基于叶绿体全基因组的云南樱花品种‘红霞'的种系分析

Phylogenetic analysis of Yunnan flowering cheery cultivar Cerasus ‘Hongxia' based on chloroplast genome

关键词:  高盆樱, 冬樱花, 重瓣, 品种起源, 系统发育

Key words:  Cerasus cerasoides, winter flowering cheery, double petal, cultivar origination, phylogenetic analysis

摘要:

云南樱花品种‘红霞'(Cerasus ‘Hongxia')广泛种植于滇中地区,3月开花,半重瓣至重瓣,粉红色,观赏价值较高。‘红霞'曾被认为是红花高盆樱(C. cerasoides var. rubea)的园艺品种,而其分子标记结果却聚在钟花樱(C. campanulata)种系,可见‘红霞'的种系归属存疑,对今后的育种及栽培极为不利。为探索‘红霞'的种系问题,该研究以‘红霞'的叶片DNA为材料,应用Illumina软件对叶绿体基因组特征进行测序,通过SPAdes 3.13.0、Gapcloser 1.12 和CPGAVAS2 2.0软件进行组装、注释,之后使用MISA和Geneious 10.0软件对叶绿体基因组特征进行分析,并使用RAxML 8.0软件构建Cerasus 分支系统发育树,分析‘红霞'在樱属植物的系统关系。结果表明:(1)‘红霞'的叶绿体全基因组长度为157 832 bp, 鸟嘌呤(Guanine)、胞嘧啶(Cytosine)含量为36.73%,包含一对反向重复(inverted repeat sequence, IR, 26 381 bp)区,由小单拷贝(short single copy, SSC, 19 120 bp)区和大单拷贝(long single copy, LSC, 85 950 bp)区分开,共编码128个基因,同时包括84个蛋白质编码基因、36个tRNA基因和8个rRNA核糖体基因。(2)通过樱属16个叶绿体全基因组的最大似然法系统发育树系统分析,发现‘红霞'与大叶早樱(C. subhirtella)和日本樱花(C. yedoensis)一支聚为姊妹群,而与高盆樱(C. cerasoides)的亲缘关系较远。因此该研究推测,‘红霞'可能不是高盆樱的品种,而有可能是钟花樱和大叶早樱或日本樱花的杂交品种。该研究结果为云南樱花品种‘红霞'的起源和遗传育种、高盆樱的品种鉴定与分类等研究提供了一定的参考资料。

Abstract:

Cerasus ‘Hongxia', a Yunnan flowering cheery cultivar blooming in March with semi-double to double pink petals, have been widely cultivated in central Yunnan for its high ornamental value. It was regarded as the cultivar of Cerasus cerasoides var. rubea. However, it was clustered in C. campanulata based on molecular markers. Therefore, the phylogeny of these cultivars are doubtful, which is not conducive to their breeding and cultivation. In order to explore the origin of Cerasus ‘Hongxia', with leaf DNA of Cerasus ‘Hongxia' as material, chloropast genome characteristics were sequenced by Illumina, assembled, annotated, and analyzed by bioinformatic methods, and analyzed by MISA and Genious R10. The phylogenetic tree of Cerasus was reconstructed by using RAxML 8.0, and the phylogenetic relationship of Cerasus ‘Hongxia' was analyzed. The results were as follows:(1)The chloroplast genome of Cerasus ‘Hongxia' was 157 832 bp in length, containing a pair of reverse repeat sequence(inverted repeat sequence,IR, 26 381 bp)regions, which were separated by a short single copy(SSC, 19 120 bp)region and a long single copy(LSC, 85 950 bp)region. A total of 128 genes were encoded, including 84 protein-coding genes, 36 tRNA genes and 8 rRNA ribosomal genes. The overall Guanine and Cytosine content of genome was 36.73%.(2)Based on the maximum likelihood phylogenetic tree analysis of 16 chloroplast genome of Cerasus, it was found that Cerasus ‘Hongxia' was formed as sister to C. subhirtella and C. yedoensis, and was far away from C. cerasoides. Therefore, we speculated that Cerasus ‘Hongxia' may be a hybrid cultivar of C. campanulata and C. subhirtella or C. yedoensis, rather than the cultivar of C. cerasoides. The above results are be useful for studies of the origination and genetic breeding of Cerasus ‘Hongxia', as well as the cultivar identification and classification of C. cerasoides.