| 引用本文: | 王一麾, 谢宜飞, 张志翔, 金佳怡, 邱相东, 童 阳.猴欢喜叶绿体全基因组及杜英科系统地位分析[J].广西植物,2022,42(1):39-48.[点击复制] |
| WANG Yihui, XIE Yifei, ZHANG Zhixiang, JIN Jiayi, QIU Xiangdong, TONG Yang.The complete chloroplast genome of Sloanea sinensis and the systematic status of Elaeocarpaceae[J].Guihaia,2022,42(1):39-48.[点击复制] |
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| 猴欢喜叶绿体全基因组及杜英科系统地位分析 |
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王一麾1, 谢宜飞1,2*, 张志翔3, 金佳怡1, 邱相东1, 童 阳1
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1. 赣南师范大学 生命科学学院, 江西 赣州 341000;2. 赣南师范大学 南岭植物标本馆,
江西 赣州 341000;3. 北京林业大学 生态与自然保护学院, 北京 100083
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| 摘要: |
| 最新的分子系统发育(APG IV)研究中以猴欢喜属(Sloanea L.)为代表的杜英科(Elaeocarpaceae)所在的酢浆草目(Oxalidales)被置于豆类分支(Fabids),且与卫矛目(Celastrales)、金虎尾目(Malpighiales)组成一支(COM分支),但支持率较低。为提高COM分支支持率,该文以杜英科猴欢喜属猴欢喜(Sloanea sinensis)为材料,应用Illumina Hiseq 2500对猴欢喜叶绿体基因组进行测序,并通过Geneious 11.0,PGA和Shiny软件进行组装,注释和绘制基因组图谱,之后使用MISA和IRscope软件对叶绿体基因组特征进行分析,并使用PhyloSuite软件构建豆类分支系统发育树。结果表明:(1)猴欢喜叶绿体基因组全长157 546 bp,GC含量为37.0%,包含一对25 984 bp的反向重复区、大单拷贝区(87 903 bp)和小单拷贝区(17 675 bp)。(2)在猴欢喜叶绿体基因组中有113个非重复基因,包括79个蛋白质编码基因、4个rRNA基因和30个tRNA基因; 共检测到81个SSR位点,其中大部分是单核苷酸重复序列; 通过IR边界区比较分析,发现日本杜英(Elaeocarpus japonicus)和猴欢喜在LSC/IRb和IRa/LSC边界上存在明显差异。(3)构建豆类分支叶绿体全基因组最大似然法系统发育树,猴欢喜同日本杜英亲缘关系最近,与酢浆草科(Oxaliadaceae)阳桃(Averrhoa carambola)、红花酢浆草(Oxalis corymbosa)和O. drummondii聚为一支,支持杜英科归于酢浆草目并且处在豆类分支中,且卫矛目、酢浆草目和金虎尾目演化支(COM分支)支持率高达100%。该研究基于猴欢喜叶绿体基因组进一步确定了杜英科和COM分支的系统地位。 |
| 关键词: 猴欢喜, 叶绿体基因组, 系统发育分析, 基因组比较, COM分支 |
| DOI：10.11931/guihaia.gxzw202102009 |
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| 文章编号:1000-3142(2022)01-0039-10 |
| 基金项目:国家自然科学基金(31110103911, J1310002)[Supported by the National Natural Science Foundation of China(31110103911, J1310002)]。 |
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| The complete chloroplast genome of Sloanea sinensis and the systematic status of Elaeocarpaceae |
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WANG Yihui1, XIE Yifei1,2*, ZHANG Zhixiang3, JIN Jiayi1, QIU Xiangdong1, TONG Yang1
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1. School of Life Sciences, Gannan Normal University, Ganzhou 341000, Jiangxi, China;2. Nanling Herbarium, Gannan Normal University,
Ganzhou 341000, Jiangxi, China;3. School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
1. School of Life Sciences, Gannan Normal University, Ganzhou 341000, Jiangxi, China; 2. Nanling Herbarium, Gannan Normal University,
Ganzhou 341000, Jiangxi, China; 3. School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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| Abstract: |
| APG IV has a noticeable improvement from the morphological phylogeny which revealed Elaeocarpaceae belonging Oxalidales includes the COM clade with Celastrales and Malpighiales, while the status of COM clade is not well supported based on phylogenetic calculation results of multi-molecular fragments. In order to improve the bootstrap of COM clade, with Sloanea sinensis(genus Sloanea, family Elaeocarpaceae)as materials, we used Illumina Hiseq 2500 platform to sequence, and then assembled, annotated, and analyzed by bioinformatic methods. Analysis of chloroplast genome characteristics was used by MISA and IRscope. The phylogenetic tree of Fabids was reconstructed by using PhyloSuite. The results were as follows:(1)The complete chloroplast genome of Sloanea sinensis was 157 546 bp in length including two inverted repeats(IRs)of 25 984 bp, which were separated by LSC and SSC of 87 904 bp and 17 674 bp, respectively. The GC content was 37.0%.(2)The genome encoded 113 functional genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. 81 SSR loci were detected in the S. sinensis genome, and most of SSR was composed of nucleobase A and T. Through IR expansion and contraction analysis, we found that there were obvious differences between Elaeocarpus japonicus and Sloanea sinensis in LSC/IRB and IRA/LSC boundaries.(3)The whole chloroplast genome phylogenetic studies showed Sloanea sinensis and Elaeocarpus japonicus were sister to Averrhoa carambola, Oxalis corymbosa and O. drummondii. Sloanea sinensis and Elaeocarpus japonicus representing Elaeocarpaceae belonged to Oxalidales, Fabids, and a strongly support for COM clade in Fabids group. Based on the chloroplast genome of genus Sloanea, the phylogenetic status of Elaeocarpaceae and the COM clade is confirmed. |
| Key words: Sloanea sinensis, chloroplast genome, phylogenetic analysis, genome comparison, COM clade |
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