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Linkage map construction for large yellow croaker (Larimichthys crocea)

ABSTRACT: Conon structiof Genetic Linkage Maps by RAD sequencing from a Hybrid Family of Large Yellow Croaker (Larimichthys crocea)

PROVIDER: PRJEB48286 | ENA |

REPOSITORIES: ENA

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Linkage map construction for large yellow croaker (Larimichthys crocea)

Project description:Construction of Genetic Linkage Maps by RAD sequencing from a Hybrid Family of Large Yellow Croaker (Larimichthys crocea)

| PRJEB48642 | ENA

Muscle transcriptome analysis of the large yellow croaker under fasting treatment by RNA-seq

Project description:We sequenced mRNA from 2 muscle samples of the large yellow croaker (Larimichthys crocea) taken from normal feeding fish and fasting stress treatment fish, respectively, to investigate the transcriptome and comparative expression profiles of the large yellow croaker muscle undergoing fasting.

2015-09-22 | GSE73291 | GEO

Comparative Transcriptome Analysis Reveals immunoregulation mechanism of lncRNA-mRNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection

Project description:Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually. The pathogenesis for cryptocaryonosis has been researched by a series of transcriptome studies under different infection conditions. However, little is known about the roles of tissue-specifically expressed genes during the infection of C. irritans. In this study, we analyzed the tissue-specific expression of transcripts in the major infection organs including gill and skin of L. crocea after C. irritans infection. we constructed transcriptome expression profiles of L. crocea gill and skin, including 23,172 protein-coding genes and 7,503 long noncoding RNAs (lncRNAs). By comparing transcriptome data from different tissues of L. crocea, we observed tissue specificity of transcripts in gill and skin, including 3,003 protein coding genes and 639 lncRNAs. A total of 212 of the protein coding genes were involved in immune system. Further analysis revealed that the tissue-specific DEGs in gill and skin were mainly involved in HIF-1 signaling pathway and Complement and coagulation cascades, respectively. In addition, 9 non-tissue-specific hub genes, including CCL4, DDIT4, LEP, ect., which are highly associated with C. irritans infection were identified. To our knowledge, this is the first comparative transcriptome analysis of gill and skin after C. irritans infection. Our results are helpful to understand the molecular mechanism of pathogenesis for cryptocaryonosis, espec-tissue specificity of protein-coding genes and lncRNAs involved in immune regulation.

2021-11-28 | GSE174221 | GEO

Muscle transcriptome analysis of the large yellow croaker under fasting treatment by RNA-seq

2015-09-22 | E-GEOD-73291 | biostudies-arrayexpress

Liver transcriptome analysis of the large yellow croaker under fasting or temperature treatment by RNA-seq

2015-08-06 | GSE67756 | GEO

Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea).

Project description:High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs) evenly distributed across the large yellow croaker (Larimichthys crocea) genome were identified using restriction-site associated DNA sequencing (RAD-seq). Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04%) of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.

| S-EPMC4661810 | biostudies-literature

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Project description:Brain transcriptome of Larimichthys crocea (Large yellow croaker) under hypoxia

| PRJNA246784 | ENA

Liver transcriptome analysis of the large yellow croaker under fasting or temperature treatment by RNA-seq

Project description:We sequenced mRNA from 4 liver samples of the large yellow croaker (Larimichthys crocea) taken from thermal stress treatment fish, normal temperature treatment fish, cold stress treatment fish and fasting stress treatment fish, respectively, to investigate the transcriptome and comparative expression profiles of the large yellow croaker liver undergoing thermal stress, cold stress and fasting. Liver mRNA profiles of control group (LB2A), thermal stress group (LC2A), cold stress group (LA2A) and 21-day fasting group (LF1A) were generated by RNA-seq, using Illumina HiSeq 2000.

2015-08-06 | E-GEOD-67756 | biostudies-arrayexpress

Larimichthys crocea

Project description:Larimichthys crocea Epigenomics

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Larimichthys crocea

Project description:Larimichthys crocea Epigenomics

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