Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations.
Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations.
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DOI：
10.1093/molbev/msv122
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发表时间：
2015-09
影响因子：
10.7
通讯作者：
Worden AZ
中科院分区：
文献类型：
--
作者：
Simmons MP;Bachy C;Sudek S;van Baren MJ;Sudek L;Ares M Jr;Worden AZ
剪切体内含子是真核基因的一个标志，被认为在基因组进化中发挥重要作用，但其起源却鲜为人知。虽然大多数内含子之间缺乏序列同源性，但最近在一些生物体中发现了在单个基因组中重复数百次的新的剪接体内含子家族。这些内含子元件(IES)或内含子样元件在其他类群中的普遍存在和保守性，以及它们与常规剪接体内含子的进化关系尚不清楚。在这里，我们系统地研究了广泛存在的海洋绿藻微单胞菌的内含子，报道了新的IES家族，大量的内含子存在-缺失多态，以及潜在的内含子插入热点。这些新的家族能够鉴定保守的IE二级结构特征，并建立一个新的跨基因组重复内含子增殖的通用模型。尽管有相同的二级结构，但每个小单胞菌谱系的IE家族与其他谱系的IE家族没有明显的序列相似性，表明它们的出现与物种形成过程密切相关。其中两个新的IE家族来自北极培养物(Micromonas Clade E2)，分离自极地地区，由于气候诱导的变化，该地区这种藻类的丰度正在增加。同样的两个家族在南极洲的元基因组数据中被检测到--在这个系统中，微单胞菌以前从未被报道过。北极分离株和位于IES两侧的南极编码序列之间惊人的高度同源性表明，我们假设的两个极地系统中的种群之间的联系通过深海洋流发生。墨西哥湾流下北大西洋深水中恢复的Clade E2序列支持这一假说。我们的研究阐明了一类不寻常的重复内含子、基因组进化、物种形成和这种前哨海藻的全球分布之间的动态关系。
Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.