5科11种鱼类ITS1特征分析及其在系统分类研究中的适用性

为了探讨ITS1作为分子标记用于鱼类系统演化的适用性,实验选取鲈形目5科11种鱼类为研究对象,包括尖吻鲈科、射水鱼科、军曹鱼科、剑鱼科和鲹科。通过克隆和测序等技术共获得了348条ITS1序列,长度范围为442~661 bp;通过对所有序列的长度、变异位点数量、GC含量、核苷酸多样性及单倍型多样性指数等遗传特征比较分析发现,11种鱼类ITS1序列无论是在种内还是在种间,长度和序列都表现出较为明显的多态性。特别是在军曹鱼中,70条克隆的长度范围为648~661 bp,但有一条序列存在55 bp缺失,结合该序列的GC含量,二级结构和最小自由能,推断该序列为假基因。以鮣为外类群,基于核糖体ITS1序列构建的邻接树显示在物种种类水平上,不同个体的克隆都按种类聚支,ITS1可以用于该类群物种的区分;在属级水平上,ITS1将11属鱼类完全区分开,能够用于属级水平的区分;在科级水平上,虽然鲹科分为2支的分子结果和形态分类存在差异,但ITS1构建的系统关系与线粒体分子标记构建的系统进化树相似。研究表明,核糖体ITS1可以作为一种有效的分子标记用于研究鱼类的系统分类研究,并且不同的分类阶元其解析能力不同,这将为鱼类核糖体的研究提供科学依据。

The analysis of ITS1 characteristics of 11 species from 5 families and its application in phylogenetic research

In recent years, the study on ribosomal genes has always been a hot spot. However, only a few reports on ribosomal genes of fish were reported, especially about the ITS1 (internal transcribed spacer 1) pseudogene. In order to investigate the applicability of ITS1 as a molecular marker in species identification and the phylogenetic analysis in fishes, 11 species from five families, belonging to Perciformes, were selected as the representatives, including Latidae, Toxotidae, Rachycentridae, Xiphiidae and Carangidae. A total of 348 ITS1 sequences were obtained, and the length of these sequences ranged from 442 to 661 bp. Compared with the genetic characteristics, such as the length differences, number of variable sites, GC content, nucleotide diversity and haplotype diversity, the ITS1 sequences of 11 species showed obvious polymorphism within intra-species and inter-species. The unusual case was that a shorter sequence with 55 bp deletion was detected among the 71 clones of Rachycentron canadum. Based on the data of GC content, secondary structure and minimum free energy of the shorter sequence, this sequence was inferred as pseudogene. The neighbor joining tree was constructed based on ITS1 sequences of 11 species from five families with Remora australis and Echeneis naucrates as outgroup. The result showed that the ITS1 sequences of different individuals from each species gathered together, and the species from each genus also grouped to one clade. These indicated the ITS1could be used as the molecular marker for phylogenetic analysis at the genus level. At the family level, the Carangidae was divided into two clades, which was similar to the result of phylogenetic analysis based on the mitochondrial marker, but both were contradictory with the classification based on morphological characteristics. To a certain extent, the ITS1 plays a role of molecular marker for phylogenetic analysis at the family level. These results provide useful scientific information for further studies on ITS1 in fishes and contribute to polymorphism analyses of ribosomal RNA genes in teleostean fishes.