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:2018-09-04 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