Magain Nicolas, Miadlikowska Jolanta, Mueller Olaf, Gajdeczka Michael, Truong Camille, Salamov Asaf A, Dubchak Inna, Grigoriev Igor V, Goffinet Bernard, Sérusiaux Emmanuël, Lutzoni François
Department of Biology, Duke University, Durham, NC 27708, United States.
Department of Biology, Duke University, Durham, NC 27708, United States.
Mol Phylogenet Evol. 2017 Dec;117:10-29. doi: 10.1016/j.ympev.2017.08.013. Epub 2017 Aug 30.
Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore the potential of this approach, we found 125 Collinear Orthologous Regions (COR) ranging from 1 to >10kb across nine genomes representing the Lecanoromycetes and Eurotiomycetes (Pezizomycotina, Ascomycota). Twenty-six of these COR were found in all 24 eurotiomycete genomes surveyed for this study. Given the high abundance and availability of fungal genomes we believe this approach could be adopted for other large groups of fungi outside the Pezizomycotina. Asa proof of concept, we selected three Collinear Orthologous Regions (COR1b, COR3, and COR16), based on synteny analyses of several genomes representing three classes of Ascomycota: Eurotiomycetes, Lecanoromycetes, and Lichinomycetes. COR16, for example, was found across these three classes of fungi. Here we compare the resolving power of these three new markers with five loci commonly used in phylogenetic studies of fungi, using section Polydactylon of the cyanolichen-forming genus Peltigera (Lecanoromycetes) - a clade with several challenging species complexes. Sequence data were subjected to three species discovery and two validating methods. COR markers substantially increased phylogenetic resolution and confidence, and highly contributed to species delimitation. The level of phylogenetic signal provided by each of the COR markers was higher than the commonly used fungal barcode ITS. High cryptic diversity was revealed by all methods. As redefined here, most species represent lineages that have relatively narrower, and more homogeneous biogeographical ranges than previously understood. The scabrosoid clade consists of ten species, seven of which are new. For the dolichorhizoid clade, twenty-two new species were discovered for a total of twenty-nine species in this clade.
在广泛的系统发育类群中，某些基因组区域的共线性可以得到维持。在这些同源基因组区域中，处于宽松净化选择下的位点，如基因间区域，可以广泛用作物种复合体群体遗传和系统发育研究的标记。为了探索这种方法的潜力，我们在代表茶渍纲和散囊菌纲（粪壳菌亚门，子囊菌门）的九个基因组中发现了125个共线直系同源区域（COR），长度从1kb到大于10kb不等。在本研究调查的所有24个散囊菌纲基因组中都发现了其中26个COR。鉴于真菌基因组的高丰度和可得性，我们认为这种方法可应用于粪壳菌亚门外的其他大型真菌类群。作为概念验证，我们基于对代表子囊菌门三个纲（散囊菌纲、茶渍纲和地卷菌纲）的几个基因组的共线性分析，选择了三个共线直系同源区域（COR1b、COR3和COR16）。例如，在这三个真菌纲中都发现了COR16。在这里，我们使用形成蓝藻地衣的脐衣属（茶渍纲）多指叶组——一个包含几个具有挑战性的物种复合体的进化枝，将这三个新标记的分辨能力与真菌系统发育研究中常用的五个位点进行比较。序列数据采用了三种物种发现方法和两种验证方法。COR标记显著提高了系统发育分辨率和可信度，并对物种界定有很大贡献。每个COR标记提供的系统发育信号水平高于常用的真菌条形码ITS。所有方法都揭示了高度的隐存多样性。如此处重新定义的，大多数物种所代表的谱系的生物地理范围比以前理解的相对更窄、更均匀。粗糙叶组由十个物种组成，其中七个是新物种。对于长根叶组，发现了22个新物种，该组共有29个物种。
