Supplementary data: Details of the conserved hairpins of M. galloprovincialis (MGR), P. fucata (PFU), R. philippinarum (RPH), S. broughtonii (SBR) and T. granosa (TGR) from Digging into bivalve miRNAomes: between conservation and innovation

Bivalves are a diverse mollusc group of economic and ecological importance. An evident resilience to pollution, parasites and extreme environments makes some bivalve species important models for studying adaptation and immunity. Despite substantial progress in sequencing projects of bivalves, information on non-coding genes and gene-regulatory aspects is still lacking. Here, we review the current repertoire of bivalve microRNAs (miRNAs), important regulators of gene expression in Metazoa. We exploited available sncRNA data for <i>Pinctada martensii, Crassostrea gigas, Corbicula fluminea, Tegillarca granosa</i> and <i>Ruditapes philippinarum</i>, and we produced new sncRNA data for two additional bivalves, the Mediterranean mussel <i>Mytilus galloprovincialis</i> and the blood clam <i>Scapharca broughtonii</i>. We found substantial heterogeneity and incorrect annotations of miRNAs; hence, we reannotated conserved miRNA families using recently established criteria for <i>bona fide</i> microRNA annotation. We found 106 miRNA families missing in the previously published bivalve datasets and 89 and 87 miRNA complements were identified in the two additional species. The overall results provide a homogeneous and evolutionary consistent picture of miRNAs in bivalves and enable future comparative studies. The identification of two bivalve-specific miRNA families sheds further light on the complexity of transcription and its regulation in bivalve molluscs.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

双壳类是一类物种多样的软体动物类群，兼具经济与生态价值。其对污染、寄生虫及极端环境具备显著耐受能力，使得部分双壳类物种成为研究适应性与免疫机制的重要模型。尽管双壳类的测序研究已取得长足进展，但目前仍缺乏关于非编码基因及基因调控层面的相关信息。本综述梳理了当前双壳类微小RNA（microRNA, miRNA）的研究现状——微小RNA是后生动物（Metazoa）中重要的基因表达调控因子。我们利用已公开的马氏珠母贝（Pinctada martensii）、长牡蛎（Crassostrea gigas）、河蚬（Corbicula fluminea）、泥蚶（Tegillarca granosa）以及菲律宾蛤仔（Ruditapes philippinarum）的小非编码RNA（small non-coding RNA, sncRNA）数据，并新增了另外两种双壳类的sncRNA数据：地中海贻贝（Mytilus galloprovincialis）与魁蚶（Scapharca broughtonii）。研究发现当前miRNA注释存在大量异质性与错误情况，因此我们依据近期确立的真实合规的微小RNA注释标准，重新注释了保守miRNA家族。我们在已发表的双壳类数据集中补全了106个此前遗漏的miRNA家族，并在新增的两个物种中分别鉴定出89和87个miRNA集合。本研究的整体结果为双壳类miRNA提供了一套统一且进化层面一致的图谱，可为后续比较研究奠定基础。本次鉴定出的两个双壳类特异性miRNA家族，进一步揭示了双壳类软体动物转录及其调控过程的复杂性。本文属于《Theo Murphy会议专题：软体动物基因组学：被忽视类群的广泛认知与未来方向》的一部分。