Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences.
Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences.
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基于叶绿体全基因组序列的石竹品种分子标记综合比较分析及开发
DOI：
10.3390/ijms232012567
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发表时间：
2022-10-19
影响因子：
5.6
通讯作者：
中科院分区：
文献类型：
--
作者：
Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our daily lives, its genome information and phylogenetic relationships remain elusive. Thus, we performed the assembly and annotation of chloroplast genomes for 12 individuals from seven Dianthus species. On this basis, we carried out the first comprehensive and systematic analysis of the chloroplast genome sequence characteristics and the phylogenetic evolution of Dianthus. The chloroplast genome of 12 Dianthus individuals ranged from 149,192 bp to 149,800 bp, containing 124 to 126 functional genes. Sequence repetition analysis showed the number of simple sequence repeats (SSRs) ranged from 75 to 80, tandem repeats ranged from 23 to 41, and pair-dispersed repeats ranged from 28 to 43. Next, we calculated the synonymous nucleotide substitution rates (Ks) of all 76 protein coding genes to obtain the evolution rate of these coding genes in Dianthus species; rpl22 showed the highest Ks (0.0471), which suggested that it evolved the swiftest. By reconstructing the phylogenetic relationships within Dianthus and other species of Caryophyllales, 16 Dianthus individuals (12 individuals reported in this study and four individuals downloaded from NCBI) were divided into two strongly supported sister clades (Clade A and Clade B). The Clade A contained five species, namely D. caryophyllus, D. barbatus, D. gratianopolitanus, and two cultivars (‘HY’ and ‘WC’). The Clade B included four species, in which D. superbus was a sister branch with D. chinensis, D. longicalyx, and F1 ‘87M’ (the hybrid offspring F1 from D. chinensis and ‘HY’). Further, based on sequence divergence analysis and hypervariable region analysis, we selected several regions that had more divergent sequences, to develop DNA markers. Additionally, we found that one DNA marker can be used to differentiate Clade A and Clade B in Dianthus. Taken together, our results provide useful information for our understanding of Dianthus classification and chloroplast genome evolution.
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影响因子：
5.3
作者：
Gu, Cuihua;Ma, Li;Wang, Yixiang
通讯作者：
Wang, Yixiang
影响因子：
4.4
作者：
Henriquez, Claudia L.;Abdullah;McKain, Michael R.
通讯作者：
McKain, Michael R.
DOI：
10.1080/23802359.2018.1521313
发表时间：
2018-10-08
期刊：
Mitochondrial DNA. Part B, Resources
影响因子：
--
作者：
Chen S;Xu Z;Zhao Y;Zhong X;Li C;Yang G
通讯作者：
Yang G
兰花物种叶绿体基因组的分子进化：深入了解系统发育关系和适应性进化
影响因子：
5.6
作者：
Dong WL;Wang RN;Zhang NY;Fan WB;Fang MF;Li ZH
通讯作者：
Li ZH
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM