Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus
Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus
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DOI：
10.3852/10-331
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发表时间：
2011-07-01
期刊：
影响因子：
2.8
通讯作者：
Banik, Mark T.
中科院分区：
文献类型：
--
作者：
Lindner, Daniel L.;Banik, Mark T.
rDNA的区域通常用于推断真菌物种之间的系统发育关系，并作为DNA条形码用于鉴定。这些区域出现在大的串联阵列中，协同进化被认为减少了这些阵列中拷贝之间的基因组内变异，尽管仍然可能存在一些变异。系统发育研究通常使用一致性测序，其有效地隐藏了大多数基因组内变异，但是含有基因组内变异的克隆序列在DNA数据库中变得普遍。为了了解使用克隆的rDNA序列在系统发育分析中的影响，我们扩增和克隆的ITS区从纯培养物的六个Laetiporus物种和一个Wolfiporia物种（担子菌门，多孔菌目）。从21个培养物中随机选择平均66个克隆并测序，总共产生1399个可解释的序列。在来自三个物种分支的六个培养物中观察到ITS拷贝之间的显著变异（序列相似性的变异>= 5%）。cincinnatus，L.进化枝J和Wolfiporiacetonophypha），用克隆序列进行系统发育分析产生了相对于用共有序列进行分析的不同的树。克隆了L. cincinnatus属于多个种的分支，有大量的克隆L. cincinnatus序列落入完全新的分支，如果对它们本身进行分析，最有可能被认为是“未描述的”或“新的”分类群。使用95%的截止值来定义操作分类单位（OTU）产生了7个具有共有ITS序列的Laetiporus OTU和20个具有克隆ITS序列的OTU。克隆rDNA序列的使用可能是有问题的真菌系统发育分析，以及在真菌条形码的倡议和努力，以检测环境样品中的真菌病原体。
Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus sequencing, which effectively conceals most intragenomic variation, but cloned sequences containing intragenomic variation are becoming prevalent in DNA databases. To understand effects of using cloned rDNA sequences in phylogenetic analyses we amplified and cloned the ITS region from pure cultures of six Laetiporus species and one Wolfiporia species (Basidiomycota, Polyporales). An average of 66 clones were selected randomly and sequenced from 21 cultures, producing a total of 1399 interpretable sequences. Significant variation (>= 5% variation in sequence similarity) was observed among ITS copies within six cultures from three species clades (L. cincinnatus, L. sp. clade J, and Wolfiporia dilatohypha) and phylogenetic analyses with the cloned sequences produced different trees relative to analyses with consensus sequences. Cloned sequences from L. cincinnatus fell into more than one species clade and numerous cloned L. cincinnatus sequences fell into entirely new clades, which if analyzed on their own most likely would be recognized as "undescribed" or "novel" taxa. The use of a 95% cut off for defining operational taxonomic units (OTUs) produced seven Laetiporus OTUs with consensus ITS sequences and 20 OTUs with cloned ITS sequences. The use of cloned rDNA sequences might be problematic in fungal phylogenetic analyses, as well as in fungal bar-coding initiatives and efforts to detect fungal pathogens in environmental samples.