J Syst Evol ›› 2019, Vol. 57 ›› Issue (1): 15-22.doi: 10.1111/jse.12453

• Research Articles • Previous Articles     Next Articles

Molecular markers for phylogenetic applications derived from comparative plastome analysis of Prunus species

Hyoung Tae Kim1, Jung Sung Kim2, You Mi Lee3, Jeong-Hwan Mun4*, and Joo-Hwan Kim5*   

  1. 1Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 41566, Korea
    2Department of Forest Science, Chungbuk National University, Cheongju, Chungbuk 28644, Korea
    3Korea National Arboretum, Pocheon-si, Gyenggi-do 11186, Korea
    4Department of Bioscience and Bioinformatics, Myoungji University, Yongin-si, Gyeonggi-do 17058, Korea
    5Department of Life Sciences, Gachon University, Seongnam-si, Gyeonggi-do 3120, Korea
  • Received:2017-01-10 Accepted:2018-07-18 Online:2019-01-10 Published:2019-01-10


Interspecific and intergeneric relationships of Prunus s.l. are still unclear due to low levels of genetic variation among species, and resulting partially unresolved phylogenetic inferences. Here we sequenced and compared six complete plastomes from two subgenera of Prunus in order to choose molecular markers to increase the amount of genetic variation suitable for inference of Prunus phylogeny. The plastomes range between 157 817 and 158 995 bp in length, and we found different levels of inverted repeat (IR) contraction among the three sampled subgenera of Prunus s.l. Most regions in Prunus plastomes considered individually provide low phylogenetic resolution at the subgenus or species level compared to a tree constructed using all 78 coding regions combined. We compared levels of variation among 206 coding regions and noncoding (intergenic and intron) plastid regions and inferred phylogenies from each region considered individually. We then chose using two regions together for future studies of relationships in Prunus, ycf1 and trnT-L, that display high to moderate levels of variation among coding and intergenic regions, respectively, and that individually permit inference of resolved species-level trees in Prunus with moderate to strong branch support. Considered together, these two regions allow inference of the same topology of Prunus inferred using all coding plastid regions combined, with comparable levels of tree support to the full plastome set. These two loci should therefore be useful as a plastid phylogenetic marker set for further inference of relationships within Prunus s.l.

Key words: molecular markers, p-distance, phylogeny of Prunus s.l., plastome

[1] Xu Zhang, Hua-Jie Zhang, Jacob B. Landis, Tao Deng, Ai-Ping Meng, Hang Sun, Yan-Song Peng, Heng-Chang Wang, and Yan-Xia Sun. Plastome phylogenomic analysis of Torreya (Taxaceae) . J Syst Evol, 2019, 57(6): 607-615.
[2] Samar O. Rabah, Bikash Shrestha, Nahid H. Hajrah, Mumdooh J. Sabir, Hesham F. Alharby, Mernan J. Sabir, Alawiah M. Alhebshi, Jamal S. M. Sabir, Lawrence E. Gilbert, Tracey A. Ruhlman, and Robert K. Jansen. Passiflora plastome sequencing reveals widespread genomic rearrangements . J Syst Evol, 2019, 57(1): 1-14.
[3] Jun Wen, AJ Harris, Yash Kalburgi, Ning Zhang, Yuan Xu, Wei Zheng, Stefanie M. Ickert-Bond, Gabriel Johnson, Elizabeth A. Zimmer. Chloroplast phylogenomics of the New World grape species (Vitis, Vitaceae) . J Syst Evol, 2018, 56(4): 297-308.
[4] Maria D. Logacheva, Alexey B. Shipunov. Phylogenomic analysis of Picramnia, Alvaradoa, and Leitneria supports the independent Picramniales . J Syst Evol, 2017, 55(3): 171-176.
[5] Zhuo-Jun Song, Zhe Wang, Yang Feng, Nan Yao, Ji Yang, Bao-Rong Lu. Genetic divergence of weedy rice populations associated with their geographic location and coexisting conspecific crop: Implications on adaptive evolution of agricultural weeds . J Syst Evol, 2015, 53(4): 330-338.
Full text



[1] Yang Li-rui and Cheng Mu-chu. Relationship between Plant Stress Resistance and Photorespiration[J]. Chin Bull Bot, 1991, 8(01): 43 -47 .
[2] Duan Guang-ming Guo Ya-qiong. The Role of Kinetin in Antisenescence and Preservation for Fruits of Green Pepper[J]. Chin Bull Bot, 1995, 12(专辑3): 116 -119 .
[3] He Ping. Investigation of Pest Species and the Control of the Main Insect Pests in the Exhibition Green House of Beijing Botanical Garden[J]. Chin Bull Bot, 1996, 13(02): 44 -47 .
[4] Cui Kai-rong;Chen Ke-ming;Wang Xiao-zhe and Wang Ya-fu. Current Reseach on Plant Somatic Embryogenesis[J]. Chin Bull Bot, 1993, 10(03): 14 -20 .
[5] WANG Pu ZHAO Xiu-Qin. The Effect of Extracting Condition on the Analysis Result of Allelochemicals in Wheat Straw[J]. Chin Bull Bot, 2001, 18(06): 735 -738 .
[6] Yanxia He;Zicheng Wang*. Variation of DNA Methylation in Arabidopsis thaliana Seedlings After the Cryopreservation[J]. Chin Bull Bot, 2009, 44(03): 317 -322 .
[7] Yiting Shi, ShuhuaYang. Chinese Scientists Made Breakthrough in Study on Ethylene Signaling Transduction in Plants[J]. Chin Bull Bot, 2016, 51(3): 287 -289 .
[8] Rongpei Yu, Yang Li, Dong Li, Xuanhuai Zhan, Lei Shi. Radiosensitivity of Green Globular Bodies of Matteuccia struthiopteris Exposed to 60Coγ Radiation[J]. Chin Bull Bot, 2015, 50(5): 565 -572 .
[10] CAO Cheng-You, KOU Zhen-Wu, JIANG De-Ming, LUO Yong-Ming, DING Xiao-Ping. Interdune Succession in the Kerqin Sandy Region[J]. Chin J Plan Ecolo, 2000, 24(3): 262 -267 .