Genome skimming and plastid microsatellite profiling of alder trees (Alnus spp., Betulaceae): phylogenetic and phylogeographical prospects
Genome skimming and plastid microsatellite profiling of alder trees (Alnus spp., Betulaceae): phylogenetic and phylogeographical prospects
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DOI：
10.1007/s11295-017-1204-2
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发表时间：
2017-12-01
影响因子：
2.4
通讯作者：
Besnard, Guillaume
中科院分区：
文献类型：
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作者：
Gryta, Herve;Van de Paer, Celine;Besnard, Guillaume
桤木 (Alnus spp.) 是北半球河岸和山区栖息地的关键树种。先前的遗传学研究表明，存在复杂的属内多样化，其中包括许多种间杂交和多倍体化事件。在这里，我们首先旨在通过从属于三个主要桤木亚属（Alnus、Alnobetula 和 Clethropsis）的物种获得的质体和核数据生成系统发育假设，来测试目前对 Alnus 的分类处理。使用基因组撇脂策略组装了 22 个欧亚和美洲桤木个体的完整质体和核糖体 DNA 簇。基于这些数据的系统发育强烈支持早期分化的Alnobetula亚属，而Clethropsis亚属的成员并不构成单系进化枝，而是嵌入Alnus亚属内。不一致的拓扑结构也维持了该群体内的网状演化。因此，我们的结果表明将 Clethropsis 和 Alnus 亚属考虑在同一分类单位内。我们的第二个目标是测试高度可变的质体标记（微卫星）的效用，以研究欧亚桤木物种的系统发育地理模式。开发了 52 个多态性质体微卫星标记，并在欧亚大陆西部的 33 个赤杨亚属种群上进行了测试。平均而言，在 131 个桤木个体中，每个基因座发现 4.3 个等位基因，从而可以鉴定 30 种氯型（多基因座谱）。揭示了共存物种之间强烈的系统发育信号和重复的细胞质捕获，证明我们的质体微卫星分析方法适合追踪桤木物种中母系谱系的冰河后传播。所有这些结果最终支持使用核基因组区域进行物种鉴定以及使用质体标记进行系统发育地理学和遗传资源管理中的起源认证。
Alders (Alnus spp.) represent keystone species trees of riparian and mountainous habitats of the northern hemisphere. Previous genetic studies have suggested a complex intrageneric diversification with numerous events of interspecific hybridization and polyploidization. Here, we first aim to test the present taxonomical treatment of Alnus by generating phylogenetic hypotheses based on plastid and nuclear data obtained from species belonging to the three main alder subgenera (Alnus, Alnobetula, and Clethropsis). A genome-skimming strategy was used to assemble the complete plastome and the nuclear ribosomal DNA cluster of 22 Eurasian and American alder individuals. Phylogenies based on these data strongly support an early diverging subgenus Alnobetula, while members of the subgenus Clethropsis do not constitute a monophyletic clade and are embedded within the subgenus Alnus. Incongruent topologies also sustain reticulate evolution within this group. Our results thus suggest considering the subgenera Clethropsis and Alnus within the same taxonomical unit. Our second aim is to test for the utility of highly variable plastid markers (microsatellites) to investigate the phylogeographic patterns of Eurasian alder species. Fifty-two polymorphic plastid microsatellite markers were developed and tested on 33 populations of the subgenus Alnus in western Eurasia. On average, 4.3 alleles per locus were revealed in 131 individuals of Alnus glutinosa, allowing the identification of 30 chlorotypes (multiloci profiles). Strong phylogeographic signals and recurrent cytoplasmic captures between co-occurring species are revealed, demonstrating that our plastid microsatellite profiling method is suitable for tracing the post-glacial spread of maternal lineages among alder species. All these results finally support the use of nuclear genomic regions for species identification and of plastid markers for phylogeographic aspects and origin certification in genetic resource management.