Comparative transcriptome reveals the thermal stress response differences between Heilongjiang population and Xinjiang population of Lota lota

Lou, Fangrui; Liu, Manhong; Han, Zhiqiang; Gao, Tianxiang

doi:10.1016/j.cbd.2022.100960

Cited by 3 publications

(5 citation statements)

References 45 publications

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“…Such interspecific distinctness in both categories and expression profiles of cold-responsive hub genes may arise from an adaptive alteration in the gene-expression-regulation network that may evolve under directional selection and confer the contrasted cold resistance capacity between the two eel gobies. This evolutionary force has been widely detected in other taxa of teleost species such as in Oncorhynchus mykiss [3] and Lota lota [76], where divergence in gene expression does not accord with genetic relatedness but is associated with phenotypic traits. Even in the hub genes that were shared between the two sister species, such interspecific variation of gene expression was also prevalent.…”

Section: Distinct Degs Corresponding With Divergent Thermal Adaptationmentioning

confidence: 95%

Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies

Liu,

Liu

et al. 2023

CIMB

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Adaptation to thermal conditions in tidal mudflats always involves tolerating frequent fluctuations and often extreme environmental temperatures. Regulation of gene expression plays a fundamental role in the evolution of these thermal adaptations. To identify the key gene regulatory networks associated with the thermal adaptation, we investigated the capability of cold tolerance, as well as the transcriptomic changes under cold stress in two mudflat inhabitants (Odontamblyopus lacepedii and O. rebecca) with contrasting latitude affinity. Our results revealed a remarkable divergent capacity of cold tolerance (CTmin: 0.61 °C vs. 9.57 °C) between the two gobies. Analysis of transcriptomic changes under cold stress unveiled 193 differentially expressed genes exhibiting similar expression profiles across all tissues and species, including several classic metabolic and circadian rhythm molecules such as ACOD and CIART that may represent the core cold response machinery in eel gobies. Meanwhile, some genes show a unique expression spectrum in the more cold-tolerant O. lacepedii suggesting their roles in the enhanced cold tolerance and hence the extreme thermal adaptations. In addition, a weighted gene co-expression network analysis (WGCNA) revealed a subset of metabolic hub genes including MYH11 and LIPT2 showing distinct down-regulation in O. lacepedii when exposed to cold stress which highlights the role of reduced energy consumption in the enhanced cold tolerance of eel gobies. These findings not only provide new insights into how mudflat teleosts could cope with cold stress and their potential evolutionary strategies for adapting to their thermal environment, but also have important implications for sound management and conservation of their fishery resources in a scenario of global climate warming in the marine realm.

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Section: Distinct Degs Corresponding With Divergent Thermal Adaptationmentioning

confidence: 95%

Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies

Liu,

Liu

et al. 2023

CIMB

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“…Temperature is indeed the key factor in current climate change, and many studies describe genes involved in fish adaptation to changes in temperature (e.g. Hori et al, 2010;Dietrich et al, 2018;Lou et al, 2022). Heavy metals are main pollutants in West African waters, as explained above.…”

Section: Candidate Gene Selectionmentioning

confidence: 99%

A new Merluccius polli reference genome to investigate the effects of global change in West African waters

et al. 2023

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Genome resources have become crucial to assess genome-wide level of variation as well as to detect adaptive variation. This is particularly important for studying diversity in marine species inhabiting regions highly affected by accelerated climate warming and pollution, also known as global change. A greater awareness of the impacts of global change is urgently needed to ensure sustainable marine fisheries. Despite recent efforts, there are still many gaps in fish reference genomes, both geographical and taxonomic. Here, we sequence, assemble and annotate the genome of Merluccius polli. The total length of this new assembly (~582 Kb, N50 = 168Kb) is approximately 40% longer and much less fragmented than a previous version. Even though it might not be intrinsic of this species, low level of heterozygosity (1.16 SNPs/Kb) and low proportion of repeat content (9.21%) was found in this genome. This hake species has a wide latitudinal distribution; therefore, it is exposed to a changing temperature gradient and to a variety of contaminants in part of its distribution along West African coast. Special emphasis was laid on the identification and characterization of candidate genes known to respond to different stressors (depth, temperature, hypoxia, and heavy metals) happening along its geographical distribution. A total of 68 of the selected candidate genes known to be associated with responses to these stressors were found in the current assembly of the genome, and their predicted sequence can be considered as full-length. Therefore, it is expected that this genome would serve as a tool to further investigations of global change in one of the most stressed marine regions in the planet.

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“…Lota lota is the only freshwater Gadiformes and is widely distributed in inland lakes and bays of Europe, Asia, and North America north of latitude 45°N (14). Climate warming caused by human activities and other factors is assumed to have resulted in a rapid decrease of L. lota resources, which are ecologically dependent on low temperature (15,16), and L. lota has been listed in the Rare Aquatic Wildlife of China. The gradual development of artificial culture can meet the market demand for aquatic food under the background of the decline of L. lota resources (17).…”

Section: Introductionmentioning

confidence: 99%

“…Transcriptional processes usually represent the complex dynamics of biological internal regulatory mechanisms (16), which can be used to reveal the response mechanisms of L. lota to invading viruses. High-throughput sequencing technologies such as RNA sequencing (RNA-seq) have advantages in obtaining complete transcripts of organisms (19), and thus have been successfully applied to analyze the transcriptional responses of a variety of aquatic fishes to viral invasion (20)(21)(22).…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, RNAseq can also serve as a useful technique for identifying the transcriptional divergences of L. lota associated with viral invasion. Unfortunately, transcriptome studies of L. lota have only focused on the response mechanisms of high temperature (16,23), and the transcriptional regulation mechanisms of L. lota in response to viral invasion have not been reported.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional responses of liver and spleen in Lota lota to polyriboinosinic polyribocytidylic acid

Lou,

Zhang,

et al. 2023

Front. Immunol.

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IntroductionThe cultured Lota lota can meet the market demand in the context of the decline of wild resources, but the disease in the high-density culture process also deserves attention. Therefore, understanding the immune regulation mechanisms of L. lota will be the basis for obtaining high benefits in artificial culture.MethodsTo explore the viral response mechanism of L. lota, RNA-seq was applied to identify the transcriptomic changes of the liver and spleen in L. lota by poly (I:C) stress.ResultsThe DEGs (liver: 2186 to 3123; spleen 1542 to 2622) and up-regulated genes (liver: 1231 to 1776; spleen 769 to 1502) in the liver and spleen increased with the prolongation (12h to 48h) of poly (I:C)-stimulation time. This means L. lota needs to mobilize more functional genes in response to longer periods of poly (I:C)-stimulation. Despite the responses of L. lota to poly (I:C) showed tissue-specificity, we hypothesized that both liver and spleen of L. lota can respond to poly (I:C) challenge may be through promoting apoptosis of DNA-damaged cells, increasing the activity of immune-enhancing enzymes, and increasing energy supply based on DEGs annotation information.ConclusionsOur results demonstrate the transcriptional responses of L. lota to poly (I:C)-stimulation, and these data provide the first resource on the genetic regulation mechanisms of L. lota against viruses. Furthermore, the present study can provide basic information for the prevention of viral diseases in L. lota artificial culture process.

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Comparative transcriptome reveals the thermal stress response differences between Heilongjiang population and Xinjiang population of Lota lota

Cited by 3 publications

References 45 publications

Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies

Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies

A new Merluccius polli reference genome to investigate the effects of global change in West African waters

Transcriptional responses of liver and spleen in Lota lota to polyriboinosinic polyribocytidylic acid

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