Genome-Wide Identification of Long Non-coding RNAs in Crassostrea gigas and Their Association with Heat Stress

Song, Kai

doi:10.1007/s10126-022-10140-0

Cited by 2 publications

(1 citation statement)

References 39 publications

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“…It was suggested that these differentially expressed lncRNAs may shape the phenotypic plasticity of abalone by regulating the expression of genes involved in signal transduction, autophagy and apoptosis, and hormone regulation. So far, a lot of lncRNAs have been identified and classified in mammals and plants, , and there is also information available regarding the involvement of lncRNAs in fish, , mollusks, − and other marine invertebrates under certain environmental conditions. However, the exact function identification of lncRNAs in these non-model animals requires more efforts and breakthroughs in the future.…”

Section: Discussionmentioning

confidence: 99%

Divergent Carry-Over Effects of Hypoxia during the Early Development of Abalone

Shen

Gao

Xiao

et al. 2022

Environ. Sci. Technol.

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After being exposed to environmental stimuli during early developmental stages, some organisms may gain or weaken physiological regulating abilities, which would have long-lasting effects on their performance. Environmental hypoxia events can have significant effects on marine organisms, but for breeding programs and other practical applications, it is important to further explore the long-term physiological effects of early hypoxia exposure in economically significant species. In this study, the Pacific abalone Haliotis discus hannai was exposed to moderate hypoxia (∼4 mg/L) from zygote to trochophora, and the assessments of hypoxia tolerance were conducted on the grow-out stage. The results revealed that juvenile abalones exposed to hypoxia at the early development stages were more hypoxiatolerant but with slower weight growth, a phenomenon called the tradeoff between growth and survival. These phenotypic effects driven by the hypoxia exposure were explained by strong selection of genes involved in signal transduction, autophagy, apoptosis, and hormone regulation. Moreover, long non-coding RNA regulation plays an important role modulating carry-over effects by controlling DNA replication and repair, signal transduction, myocardial activity, and hormone regulation. This study revealed that the ability to create favorable phenotypic differentiation through genetic selection and/or epigenetic regulation is important for the survival and development of aquatic animals in the face of rapidly changing environmental conditions.

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Section: Discussionmentioning

confidence: 99%

Divergent Carry-Over Effects of Hypoxia during the Early Development of Abalone

Shen

Gao

Xiao

et al. 2022

Environ. Sci. Technol.

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Integrated analysis of mRNAs and lncRNAs reveals candidate marker genes and potential hub lncRNAs associated with growth regulation of the Pacific Oyster, Crassostrea gigas

Yang

Shi

et al. 2023

BMC Genomics

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Background The Pacific oyster, Crassostrea gigas, is an economically important shellfish around the world. Great efforts have been made to improve its growth rate through genetic breeding. However, the candidate marker genes, pathways, and potential lncRNAs involved in oyster growth regulation remain largely unknown. To identify genes, lncRNAs, and pathways involved in growth regulation, C. gigas spat was cultured at a low temperature (15 ℃) to yield a growth-inhibited model, which was used to conduct comparative transcriptome analysis with spat cultured at normal temperature (25 ℃). Results In total, 8627 differentially expressed genes (DEGs) and 1072 differentially expressed lncRNAs (DELs) were identified between the normal-growth oysters (cultured at 25 ℃, hereinafter referred to as NG) and slow-growth oysters (cultured at 15 ℃, hereinafter referred to as SG). Functional enrichment analysis showed that these DEGs were mostly enriched in the AMPK signaling pathway, MAPK signaling pathway, insulin signaling pathway, autophagy, apoptosis, calcium signaling pathway, and endocytosis process. LncRNAs analysis identified 265 cis-acting pairs and 618 trans-acting pairs that might participate in oyster growth regulation. The expression levels of LNC_001270, LNC_003322, LNC_011563, LNC_006260, and LNC_012905 were inducible to the culture temperature and food abundance. These lncRNAs were located at the antisense, upstream, or downstream of the SREBP1/p62, CDC42, CaM, FAS, and PIK3CA genes, respectively. Furthermore, the expression of the trans-acting lncRNAs, including XR_9000022.2, LNC_008019, LNC_015817, LNC_000838, LNC_00839, LNC_011859, LNC_007294, LNC_006429, XR_002198885.1, and XR_902224.2 was also significantly associated with the expression of genes enriched in AMPK signaling pathway, insulin signaling pathway, autophagy, apoptosis, calcium signaling pathway, and endocytosis process. Conclusions In this study, we identified the critical growth-related genes and lncRNAs that could be utilized as candidate markers to illustrate the molecular mechanisms underlying the growth regulation of Pacific oysters.

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Genome-Wide Identification of Long Non-coding RNAs in Crassostrea gigas and Their Association with Heat Stress

Cited by 2 publications

References 39 publications

Divergent Carry-Over Effects of Hypoxia during the Early Development of Abalone

Divergent Carry-Over Effects of Hypoxia during the Early Development of Abalone

Integrated analysis of mRNAs and lncRNAs reveals candidate marker genes and potential hub lncRNAs associated with growth regulation of the Pacific Oyster, Crassostrea gigas

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