DNA barcode identification of Podocarpaceae--the second largest conifer family.
DNA barcode identification of Podocarpaceae--the second largest conifer family.
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DOI：
10.1371/journal.pone.0081008
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Schulz C
中科院分区：
文献类型：
--
作者：
Little DP;Knopf P;Schulz C
我们已经为代表罗汉松科所有18个现存属的320个标本生成了matK、rbcL和nrITS2 DNA条形码。样本包括198个已确认物种中的145个。对获得3个标记的159个个体(代表15属97种)进行了序列质量和物种鉴别的比较分析。绝大多数序列是高质量的(B 30 = 0.596-0.989)。即使是最低质量的序列也超过了条形码数据标准的最低要求。在少数产生低质量序列的情况下，无法辨别负责的机制。标记物或标记物组合的区分力差异无统计学意义(p = 0.05)。条形码标记单独和组合的识别力很低(最大为物种的56.7%)。在某些情况下，尽管存在表面上有用的变异(物种间的基因类型相同)，但物种歧视失败了，但在许多情况下，根本就没有序列变异。当同时考虑这三个标记时，50.5%的物种观察到条形码间隙(种内最大P距离和GT；种间最小P距离)。条形码间隙的存在不能预测识别成功(p = 0.02)，而且不同标记之间条形码间隙的频率在统计学上没有显著差异(p = 0.05)。此外，每个物种抽样的个体数量与条形码缺口的存在之间没有相关性(p = 0.27)。
We have generated matK, rbcL, and nrITS2 DNA barcodes for 320 specimens representing all 18 extant genera of the conifer family Podocarpaceae. The sample includes 145 of the 198 recognized species. Comparative analyses of sequence quality and species discrimination were conducted on the 159 individuals from which all three markers were recovered (representing 15 genera and 97 species). The vast majority of sequences were of high quality (B 30 = 0.596–0.989). Even the lowest quality sequences exceeded the minimum requirements of the BARCODE data standard. In the few instances that low quality sequences were generated, the responsible mechanism could not be discerned. There were no statistically significant differences in the discriminatory power of markers or marker combinations (p = 0.05). The discriminatory power of the barcode markers individually and in combination is low (56.7% of species at maximum). In some instances, species discrimination failed in spite of ostensibly useful variation being present (genotypes were shared among species), but in many cases there was simply an absence of sequence variation. Barcode gaps (maximum intraspecific p–distance > minimum interspecific p–distance) were observed in 50.5% of species when all three markers were considered simultaneously. The presence of a barcode gap was not predictive of discrimination success (p = 0.02) and there was no statistically significant difference in the frequency of barcode gaps among markers (p = 0.05). In addition, there was no correlation between number of individuals sampled per species and the presence of a barcode gap (p = 0.27).
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