Characterization and phylogenetic analysis of the complete chloroplast genome of Dictamnus dasycarpus Turcz.
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摘要:
通过高通量测序技术获取白鲜（Dictamnus dasycarpus Turcz.）叶绿体全基因组序列，并采用生物信息学方法对其结构特征和系统发育关系进行了分析。结果显示，白鲜叶绿体基因组具有典型的环状四分体结构，总长度为157 139 bp，大单拷贝区和小单拷贝区长度分别为84 478 bp和18 587 bp，一对反向重复序列长度为27 037 bp，总GC含量为38.5%。共注释到132个基因，包括87个蛋白编码基因（PCGs）、8个rRNA和37个tRNA基因。计算相对同义密码子使用频率（RSCU），发现编码最多的密码子是亮氨酸（Leu/L），编码最少的密码子是半胱氨酸（Cys/C），RSCU值大于1的密码子有32个。白鲜叶绿体基因组共包含61个简单重复序列。通过对芸香科8种植物的叶绿体基因组结构进行比较，发现白鲜属与其他属的叶绿体基因组结构基本一致，并未发生重排和倒位现象。系统进化树分析结果表明，白鲜与臭常山（Orixa japonica Thunb.）的亲缘关系最近。
Abstract:The whole genome sequence of Dictamnus dasycarpus Turcz. chloroplasts was obtained by high-throughput sequencing, and its structural features and phylogenetic relationships were analyzed by bioinformatics. Results showed that the chloroplast genome had a typical circular tetrameric structure with a total length of 157 139 bp, a large and small single-copy region of 84 478 bp and 18 587 bp, respectively, a pair of inverted repeat sequences of 27 037 bp, and a total GC content of 38.5%. In total, 132 genes were annotated, including 87 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. The frequency of relative synonymous codon use (RSCU) was calculated, showing that the most encoded codon was leucine (Leu/L) and the least encoded codon was cysteine (Cys/C), with 32 codons with RSCU values greater than 1. The D. dasycarpus chloroplast genome contained a total of 61 simple repetitive sequences. Compared with eight species of Rutaceae, the chloroplast genome structure was generally consistent between Dictamnus and other genera, with no rearrangements or inversions. Phylogenetic analysis showed that D. dasycarpus was most closely related to Orixa japonica Thunb.
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Keywords:
- Dictamnus dasycarpus /
- Chloroplast genome /
- Rutaceae /
- Codon /
- Phylogeny
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图 2 白鲜叶绿体基因组相对同义密码子使用度
Figure 2. RSCU value of chloroplast genome in Dictamnus dasycarpus
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图 4 芸香科7种植物叶绿体基因组的可视化比对
使用广东酒饼簕为参考基因组。横轴表示比对的7个芸香科物种的叶绿体基因组。垂直比例表示百分比同一性，范围为 50% ~ 100%。不同颜色表示不同基因的功能。
Figure 4. Visual alignment of chloroplast genomes of seven species of Rutaceae
Atalantia kwangtungensis was used as a reference genome. Horizontal axis indicates seven aligned chloroplast genomes. Vertical scale represents percentage identity, ranging from 50%–100%. Different colors indicate functions of different genes.
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图 5 芸香科植物叶绿体基因组IR/SC边界比对图
Figure 5. Border regions of complete chloroplast genomes of Rutaceae plants
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图 6 芸香科植物叶绿体全基因组系统发育树
Figure 6. Phylogenetic tree based on complete chloroplast genomes of Rutaceae plants
表 1 白鲜叶绿体基因组碱基组成
Table 1 Base composition of chloroplast genome in Dictamnus dasycarpus
区域
RegionA / % T / % G / % C / % 长度
Length / bpGC / % 大单拷贝区（LSC） 30.9 32.2 17.9 19 84478 36.9 小单拷贝区（SSC） 33.7 33.2 16 17.1 18587 33.1 反向重复序列A（IRA） 28.7 28.4 22.2 20.7 27037 42.9 反向重复序列B（IRB） 28.4 28.7 20.7 22.2 27037 42.9 合计 30.4 31.1 18.9 19.6 157139 38.5 
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