背景:太平洋牡蛎,Crassostreagigas,是世界上重要的经济贝类。通过遗传育种,已经做出了巨大的努力来提高其生长速率。然而,候选标记基因,通路,和参与牡蛎生长调节的潜在lncRNAs在很大程度上仍然未知。为了识别基因,lncRNAs,和参与生长调节的途径,C.gigasspat在低温(15℃)下培养,以产生生长抑制模型,用常温(25℃)培养的spat进行比较转录组分析。
结果:总计,在正常生长的牡蛎之间鉴定出8627个差异表达基因(DEGs)和1072个差异表达lncRNAs(DELs)(在25℃下培养,以下简称NG)和缓慢生长的牡蛎(在15℃下培养,以下简称SG)。功能富集分析表明,这些DEGs大多富集在AMPK信号通路中,MAPK信号通路,胰岛素信号通路,自噬,凋亡,钙信号通路,和内吞过程。LncRNAs分析确定了265个顺式作用对和618个反式作用对,它们可能参与牡蛎生长调节。LNC_001270,LNC_003322,LNC_011563,LNC_006260和LNC_012905的表达水平可诱导培养温度和食物丰度。这些lncRNAs位于反义,上游,或SREBP1/p62,CDC42,CaM,FAS,和PIK3CA基因,分别。此外,反式作用lncRNAs的表达,包括XR_9000022.2,LNC_008019,LNC_015817,LNC_000838,LNC_00839,LNC_011859,LNC_007294,LNC_006429,XR_002198885.1和XR_902224.2也与AMPK信号通路中富集基因的表达显著相关,胰岛素信号通路,自噬,凋亡,钙信号通路,和内吞过程。
结论:在这项研究中,我们确定了关键的生长相关基因和lncRNAs,它们可以用作候选标记来说明太平洋牡蛎生长调节的分子机制.
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.