Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, 266003, China.
BMC Genomics. 2023 Aug 10;24(1):453. doi: 10.1186/s12864-023-09543-7.
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 ℃).
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.
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.
太平洋牡蛎（Crassostrea gigas）是世界范围内一种具有重要经济价值的贝类。为了提高其生长速度，人们已经做出了巨大的努力来进行遗传育种。然而，与牡蛎生长调控相关的候选标记基因、途径和潜在的长非编码 RNA（lncRNA）仍知之甚少。为了鉴定参与生长调控的基因、lncRNA 和途径，我们将太平洋牡蛎的幼体在低温（15℃）下培养以建立生长抑制模型，然后与在常温和 25℃下培养的幼体进行比较转录组分析。
在正常生长（25℃，以下简称 NG）和生长缓慢（15℃，以下简称 SG）的牡蛎之间，共鉴定到 8627 个差异表达基因（DEGs）和 1072 个差异表达 lncRNA（DELs）。功能富集分析表明，这些 DEGs 主要富集在 AMPK 信号通路、MAPK 信号通路、胰岛素信号通路、自噬、细胞凋亡、钙信号通路和内吞作用过程中。lncRNA 分析鉴定出 265 对顺式作用对和 618 对反式作用对，它们可能参与了牡蛎的生长调控。LNC_001270、LNC_003322、LNC_011563、LNC_006260 和 LNC_012905 的表达水平对培养温度和食物丰度具有诱导性。这些 lncRNA 分别位于 SREBP1/p62、CDC42、CaM、FAS 和 PIK3CA 基因的反义、上游或下游。此外，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 在内的反式作用 lncRNA 的表达也与 AMPK 信号通路、胰岛素信号通路、自噬、细胞凋亡、钙信号通路和内吞作用过程中富集的基因的表达显著相关。
在本研究中，我们鉴定了关键的生长相关基因和 lncRNA，它们可作为候选标记物，阐明太平洋牡蛎生长调控的分子机制。
