Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation

Please refer to the publication Shin et al. (2021): "Shin CR, Choi EH, Kim G. et al. (2021). Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation. Scientific Reports 11: 12239.

The land snail Ellobium chinense (Pulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of E. chinense has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific E. chinense based on COI and 10 microsatellite markers. The analyses of 140 COI data from South Korea and Japan and 54 microsatellite data from South Korea revealed that E. chinense has high haplotype and low nucleotide diversity without showing any genetic structures that reflect geographical isolations. It strongly implies that the subfamily Ellobiinae may have first appeared around the Eocene Optimum immediately after the Paleocene–Eocene Thermal Maximum (PETM; ca. 55 mya) and the examined E. chinense populations in Northwestern Pacific may have been maintained in a metapopulation under the influence of the Kuroshio warm currents through the Late-Middle Pleistocene (0.350−0.126 mya) and Late Pleistocene (0.126−0.012 mya). We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in COI (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four COI hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure.

Methods
We elucidated the genetic diversity and the pattern of genetic structures among populations of northwestern Pacific E. chinense (sampled in South Korea and Japan). Our analyses were based on the popular DNA barcode region of the mitochondrial gene COI and 10 selected SSR microsatellite markers. In total, 140 COI data (consisting of 139 South Korean samples and one Japanese sample), and 54 SSR microsatellite data (from South Korea only) were analyzed. In addition, we employed four distinct covariate adenine/guanine hotspots observed on COI which are distinct key sequences to easily classify phylogenetic groups of E. chinense. Herein, this repository contains the raw data of COI alignments and G-quadruplex motifs. For these results, the population genetic diversity and structure analyses and divergence time estimation were performed. Finally, it was written as a manuscript and accepted for publication in the journal Scientific Reports.

请参阅Shin等人(2021)的研究：Shin CR, Choi EH, Kim G 等. (2021). 基于更新世扩张与4个与G-四链体(G-quadruplex)构象相关的COI鸟嘌呤热点的中国耳螺(Ellobium chinense)集合种群特征. 科学报告(Scientific Reports), 11: 12239.

栖息于西北太平洋沿岸盐沼的中国耳螺(Ellobium chinense，肺螺亚纲(Pulmonata)、耳螺目(Ellobiida)、耳螺科(Ellobiidae))是IUCN红色名录(IUCN Red List)中的濒危物种。近数十年来，受自然灾害与人类活动造成的环境干扰影响，该物种种群规模持续缩减。本研究基于细胞色素c氧化酶亚基I(COI)基因与10个微卫星(microsatellite)标记，首次对西北太平洋中国耳螺的遗传多样性及种群遗传结构展开评估。通过分析韩国与日本的140条COI序列数据，以及韩国的54条微卫星数据，研究发现中国耳螺具有较高的单倍型多样性与较低的核苷酸多样性，且未呈现出反映地理隔离的遗传结构特征。该结果强烈暗示，耳螺亚科(Ellobiinae)可能最早出现于古新世-始新世极热事件(Paleocene–Eocene Thermal Maximum, PETM，约5500万年前)之后的始新世适宜期；本次研究涉及的西北太平洋中国耳螺种群，可能在中更新世晚期(0.350~0.126百万年前)与更新世晚期(0.126~0.012百万年前)期间，受黑潮暖流(Kuroshio warm currents)影响维持为集合种群(metapopulation)。此外，研究人员发现了4个不受地理分布限制的演化支，可通过COI基因上4个单向逐步的腺嘌呤到鸟嘌呤突变位点(位点207-282-354-420：A-A-A-A、A-A-G-A、G-A-G-A与G-G-G-G)轻松区分。同时，这4个COI热点位点之间存在高度的协变性，且相关性显著。本文还讨论了这些协变性鸟嘌呤位点所形成的连续4个G-四链体的作用，以及它们在正选择压力下可能产生的有益效应。

研究方法
本研究阐明了采自韩国与日本的西北太平洋中国耳螺种群的遗传多样性与种群遗传结构模式。分析基于线粒体基因COI的通用DNA条形码区域，以及10个筛选出的简单序列重复(Simple Sequence Repeat, SSR，即微卫星)标记。本次研究共分析了140条COI序列数据(包含139个韩国样本与1个日本样本)，以及仅来自韩国的54条SSR微卫星数据。此外，本研究利用了COI基因上观测到的4个独立协变性腺嘌呤/鸟嘌呤热点位点，这些位点是区分中国耳螺演化支的关键特征序列。本数据集仓库包含COI序列比对与G-四链体基序的原始数据。基于这些数据，研究人员开展了种群遗传多样性与结构分析以及分化时间估算。最终相关研究成果撰写为论文，并被《科学报告》(Scientific Reports)期刊接收发表。