Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), are crucial sensors with a conserved structure in cytoplasm, inducing the production of cytokines, chemokines and host restriction factors which mediate a variety of intracellular activities to interfere with distinct PAMPs (pathogen-associated molecular patterns) for eliminating pathogens in innate immune system. Although RLR genes have been investigated in most vertebrates and some invertebrates, the systematic identification and characterization of RLR genes have not been reported in scallops. In this study, four RLR genes (PY-10413.4, PY-10413.5, PY-443.7 and PY-443.8, designated PyRLRs) were identified in Yesso scallop (Patinopecten yessoensis) through whole-genome scanning through in silico analysis, including two pairs of tandem duplicate genes located on the same scaffold (PY-10413.4 and PY-10413.5, PY-443.7 and PY-443.8, respectively). Phylogenetic and protein structural analyses were performed to determine the identities and evolutionary relationships of these genes. The expression profiles of PyRLRs were determined in all developmental stages, in healthy adult tissues, and in mantles that simulated ocean acidification (OA) exposure (pH = 6.5 and 7.5) at different time points (3, 6, 12 and 24 h). Spatiotemporal expression patterns suggested the functional roles of PyRLRs in all stages of development and growth of the scallop. Regulation expressions revealed PY-10413.4 and PY-10413.5 with one or two CARD(s) (caspase activation and recruitment domain) were up-regulated expressed at most time points, whereas PY-443.8 and PY-10413.4 without CARD were significantly down-regulated at each time points, suggesting functional differentiations in the two pairs of PyRLRs based on the structural differences in response to OA. Collectively, this study demonstrated gene duplication of RLR family genes and provide primary analysis for versatile roles in the response of the bivalve innate immune system to OA challenge.

中文翻译：

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全基因组鉴定，Yesso扇贝（Patinopecten yessoensis）中RLR基因的表征以及响应海洋酸化的功能调节。

维甲酸诱导型基因I（RIG-I）样受体（RLR）是细胞质中具有保守结构的关键传感器，可诱导细胞因子，趋化因子和宿主限制因子的产生，这些因子介导多种细胞内活性以干扰不同的PAMP（与病原体相关的分子模式），用于消除先天免疫系统中的病原体。尽管已在大多数脊椎动物和一些无脊椎动物中研究了RLR基因，但尚未在扇贝中报道RLR基因的系统鉴定和表征。在这项研究中，通过计算机模拟全基因组扫描，在Yesso扇贝（Patinopecten yessoensis）中鉴定了四个RLR基因（PY-10413.4，PY-10413.5，PY-443.7和PY-443.8，称为PyRLRs），包括位于同一支架上的两对串联重复基因（分别为PY-10413.4和PY-10413.5，PY-443.7和PY-443.8）。进行了系统发育和蛋白质结构分析，以确定这些基因的身份和进化关系。在所有发育阶段，健康的成人组织中以及在不同时间点（3、6、12和24小时）模拟海洋酸化（OA）暴露（pH = 6.5和7.5）的地幔中，测定PyRLRs的表达谱。时空表达模式表明PyRLRs在扇贝的发育和生长的所有阶段的功能作用。调控表达显示具有一个或两个CARD（胱天蛋白酶激活和募集结构域）的PY-10413.4和PY-10413.5在大多数时间点均被上调，而PY-443.8和PY-10413则表达。4个无CARD的化合物在每个时间点均显着下调，这表明基于对OA的结构差异，两对PyRLRs的功能存在差异。总体而言，这项研究证明了RLR家族基因的基因重复，并为双壳先天免疫系统对OA攻击的应答中的多种功能提供了初步分析。