Whole-genome sequencing reveals sex determination and liver high-fat storage mechanisms of yellowstripe goby (Mugilogobius chulae)

Cai, Lei; Liu, Guocheng; Wei, Yuanzheng; Zhu, Yabing; Li, Jianjun; Miao, Zhimin; Chen, Meili; Yue, Zhen; Yu, Lujun; Zhou, Dong; Ye, Huixin; Sun, Wenjing; Ren, Haitao

doi:10.1038/s42003-020-01541-9

Cited by 18 publications

(3 citation statements)

References 94 publications

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“…Therefore, we speculate that the shimofuri goby genome belongs to the common diploid genome. The size of the shimofuri goby genome (887.60 Mb) was similar to that of the most published species of Gobiidae, being smaller than those of Boleophthalmus pectinirostris (955.75 Mb) and Mugilogobius chulae (1003.36 Mb) [33,34]. Differences in genome size may be due to the differences in repeat sequence content and transposon insertion events [35].…”

Section: Discussionsupporting

confidence: 60%

Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus

Zhao

Liu²,

et al. 2022

Animals

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The shimofuri goby (Tridentiger bifasciatus) is a small and highly adaptable goby, distributed along the coasts of China, the Sea of Japan, and the west coastal and estuarine areas of the Northwest Pacific. Next-generation sequencing was used to generate genome-wide survey data to provide essential characterization of the shimofuri goby genome and for the further mining of genomic information. The genome size of the shimofuri goby was estimated to be approximately 887.60 Mb through K-mer analysis, with a heterozygosity ratio and repeat sequence ratio of 0.47% and 32.60%, respectively. The assembled genome was used to identify microsatellite motifs (Simple Sequence Repeats, SSRs), extract single-copy homologous genes and assemble the mitochondrial genome. A total of 288,730 SSRs were identified. The most frequent SSRs were dinucleotide repeats (with a frequency of 61.15%), followed by trinucleotide (29.87%), tetranucleotide (6.19%), pentanucleotide (1.13%), and hexanucleotide repeats (1.66%). The results of the phylogenetic analysis based on single-copy homologous genes showed that the shimofuri goby and Rhinogobius similis can be clustered into one branch. The shimofuri goby was originally thought to be the same as the chameleon goby (Tridentiger trigonocephalus) due to their close morphological resemblance. However, a complete mitochondrial genome was assembled and the results of the phylogenetic analysis support the inclusion of the shimofuri goby as a separate species. PSMC analysis indicated that the shimofuri goby experienced a bottleneck event during the Pleistocene Glacial Epoch, in which its population size decreased massively, and then it began to recover gradually after the Last Glacial Maximum. This study provides a reference for the further assembly of the complete genome map of the shimofuri goby, and is a valuable genomic resource for the study of its evolutionary biology.

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Section: Discussionsupporting

confidence: 60%

Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus

Zhao

Liu²,

et al. 2022

Animals

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“…Moreover, genomic data provides a foundation for comparative studies, helping identify unique adaptations, ecological interactions, and evolutionary innovations. While many gobioid genome assemblies have been generated recently (Adrian-Kalchhauser et al, 2020; Cai et al, 2021; Y. Hu et al, 2021; Q.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-level genome assembly of the primitive loach goby,Rhyacichthys aspro, reveals mechanisms underlying Gobioidei diversification

Wang,

Lu,

et al. 2024

Preprint

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The percomorph fish clade Gobioidei are a suborder that comprises over 2,200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their diversification, we sequenced and annotated the genome of the loach goby,Rhyacichthys aspro, the basal most group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 607 Mb, and a rise in species diversity from basal to derived lineages is mirrored by enlarged genomes and a higher presence of repeat elements (REs), particularly DNA transposons. These transposons are enriched in coding and regulatory regions and their copy number increase is strongly correlated with mutation rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an over representation of synaptic function genes, with genes putatively under selection linked to synapse organization and calcium signaling, suggesting a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed light on the loach goby’s survival mechanisms and the broader evolutionary trends within Gobioidei.

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“…The sh liver, as a target tissue that regulates lipid metabolism, plays a vital role in lipid digestion and absorption (Harvey et al, 2019). Current research has shown that there are multiple factors affecting lipid deposition in sh liver, including diets (Zhou et al, 2023;Ji et al, 2022), environment (Zhou et al, 2019), physiology (Cai et al, 2021), and species (Ando et al, 1993). Studies on grass carp have reported that a high-lipid diet (with a lipid level of 8.8%) induces lipid accumulation in the hepatopancreas (Zhang et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Regulation of lipid metabolism in grass carp hepatocytes by exosomes derived from fatty hepatocytes though GRP78

Yang,

lu,

Cao

et al. 2024

Preprint

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Exosomes regulate lipid metabolism by carrying miRNAs, nucleic acids, and proteins, thereby influencing the function of receptor cells. Glucose-regulated protein 78 (GRP78) is also involved in the regulation of lipid metabolism. However, it remains unclear whether exosomes derived from fatty hepatocytes (OA-Exo) regulate lipid metabolism through the enrichment of GRP78. In this study, we observed lipid accumulation after incubating hepatocytes with oleic acid (OA) for 24 hours (fatty hepatocytes) (P < 0.05). Interestingly, the expression of GRP78 was significantly increased in fatty hepatocytes and OA-Exo (P < 0.05). We hypothesized that GRP78 plays an important role in the regulation of lipid metabolism. Subsequently, the hepatocytes were separately incubated with OA-Exo (50 µg/mL) and GRP78 protein (1 µg/mL) for 24 hours. The results showed a significant increase in the content of Triacylglycerol (TG) and total cholesterol (TC), as well as up-regulation of the expression of GRP78 and inositol-requiring enzyme-1alpha (IRE1α) protein (P < 0.05). It suggested that exosomal GRP78 promoted lipid accumulation in hepatocytes. Therefore, we used YUM70 (an inhibitor of GRP78) to inhibit endogenous GRP78, followed by incubation of hepatocytes with OA-Exo and GRP78 for 24 hours. Compared with the control group, the content of TG and the expression of GRP78 protein were significantly decreased in the YUM70 group (P < 0.05). However, when compared with the YUM70 group, OA-Exo reversed the effect of YUM70 and increased the content of TG, TC, and the expression of GRP78 protein in hepatocytes (P < 0.05). These results suggested that OA-Exo promoted lipid accumulation in hepatocytes through the recruitment of GRP78, and the IRE1α pathway may be important in this process. Furthermore, the inhibition of the IRE1α pathway with 4µ8C resulted in a significant decrease in TG content compared to the control group (P < 0.05). However, when compared with the 4µ8C group, OA-Exo and GRP78 reversed the effect of 4µ8C and significantly increased TG content (P < 0.05). Taken together, these results indicated that OA-Exo activated IRE1α to promote lipid accumulation in hepatocytes through the enrichment of GRP78. This study provided a new perspective for further exploration of exosomal lipid metabolism in fish.

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Whole-genome sequencing reveals sex determination and liver high-fat storage mechanisms of yellowstripe goby (Mugilogobius chulae)

Cited by 18 publications

References 94 publications

Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus

Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus

Chromosome-level genome assembly of the primitive loach goby,Rhyacichthys aspro, reveals mechanisms underlying Gobioidei diversification

Regulation of lipid metabolism in grass carp hepatocytes by exosomes derived from fatty hepatocytes though GRP78

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