Abstract:

Nymphaea is primitive angiosperm with important economic， medicinal and ornamental value. The characteries analysis of codons in the coding region of chloroplast genome is of great significance for chloroplast genetic engineering and species phylogeny. The codon usage profiling of chloroplast genomes in Nymphaea was systematically analyzed， and the phylogenetic relationship was decoded among the 22 Nymphaea plants. The results showed that the codon adaptation index of chloroplast genome from total 22 Nymphaea ranged from 0.168 to 0.170， and the effective codon number ranged from 51.301 to 51.577， which indicated weak codon preference in Nymphaea. The GC contents of bases at different positions of codon were 46.26% （GC1）， 38.67% （GC2） and 32.54% （GC3）， respectively， indicating that A and U used in chloroplast codons were rich in Nymphaea. The analysis of ENC plot， PR2 plot and neutral plot showed that the codon bias in the chloroplast genome was mainly affected by selection pressure. Correlation analysis showed that ENC value was significantly correlated with GC2 and GC3 （P<0.05）， which indicated that the composition of bases in the 1^st and 2^nd had great influence on codon using pattern. The optimal codon analysis showed that there were quantitative differences of the optimal codons among these species （5~11）， and two optimal codons （CCA and AAU） were determined. Phylogenetic analysis showed that the classification results based on relative synonymous codon usage （RSCU） value were consistent to those based on chloroplast gene sequences （matK， trnL?trnF and coding sequence）， which indicated that the codon using characteristics among related species of Nymphaea were similar， and the classification results based on codon RSCU value divided Nymphaea into 3 subgenera， which provided a theoretical basis for the phylogeny， species classification and chloroplast genetic engineering of Nymphaea.

Key words: Nymphaea, chloroplast genome, codon usage bias, phylogeny

摘要：

睡莲属植物是具有重要的经济、药用和观赏价值的原始被子植物。分析其叶绿体基因组编码区密码子的使用特征，以22种睡莲的叶绿体基因组为研究对象，对睡莲叶绿体基因组密码子的偏好性及睡莲属植物间的进化关系进行了系统分析。结果表明，22种睡莲植物叶绿体基因组密码子适应指数（codon adaptation index，CAI）为0.168~0.170，有效密码子数（effective number of codon，ENC）为51.301~51.577，表明睡莲属叶绿体基因组密码子偏好性较弱；密码子不同位置的GC含量分别为46.26%（第1位，GC1）、38.67%（第2位，GC2）和32.54%（第3位，GC3），表明睡莲属植物叶绿体密码子偏好使用A/U结尾。ENC-plot、PR2-plot和中性绘图分析表明，选择压力是影响睡莲属叶绿体编码区密码子偏好性的重要因素。相关性分析表明，ENC与GC2、GC3呈显著相关（P<0.05），密码子第2、3位碱基组成对密码子使用模式存在较大影响。最优密码子分析表明，22种睡莲最优密码子存在数量差异（5~11个），共有的2个最优密码子为CCA、AAU。系统发育分析显示，基于同义密码子相对使用度（relative synonymous codon usage，RSCU）和基于叶绿体基因序列（matK、trnL?trnF和编码序列）的分类结果相似，说明睡莲属近缘种之间密码子使用特征相似，基于RSCU将睡莲属划分为3个亚属，为睡莲属植物系统进化、物种分类及叶绿体基因工程的相关研究提供了理论依据。

关键词: 睡莲属, 叶绿体基因组, 密码子偏好性, 系统发育