Liver transcriptome sequencing and de novo annotation of the large yellow croaker ( Larimichthy crocea ) under heat and cold stress

Qian, Baoying; Xue, Liyan

doi:10.1016/j.margen.2015.12.001

Cited by 106 publications

(49 citation statements)

References 24 publications

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“…Despite the lack of biological replicates in the transcriptome data [19], the expression results are still an indication. The pooling sample strategy in thermal treatments could have eliminated individual variation.…”

Section: Discussionmentioning

confidence: 99%

“…There is still no genome-wide characterization of the hsp70 gene family in the large yellow croaker to date. The large yellow croaker genomic resources and transcriptome sequences have been well developed in recent years [13,19]. These resources have made it feasible to conduct a systematic analysis of the genes of interest in the large yellow croaker genome.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification of Hsp70 Genes in the Large Yellow Croaker (Larimichthys crocea) and Their Regulated Expression Under Cold and Heat Stress

Han

2018

Genes

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Heat shock proteins 70 (Hsp70) are required for key cellular processes and responses to environmental changes, however, there are an unknown number of hsp70 gene family members in the large yellow croaker (Larimichthys crocea). In the present study, 17 hsp70 genes were identified through the genome of the large yellow croaker. These genes are divided into seven evolutionarily distinct groups according to a phylogenetic tree. The orthologs of these hsp70 genes were found in humans and zebrafish. The expression patterns of the hsp70 gene family in the large yellow croaker under cold and heat stress were studied by examining transcriptome data. Six out of 17 genes were significantly unregulated or downregulated after cold or heat stress. There were two genes significantly upregulated and two genes downregulated in the liver after cold treatment, while after heat treatment, five genes were significantly upregulated, and no genes were significantly downregulated. Three expression patterns were detected: strictly heat-inducible hsp70, constitutively expressed and moderately heat-inducible hsp70, and constitutively expressed and less stress-dependent hsp70 genes. All the findings will contribute to a better understanding of the biological function of hsp70s in defending against thermal challenges.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of Hsp70 Genes in the Large Yellow Croaker (Larimichthys crocea) and Their Regulated Expression Under Cold and Heat Stress

Han

2018

Genes

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“…In addition to its economic value, L. crocea is a unique model species with some peculiar traits: it produces loud sounds, has a well-developed olfactory system, and is sensitive to various environmental stressors, such as hypoxia and chemical pollution 2 . The transcriptomic and proteomic responses of L. crocea to various stimuli, including pathogens, hypoxia, and high temperature have been investigated extensively to determine the specific defense mechanisms it uses to handle physiological responses 3 – 9 . The whole genome of L. crocea was previously sequenced with Ilumina HiSeq 2000 system 2 , 10 .…”

Section: Introductionmentioning

confidence: 99%

An improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function

Huo

Guan

et al. 2018

Commun Biol

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Larimichthys crocea (large yellow croaker) is a type of perciform fish well known for its peculiar physiological properties and economic value. Here, we constructed an improved version of the L. crocea genome assembly, which contained 26,100 protein-coding genes. Twenty-four pseudo-chromosomes of L. crocea were also reconstructed, comprising 90% of the genome assembly. This improved assembly revealed several expansions in gene families associated with olfactory detection, detoxification, and innate immunity. Specifically, six hepcidin genes (LcHamps) were identified in L. crocea, possibly resulting from lineage-specific gene duplication. All LcHamps possessed similar genomic structures and functional domains, but varied substantially with respect to expression pattern, transcriptional regulation, and biological function. LcHamp1 was associated specifically with iron metabolism, while LcHamp2s were functionally diverse, involving in antibacterial activity, antiviral activity, and regulation of intracellular iron metabolism. This functional diversity among gene copies may have allowed L. crocea to adapt to diverse environmental conditions.

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“…For instance, the transcriptional profiling of cold adapting polar fishes implies that routine protein homeostasis is a significant cost in extreme cold and that the ubiquitin-mediated protein degradation pathway is of special importance during this adaptation process [2]. Also, ubiquitination-related genes are significantly expressed in temperate fish such as Cyprinus carpio [3][4][5], tropical fish such as Danio rerio [6,7] and other fishes [8][9][10][11] when exposed to acute cold stress.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona)

et al. 2020

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Background Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. The tiger barb Puntius tetrazona is a tropical stenothermal fish, with great popularity in aquarium trade and research. Results To investigate the response mechanism of P. tetrazona to low temperature, fish were exposed to increasing levels of acute cold stress. Histopathological analysis showed that the brain, gill, liver and muscle tissues appeared serious damage after cold stress (13 °C). Brain, gill, liver and muscle tissues from control (CTRL) groups (27 °C) and COLD stress groups (13 °C) of eight-month fish (gender-neutral) were sampled and assessed for transcriptomic profiling by high-throughput sequencing. 83.0 Gb of raw data were generated, filtered and assembled for de novo transcriptome assembly. According to the transcriptome reference, we obtained 392,878 transcripts and 238,878 unigenes, of which 89.29% of the latter were annotated. There were 23,743 differently expressed genes (DEGs) been filtered from four pairs of tissues (brain, gill, liver and muscle) between these cold stress and control groups. These DEGs were mainly involved in circadian entrainment, circadian rhythm, biosynthesis of steroid and fatty acid. There were 64 shared DEGs between the four pairs of groups, and five were related to ubiquitylation/deubiquitylation. Our results suggested that ubiquitin-mediated protein degradation might be necessary for tropical stenothermal fish coping with acute cold stress. Also, the significant cold-induced expression of heat shock 70 kDa protein (HSP70) and cold-induced RNA-binding protein (CIRBP) was verified. These results suggested that the expression of the molecular chaperones HSP70 and CIRBP in P. tetrazona might play a critical role in coping with acute cold stress. Conclusions This is the first transcriptome analysis of P. tetrazona using RNA-Seq technology. Novel findings about tropical stenothermal fish under cold stress (such as HSP70 and CIRBP genes) are presented here. This study contributes new insights into the molecular mechanisms of tropical stenothermal species response to acute cold stress.

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Liver transcriptome sequencing and de novo annotation of the large yellow croaker ( Larimichthy crocea ) under heat and cold stress

Cited by 106 publications

References 24 publications

Genome-Wide Identification of Hsp70 Genes in the Large Yellow Croaker (Larimichthys crocea) and Their Regulated Expression Under Cold and Heat Stress

Genome-Wide Identification of Hsp70 Genes in the Large Yellow Croaker (Larimichthys crocea) and Their Regulated Expression Under Cold and Heat Stress

An improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function

Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona)

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