外来入侵物种的基因签名及其遗传多样性聚类分析

Genomic signature and cluster analysis of genetic diversity of alien invasive species

密码子的使用频率分布能够反映一定的生物特性,因而可作为一种基因签名。本文使用CGR方法来研究外来入侵物种不同组织序列的基因签名及遗传多样性聚类分析,首先得出了刺花莲子草(Alternanthera pungens),紫茎泽兰(Ageratinaadenophora),水葫芦(Eichhornia crassipes),微甘菊(Mikania micrantha),土荆芥(Chenopodium ambrosioides),一枝黄花(Solidagocanadensis)等6种外来入侵植物的31条序列核苷酸字串长k=1到k=6的情况,并选取k=3,即基因序列的密码子,作为生物特性的一个重要表达。并且构造序列间的CGR欧式距离,进而对外来入侵植物序列遗传多样性进行了聚类分析。通过对所获得的6种外来入侵植物的31条序列的基因签名,得出如下结果:CGR是一种简便且计算量小的方法,且基于CGR方法的基因签名,具有典型的生物特性;入侵植物的基因序列在密码子的使用上是非均衡的,且物种亲缘关系近的,则基因签名相似越高;而且基因签名也揭示出了密码子的第三位碱基偏好使用碱基T的现象,与一般物种密码子第三位碱基偏好G/C情况有强烈反差。此外,从获得的6个物种的31条序列聚类谱系图可以直观看出,入侵植物间存在着一定的亲缘关系,遗传多样性较丰富。由于我们所建立的基于CGR方法的基因签名,不仅能够反映植物特性和进化关系,而且能揭示序列中密码子和碱基的偏好使用情况,因而该方法有利于对外来入侵物种的遗传多样性分析、风险评估及预防控制等提供科学依据。

Alien invasive species had been a global eco-environmental problem, resulting in huge economic loss. The distribution of codon usage could reflect some biological characteristics, therefore it could be a genomic signature. The paper proposed a genomic signature-based approach, using CGR with word length of k=3, which could be applied to analyse the sequences of alien invasive species and cluster analysis of genetic diversity. Firstly, we gained these cases of nucleotide word lengths （k= 1 to 6） on 31 sequences of 6 alien invasive plants, which were altemanthera pungens, ageratina adenophora, eichhomia crassipes, mikania micrantha, chenopodium ambrosioides and solidago, respectively, and chosen word length of k=3, also was the codons, which be as the important biological expression. And then we constructed the Euclidean distance of CGR, and finally gained the dendrograms of alien invasive species. And these results were shown by analyzing these genomic signatures of 31 sequences of 6 alien invasive, respectively. CGR was a handy method with small calculation. And the genomic signature based on CGR could reflect some typical biological properties. The usage of codon in the gene sequence of alien invasive plant was unbalanced. The more closed genetic relationship of alien invasive species were, the more similar their genomic signatures were. Among these genomic signatures, a especial phenomena was revealed, and that was the third base of codons of gene sequence preferred to using nucleotide T, which was very different to these common species preferring to using nucleotide G or C. What＇s more, from the dendrograms of clustering of 31 sequences of 6 alien invasive plants, we could see clearly alien invasive plants had some relationships, and genetic diversity was abundant. By using this constructed method of genomic signature based on CGR, not only efficiently reflected these biological characteristics and evolutionary relationship of alien invasive plants, but also revealed the usage condition of codon and base in the codon of alien invasive plants. Therefore, the structured method which was benefit to offering scientific basis for analysis of genetic diversity, risk assessment, prevention and control of alien invasive plants.