11种鲈形目鱼类的核糖体基因GC含量及其与硬骨鱼类的特征比较

核糖体基因为串联重复多拷贝的基因,包括3个编码基因(18S,5.8S,28S)和两个间隔区ITS1(internal transcribed spacer 1)和ITS2(internal transcribed spacer 2)。目前,对核糖体基因的相关报道主要集中在个体内不同拷贝间的多态特征,以及其作为分子标记在系统演化关系中的应用,GC含量作为一项非常重要的核苷酸序列指标,而鲜有报道。为了探讨鱼类的核糖体基因GC含量特征以及间隔区是否也存在GC平衡现象,本研究选择了鲈形目(Perciformes)5科11种鱼类5个片段的核糖体基因进行研究,包括尖吻鲈科(Latidae)、射水鱼科(Toxotidae)、军曹鱼科(Rachycentridae)、剑鱼科(Xiphiidae)、鲹科(Carangidae)。获得了1651个单克隆序列,通过分析并比较已有的其他硬骨鱼序列片段的GC含量变化特征,结果发现:本研究鱼类的18S的GC含量为52.6%~57.1%(平均54.6%),5.8S为55.6%~58.9%(平均57.4%),28S为64.2%~65.8%(平均64.6%),ITS1为56.5%~73.0%(平均65.0%),ITS2为62.3%~77.5%(平均69.1%)。编码区的GC含量相对较保守,变异范围较小,18S和5.8S变化范围明显小于间隔区,28S则位于间隔区的最低值和最高值之间。因此,我们发现硬骨鱼核糖体ITS高于60%的GC含量是该类群的一个特征,并且高GC含量的ITS1和ITS2序列中不存在明显的高GC富集区,其含量高低的变化与序列长度也没有相关性。本研究11种鱼类的ITS1和ITS2的GC含量在种内的相似性既有大于也有小于种间相同片段的相似性,因此GC平衡现象只存在部分种类中。本研究结果可为鱼类核糖体基因序列特征的进一步研究及利用提供科学依据。

Analysis of the GC content of ribosomal genes of 11 species of Perci-formes and comparison with other teleostean fishes

The ribosomal RNA gene (rDNA) cluster consists of multiple units of three coding genes (18S, 5.8S, and 28S) as well as two internal transcribed spacers (ITS1 and ITS2) separating the coding regions. Thus far, stu-dies on these five fragments mainly focused on the polymorphism of different copies within each individual sam-ple and identification of useful markers for phylogenetic relationship analysis. However, there are limited studies related to the features of GC content, which is a very important characteristic of ribosomal RNA gene. The cha-racteristics of rDNA GC content and whether the GC balance phenomenon exists in the coding regions in fishes were investigated by selecting 11 species from five families of Perciformes, including Latidae, Toxotidae, Rachy-centridae, Xiphiidae, and Carangidae. In all, 1651 monoclones from the five fragments mentioned above were obtained. The GC content features were analyzed based on the sequences from the 11 species or the datasets from other teleostean fishes retrieved from GenBank. The results from the above two analyses were compared. The fol-lowing results were obtained. First, the GC content of 18S, 5.8S, 28S, ITS1, and ITS2 ranged from 52.6% to 57.1% (average, 54.6%), 55.6% to 58.9% (average, 57.4%), 64.2% to 65.8% (average, 64.6%), 56.5% to 73.0%(average, 65.0%), and 62.3% to 77.5% (average, 69.1%), respectively. Second, compared with non-coding regions, coding regions were relatively conserved. The GC content of the coding genes varied in smaller ranges than those of the internal transcribed spacers. The GC contents of 18S and 5.8S were lower than those of ITS1 and ITS2, but that of 28S was between the lowest and highest values of ITS1 and ITS2. Therefore, we found that the GC content of non-coding regions was higher than 60%, which was a remarkable characteristic of these fishes, and no correla-tion was found between fragment length and higher GC content. Further, no obvious G, C, or GC rich block was found in the high-GC-content regions of ITS1 and ITS2 sequences. Third, the similarity of GC content between ITS1 and ITS2 within the same species could be higher or lower than that of the same fragment among different species within the 11 species. Therefore, the GC balance phenomenon is not universal and only exists in species whose intra-species GC content similarity is lower than the inter-species GC content similarity. The results of this study might provide a scientific basis for further studies and facilitate the utilization of the ribosomal gene cha-racteristics of fish.