| 摘要: |
| 为确定桃叶珊瑚属（Aucuba）植物叶绿体基因组的结构组成及其序列差异，揭示其属下种间亲缘关系，本研究对桃叶珊瑚（A. chinensis）、花叶青木（A. japonica var. variegata）等6种桃叶珊瑚属植物和丝缨花属植物黄杨叶丝缨花（Garrya buxifolia）进行二代测序，利用生物信息学软件对其叶绿体基因组序列进行组装和注释，对6种桃叶珊瑚属植物叶绿体基因组序列进行基本特征分析、序列比较以及系统发育分析。结果表明：（1）桃叶珊瑚属植物叶绿体基因组具典型的环状四分体结构，6条序列全长157 891~158 325 bp，均编码114个基因，包括80个蛋白质编码基因、30个tRNA基因和4个rRNA基因；（2）6种植物叶绿体基因组高频密码子数均为29个，偏好以A/U结尾，确定了这6条序列的最优密码子共100个，包含12个共有的最优密码子；（3）6条叶绿体基因组序列共检测到270条散在重复序列，133条串联重复序列以及412个SSR位点；（4）比较基因组学分析结果表明，该属植物叶绿体基因组序列高度保守；（5）从叶绿体基因组中筛选出10个高变片段；（6）系统发育分析结果支持桃叶珊瑚属为一支持率高的单系，其与丝缨花属关系较近。该研究对象的5种桃叶珊瑚属植物以及1种丝缨花属植物的叶绿体基因组均为首次测序组装，揭示了桃叶珊瑚属及其属下种间的系统发育关系，为桃叶珊瑚属植物的分类鉴定和系统发育提供了参考资料。 |
| 关键词: 桃叶珊瑚属，叶绿体基因组，序列变异，重复序列，密码子偏好性，系统发育分析 |
| DOI： |
| 分类号: |
| 基金项目:广州中医药大学“青年英才培养工程”项目（QNYC20190105）；国家自然科学青年科学基金项目（No.31700166）；2019年医疗服务与保障能力提升补助资金（中医药事业传承与发展部分）“全国中药资源普查项目”（财社〔2019〕39号） |
|
| The sequence characteristics of chloroplast genomes and phylogenic analysis of genus Aucuba |
|
LI Juan, TONG Yi, FAN Zhichao, TONG Jiayun
|
|
Guangzhou University of Chinese Medicine
|
| Abstract: |
| To determine the genetic structure and sequence differences of the chloroplast genome of genus Aucuba and to reveal their interspecies relationship, the chloroplast genomes of six Aucuba species including A. chinensis and A. japonica var. variegata as well as Garrya buxifolia were sequenced using high-throughput sequencing technology. The chloroplast genomes were assembled and annotated using Bioinformatics software. Phylogenetic analysis was conducted combined with the published chloroplast genomes of A. japonica. The results were as follows: (1) Six Aucuba plants chloroplast genomes exhibited typical quadripartite circular structure (i.e., LSC, SSC, IRB and IRA) and were between 157 891-158 325 bp in length; (2) A total of 114 genes were annotated (except the duplicate genes on IRs), including 80 protein-coding genes (CDS), 30 tRNA genes and 4 rRNA genes; (3) 270 interspersed repeats, 133 tandem repeats and 412 SSR loci were detected in the six Aucuba chloroplast genomes; (4) A total of 29 high frequency codons prefer ending in A/U. 100 optimal codons were filtered out in total, 12 of which were shared by six Aucuba species; (5) Comparative analysis of six Aucuba species reveals a highly conserved chloroplast genome sequence; (6) Ten highly divergent regions were identified based on nucleotide diversity analysis; (7) The phylogenetic trees were constructed using maximum likelihood (ML) and Bayesian (BI) showing a similar topology. The results support that genus Aucuba was monophyletic, as a sister to genus Garrya. We first sequenced the complete chloroplast genomes of these five Aucuba species and one Garrya species. The results reveal the interspecies relationships and the taxonomic status of genus Aucuba, providing genetic resources for the classification, identification and phylogeny of the genus Aucuba. |
| Key words: genus Aucuba, chloroplast genome, sequence variation, repeated sequences, codon preference, phylogeny |
