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    徐家洪, 曾晴, 叶富余, 胡杨阳, 时寰宇, 张璇, 陈金辉. 基于全长转录组序列、核基因与叶绿体基因分析琼岛杨在杨属的亲缘关系[J]. 北京林业大学学报, 2021, 43(10): 28-37. DOI: 10.12171/j.1000-1522.20200286
    引用本文: 徐家洪, 曾晴, 叶富余, 胡杨阳, 时寰宇, 张璇, 陈金辉. 基于全长转录组序列、核基因与叶绿体基因分析琼岛杨在杨属的亲缘关系[J]. 北京林业大学学报, 2021, 43(10): 28-37. DOI: 10.12171/j.1000-1522.20200286
    Xu Jiahong, Zeng Qing, Ye Fuyu, Hu Yangyang, Shi Huanyu, Zhang Xuan, Chen Jinhui. Genetic relationship of Populus qiongdaoensis in Populus based on full-length transcriptome sequences, nuclear genes and chloroplast genes[J]. Journal of Beijing Forestry University, 2021, 43(10): 28-37. DOI: 10.12171/j.1000-1522.20200286
    Citation: Xu Jiahong, Zeng Qing, Ye Fuyu, Hu Yangyang, Shi Huanyu, Zhang Xuan, Chen Jinhui. Genetic relationship of Populus qiongdaoensis in Populus based on full-length transcriptome sequences, nuclear genes and chloroplast genes[J]. Journal of Beijing Forestry University, 2021, 43(10): 28-37. DOI: 10.12171/j.1000-1522.20200286

    基于全长转录组序列、核基因与叶绿体基因分析琼岛杨在杨属的亲缘关系

    Genetic relationship of Populus qiongdaoensis in Populus based on full-length transcriptome sequences, nuclear genes and chloroplast genes

    • 摘要:
        目的  琼岛杨是我国热带地区发现的一种杨树,至今其分类和进化鲜有报道。本研究旨在通过三代全长转录组测序等方法了解琼岛杨在杨属中的分类与进化。
        方法  基于Pacbio Sequel测序技术获取的热胁迫下琼岛杨、加杨和小叶杨完整全长转录本数据,通过直系同源基因计算非同义替换值(Ka)、同义替换值(Ks)及Ka/Ks值,比较直系同源基因在热胁迫下的表达模式,并结合毛果杨和簸箕柳的直系同源基因,构建了5个树种的进化树来分析杨树亲缘关系。通过克隆琼岛杨核基因(nrDNA:UDP-SQPOPTRDRAFT_575699)和叶绿体基因(cpDNA:atpⅠ和trnF),分析基因序列在琼岛杨种群中的多态性,计算琼岛杨种内遗传距离,及与19个树种(5个杨树组和1个类外群组)的种间遗传距离。基于最大似然法和最小进化法构建了琼岛杨与19个树种的进化树,以分析琼岛杨在杨属的亲缘关系。
        结果  三代转录组测序共获得660组琼岛杨、小叶杨和加杨的直系同源基因,Ks平均值为0.150 5,峰值为0.02,Ka/Ks < 1,占比97.27%,这显示了3种杨树较近的亲缘关系。直系同源基因表达模式分析发现,3种杨树在热胁迫下具有相同的表达模式。利用遗传距离法计算琼岛杨与19个树种中atpⅠ、trnFUDP-SQPOPTRDRAFT_575699等4种基因遗传距离的平均值,发现琼岛杨与白杨组具有最近亲缘关系,平均值为0.011。
        结论  基于三代全长转录组测序获得的直系同源基因分析显示出,琼岛杨与其他杨树具有较近亲缘关系。克隆cpDNA和nrDNA基因,计算遗传距离和构建的进化树均表明琼岛杨与白杨组具有最近亲缘关系。cpDNA的多态性以及进化分支置信度明显高于nrDNA,表明在琼岛杨中cpDNA比nrDNA基因更具备物种鉴别能力。

       

      Abstract:
        Objective  Populus qiongdaoensis is a plant of the Populus genus found in tropical regions of China. So far, there is few studies focus on its classification and evolution. This study aimed to understand the classification and evolution of P. qiongdaoensis in genus by third-generation full-length transcriptome sequencing and other methods.
        Method  Based on the Pacbio Sequel sequencing technology, the complete full-length transcript data of P. qiongdaoensis, P. canadensis and P. simonii under heat stress were obtained. Then, the non-synonymous substitutions (Ka), sense substitution (Ks) and Ka/Ks value of homologous genes of three Populus were calculated. We further compared the expression patterns of orthologous genes under heat stress, and constructed the phylogenetic tree of five species to analyze the genetic relationship of Populus by combining the orthologous genes of P. trichocarpa and Salix suchowensis. Finally, we cloned nuclear genes (nrDNA; UDP-SQ and POPTRDRAFT_575699) and chloroplast genes (cpDNA; atpⅠ and trnF) of P. qiongdaoensis to analyze the polymorphism of these gene sequences in the population of P. qiongdaoensis, calculated the intraspecific genetic distances of P. qiongdaoensis, and the interspecific genetic distances between P. qiongdaoensis and 19 species (five Populus groups and one out-of-class group). Based on the maximum likelihood method and the minimum evolution method, the evolutionary tree of P. qiongdaoensis and 19 tree species were constructed to analyze the genetic relationship of P. qiongdaoensis.
        Result  Third-generations of transcriptome sequencing obtained a total of 660 groups of orthologous genes from P. qiongdaoensis, P. canadensis and P. simonii. The average of Ks was 0.1505, the peak value was 0.02, and the ratio of Ka/Ks < 1 was 97.27%, showing the close relationship of the three Populus species. Analysis of orthologous gene expression patterns revealed that they had the same expression pattern under heat stress. The average genetic distance of four genes including atpⅠ, trnF, UDP-SQ and POPTRDRAFT_575699 between P. qiongdaoensis and 19 tree species was 0.011, indicating that genetic relationship between P. qiongdaoensis and poplar group was closest.
        Conclusion  The analysis of orthologous genes based on third-generation full-length transcriptome sequencing reveals that P. qiongdaoensis has a close relationship with other Populus. The results of genetic distances and constructing evolutionary trees show that P. qiongdaoensis has a close relationship with Leuce by cloning sequences of cpDNA and nrDNA genes. The polymorphism and evolutionary branch confidence of cpDNA are significantly higher than that of nrDNA, indicating that cpDNA is more capable of species discrimination than nrDNA genes in P. qiongdaoensis.

       

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