Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: A case study of the Lecanoromycetes (Ascomycota)
Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: A case study of the Lecanoromycetes (Ascomycota)
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DOI：
10.1016/j.ympev.2006.10.016
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发表时间：
2007-07-01
影响因子：
4.1
通讯作者：
Lutzoni, Francois
中科院分区：
文献类型：
--
作者：
Hofstetter, Valerie;Miadlikowska, Jolanta;Lutzoni, Francois
两个蛋白质编码（RPB 1和RPB 2）和三个核糖体RNA编码（nucSSU，nucLSU和mitSSU）基因单独和各种组合的分辨率和统计支持进行了研究的基础上最大似然引导分析地衣形成真菌类蜡蚧菌（子囊菌）。我们的研究结果表明，最佳位点（单一和组合）用于地衣形成子囊菌门的分子系统学是蛋白质编码基因（RPB 1和RPB 2）。RPB 1和RPB 2基因单独的遗传效率比所有的两个和三个位点的核糖体位点的组合。这两个位点的第3位密码子位置提供了支持蜡蚧菌门内系统发育关系的最多特征。我们在这项研究中使用的三个核糖体位点，mitSSU贡献最大的系统发育分析时，结合RPB 1和RPB 2。除了mitSSU，核糖体基因是最难恢复的，因为它们往往含有许多内含子，导致PCR偏向于众多和无内含子共提取的污染真菌（主要是Dothideomycetes，Chaetoacetomycetes，并Sordariomycetes在子囊菌门，和成员的担子菌门），其中栖息地衣菌体。最大似然分析相结合的五个位点的数据集为82个成员的蜡蚧菌提供了一个很好的解决和支持树相比，现有的craconogenies。我们证实了单系性的三个公认的亚类的蜡蚧，Acarosporomycetidae，Ostropomycetidae，和蜡蚧菌亚科;后者划定为单系的第一次，与家庭Umbilicariaceae和Hypocenomycescalaris排除。Candelariella属（以前属于Candelariaceae，现在属于蜡蚧科）代表了蜡蚧菌纲中的第一个进化分裂，在Acarosporomycetidae分化之前。本研究为今后地衣及相关子囊菌多位点系统发育研究提供了必要的位点选择依据。(c)2006年爱思唯尔公司All rights reserved.
The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood boot-strap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes. (c) 2006 Elsevier Inc. All rights reserved.