TY - JOUR
T1 - Plastome characterization and comparative analyses of wild crabapples (Malus baccata and M. toringo)
T2 - insights into infraspecific plastome variation and phylogenetic relationships
AU - Cho, Myong Suk
AU - Kim, Jin Hyeong
AU - Yamada, Takayuki
AU - Maki, Masayuki
AU - Kim, Seung Chul
N1 - Funding Information:
This work was supported by “A Study on Utilization of Digitalized DNA Sequences in Plant Resources Based on Next Generation Sequence Analysis” (project number NIBR201803201) and “A study on plant resources based on DNA sequences utilizing Next Generation Sequencing technique (2nd year)” (project number NIBR201905201), which were funded by the National Institute of Biological Resources, Korea.
Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
PY - 2021/10
Y1 - 2021/10
N2 - Malus baccata (L.) Borkh. and Malus toringo (Siebold) Siebold ex de Vriese of the genus Malus Mill. (Rosaceae) are wild crabapples occurring in temperate East Asia. Despite their horticultural importance as ornamental trees and the natural resources in apple breeding, their phylogenetic relationships have never been determined clearly owing to lack of resolution in previous studies. We characterized four complete chloroplast genomes of these two species and conducted various phylogenomic analyses comparatively to the previously reported plastomes of other wild Malus species. They were highly conserved in genomic structures and gene contents, containing 129 genes including 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Phylogenetic analysis of 23 representative Malus plastomes did not support the current classification of the major sections in Malus, revealing non-monophylies. The plastomes of M. toringo revealed two chloroplast types corresponding to their geographic distribution; M. toringo from China was more closely related to other sympatric species, while two conspecific M. toringo from Japan and Korea were in a sister relationship with M. baccata from Korea. We identified one positively selected gene (ndhD) and seven mutation hotspots (trnK-rps16, trnR-atpA, petN-psbM, trnT-psbD, psbZ-trnG, ndhC-trnV, and ycf1) and variable SSRs as potential useful plastid markers.
AB - Malus baccata (L.) Borkh. and Malus toringo (Siebold) Siebold ex de Vriese of the genus Malus Mill. (Rosaceae) are wild crabapples occurring in temperate East Asia. Despite their horticultural importance as ornamental trees and the natural resources in apple breeding, their phylogenetic relationships have never been determined clearly owing to lack of resolution in previous studies. We characterized four complete chloroplast genomes of these two species and conducted various phylogenomic analyses comparatively to the previously reported plastomes of other wild Malus species. They were highly conserved in genomic structures and gene contents, containing 129 genes including 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Phylogenetic analysis of 23 representative Malus plastomes did not support the current classification of the major sections in Malus, revealing non-monophylies. The plastomes of M. toringo revealed two chloroplast types corresponding to their geographic distribution; M. toringo from China was more closely related to other sympatric species, while two conspecific M. toringo from Japan and Korea were in a sister relationship with M. baccata from Korea. We identified one positively selected gene (ndhD) and seven mutation hotspots (trnK-rps16, trnR-atpA, petN-psbM, trnT-psbD, psbZ-trnG, ndhC-trnV, and ycf1) and variable SSRs as potential useful plastid markers.
KW - Chloroplast genome
KW - Comparative phylogenomic analysis
KW - Malus baccata
KW - Malus toringo
KW - Plastome
KW - Wild crabapples
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U2 - 10.1007/s11295-021-01520-z
DO - 10.1007/s11295-021-01520-z
M3 - Article
AN - SCOPUS:85113384947
VL - 17
JO - Tree Genetics and Genomes
JF - Tree Genetics and Genomes
SN - 1614-2942
IS - 5
M1 - 41
ER -