Kretzer A M, Bruns T D
Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, California, 94720-3102, USA.
Mol Phylogenet Evol. 1999 Dec;13(3):483-92. doi: 10.1006/mpev.1999.0680.
Complete nucleotide sequences have been determined for atp6 from Suillus luteus and cox3 from Suillus sinuspaulianus (Boletales, Hymenomycetes, Basidiomycota), which code for ATPase subunit 6 and cytochrome oxidase subunit 3, respectively. These sequences were used to design PCR primers for the amplification of partial atp6 and cox3 sequences from other members of the Boletales and outgroup taxa. In atp6 and cox3 from Russula rosacea, one of the outgroup taxa, we observed a number of in-frame TGA(trp) codons, which imply a Neurospora crassa-type mitochondrial code in R. rosacea and possibly in basidiomycetes in general. Interestingly, however, most basidiomycetes other than R. rosacea appear to strongly prefer the TGG(trp) codon, which is unusual, given the strong A + T bias in fungal mitochondrial genomes. Pairwise comparisons were performed between atp6 sequences from increasingly divergent fungal lineages, and results show that all three codon positions become saturated in substitutions after an estimated divergence time of approx 300 Ma. This means that atp6 is likely to provide phylogenetic resolution within fungal classes but not at higher taxonomic levels. Also, because of the strong A + T bias in fungal mitochondrial genomes, A/T transversions were found to be more common than any other type of substitution, resulting in transversions being about two to three times more common in most pairwise sequence comparisons. Finally, atp6 sequences were used to infer phylogenetic relationships between 27 taxa from the Boletales and 4 outgroup taxa. Analyses were performed (i) on nucleotide sequence data using parsimony (successive approximation) as well as maximum likelihood methods and (ii) on deduced amino acid sequences using distance methods based on empirical substitution probabilities. Results from the various analyses are largely concordant with each other as well as with prior analyses of partial mitochondrial large-subunit rDNA (mtLSU rDNA). Analysis of the combined atp6 and mtLSU rDNA sequences results in increased bootstrap support for several key branches. Relationships that have been resolved for the first time in the current analysis are discussed.
已确定了黄斑牛肝菌的atp6基因和保罗牛肝菌（牛肝菌目、层菌纲、担子菌门）的cox3基因的完整核苷酸序列，它们分别编码ATP酶亚基6和细胞色素氧化酶亚基3。这些序列被用于设计PCR引物，以扩增牛肝菌目其他成员和外类群分类单元的部分atp6和cox3序列。在其中一个外类群分类单元——酒红乳菇的atp6和cox3中，我们观察到许多框内TGA（色氨酸）密码子，这意味着酒红乳菇以及可能一般担子菌中存在粗糙脉孢菌型线粒体密码子。然而，有趣的是，除酒红乳菇外的大多数担子菌似乎强烈偏好TGG（色氨酸）密码子，鉴于真菌线粒体基因组中强烈的A + T偏向，这是不寻常的。对来自分歧越来越大的真菌谱系的atp6序列进行了成对比较，结果表明，在估计的分歧时间约300百万年后，所有三个密码子位置的替换都达到了饱和。这意味着atp6可能在真菌类内提供系统发育分辨率，但在更高的分类水平上则不然。此外，由于真菌线粒体基因组中强烈的A + T偏向，发现A/T颠换比任何其他类型的替换更常见，导致在大多数成对序列比较中，颠换的频率大约是其他替换的两到三倍。最后，atp6序列被用于推断牛肝菌目中27个分类单元与4个外类群分类单元之间的系统发育关系。分析分别进行：（i）使用简约法（逐步逼近）以及最大似然法对核苷酸序列数据进行分析，（ii）使用基于经验替换概率的距离法对推导的氨基酸序列进行分析。各种分析的结果彼此之间以及与先前对部分线粒体大亚基rDNA（mtLSU rDNA）的分析结果基本一致。讨论了在当前分析中首次解析的关系。
