大花君子兰叶绿体基因组及其特征

采用Illumina MiSeq测序平台对大花君子兰(Clivia miniata)叶片总DNA进行测序,通过组装获得了其叶绿体基因组(cpDNA)全长序列(158 114 bp)。对其cpDNA注释得到135个基因,包含87个蛋白编码基因、40个tRNA基因和8个r RNA基因。采用生物信息学方法对获得的cpDNA进行简单序列重复(SSR)分析和密码子偏好性分析。结果显示:①大花君子兰cpDNA中共有61个SSR位点,其中单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸和六核苷酸重复数分别为38、9、2、8、3和1个,多数SSR分布在基因间隔区;②大花君子兰cpDNA密码子偏爱以A或U(T)结尾,亮氨酸使用频率最高,半胱氨酸使用频率最低。基于24种植物的cpDNA全长和23种植物的叶绿体ycf2基因序列进行系统发育分析,结果显示大花君子兰与石蒜科植物在同一分支,显示最近的亲缘关系,支持大花君子兰属于石蒜科。基于叶绿体ycf2的系统发育分析结果与基于cpDNA全长的系统发育分析研究结果大部分相同,支持ycf2基因可以代替cpDNA全长用于植物系统发育分析。

Complete Chloroplast Genome Sequence of Clivia miniata and Its Characteristics

The total DNA of Clivia miniata leaves was sequenced by Illumina MiSeq sequencing platform，and the full-length sequence（158 114 bp）of chloroplast genome（cpDNA）was obtained by assembly. A total of 135 genes were annotated in the cpDNA. The 135 genes included 87 protein coding genes，40 tRNA genes and 8 rRNA genes. Both simple sequence repeat（SSR）and codon preference of the cpDNA were analyzed using bioinformatics method. The results showed that（1）the total number of SSR loci in the cpDNA of C. miniata was 61，of which 38，9，2，8，3 and 1 were mononucleotide，dinucleotide，tirnucleotide，tetranucleotide，pentanucleotide and hexanucleotide repeats，respectively，and most of the SSRs were located in the intergenic regions；（2）the codons in cpDNA of C. miniata tended to end with A or U(T)，the frequency of serine was the highest and that of cysteine was the lowest. In addition，the phylogenetic analysis was carried out based on the full sequence of 24 cpDNAs and the sequence of 23 ycf2 genes of chloroplasts. The results showed that both C. miniata and Amaryllidaceae plants were clustered into one branch，which not only indicated the closest genetic relationship of them but also supported that C. miniata belongs to Amaryllidaceae. The results of phylogenetic analysis based on chloroplast ycf2 are mostly the same as that based on full sequence of cpDNA，which indicated that the ycf2 genes could replace full-length cpDNAs for plant phylogenetic analysis.