Kartavtsev Yuri P, Jung Sang-Oun, Lee Young-Mi, Byeon Hwa-Kun, Lee Jae-Seong
Department of Chemistry, and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea.
Gene. 2007 Jul 1;396(1):13-27. doi: 10.1016/j.gene.2007.01.027. Epub 2007 Feb 12.
Mitochondrial DNA (mtDNA) from the bullhead torrent catfish, Liobagrus obesus, was isolated by long-polymerase chain reaction (Long-PCR) with universal primers and was fully sequenced by primer working using flanking sequences. The complete mtDNA from L. obesus was 16,531 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, demonstrating a structure very similar to that of other bony fish. An analysis of the protein-coding genes revealed a statistically substantiated bias in (T+C): (A+G) content, supporting earlier findings regarding this peculiarity. As indicated by a chi-square test, the observed scores for pyrimidine and purine content were different from those expected assuming a 50:50 ratio: chi(2)=41.63, d.f.=5, p<0.000001 for three categories, including the 1st, 2nd, and 3rd codon positions. Further, there was a difference in nucleotide content between ND6 and the other 12 protein-coding genes in L. obesus. The values of p-distances, as summarized for different scales of evolutionary history at the Cyt b gene, revealed a clear pattern of increased nucleotide diversity at four levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. Scores of average p-distances of the four categories in catfish were (1) 1.59+/-0.54%, (2) 5.28+/-1.72% (3) 16.37+/-1.26%, and (4) 19.81+/-0.14%, respectively. These data support the hypothesis that speciation in the order Siluriformes, in most cases, follows a geographic mode through the accumulation of a numerous small genetic changes over a long time period. A phylogenetic tree for the bullhead torrent catfish and several other fish species belonging to the order Siluriformes was developed on the basis of respective Cyt b sequences (1138 bp); the analysis revealed a monophyletic origin for the five examined families. A species-specific clustering of sequences from single species was obtained, supporting additionally basic phylogenetic information for the catfish and the barcoding suitability of Cyt b sequence data. Lastly, one of the well-supported properties of our phylogenetic tree (99% repetition level in our analysis) was the monophyletic placement of all catfish (order Siluriformes) among other ray-finned fish of the class Actinopterigii. Also discussed herein are the aspects of phylogeny based on the 16S rRNA gene.
通过使用通用引物的长聚合酶链反应（Long-PCR）从钝头鮡（Liobagrus obesus）中分离出线粒体DNA（mtDNA），并利用侧翼序列通过引物步移法对其进行了全序列测定。钝头鮡的完整mtDNA长度为16,531 bp，包含13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和一个控制区，其结构与其他硬骨鱼非常相似。对蛋白质编码基因的分析揭示了（T+C）:（A+G）含量在统计学上有显著偏差，支持了关于这一特性的早期研究结果。卡方检验表明，嘧啶和嘌呤含量的观察值与假设为50:50比例时的预期值不同：对于包括第一、第二和第三密码子位置在内的三个类别，卡方值（χ2）=41.63，自由度（d.f.）=5，p<0.000001。此外，钝头鮡的ND6基因与其他12个蛋白质编码基因在核苷酸含量上存在差异。根据细胞色素b（Cyt b）基因在不同进化历史尺度上总结的p距离值，揭示了在四个水平上核苷酸多样性增加的明显模式：（1）种内，（2）属内，（3）科内，（4）目内。鲶形目鱼类这四个类别的平均p距离得分分别为：（1）1.59±0.54%，（2）5.28±1.72%，（3）16.37±1.26%，（4）19.81±0.14%。这些数据支持了这样一个假说，即鲶形目在大多数情况下的物种形成是通过在很长一段时间内积累大量小的遗传变化而遵循地理模式的。基于各自的细胞色素b序列（1138 bp）构建了钝头鮡和其他几种鲶形目鱼类的系统发育树；分析揭示了所研究的五个科具有单系起源。获得了来自单个物种的序列的物种特异性聚类，这进一步支持了鲶形目鱼类的基本系统发育信息以及细胞色素b序列数据的条形码适用性。最后，我们的系统发育树的一个得到充分支持的特性（在我们的分析中重复水平为99%）是所有鲶形目鱼类（鲶形目）在其他辐鳍鱼纲硬骨鱼中的单系定位。本文还讨论了基于16S rRNA基因的系统发育方面的问题。
