus)

Conservation Genetics (2008)

Tianjun Xu Changwei Shao Xiaolin Liao Xiang Shan Ji Songlin Chen

Linkage Disequilibrium

genomic DNA

10.1007/s10592-008-9557-6