Chloroplast genomes and nuclear sequences reveal the interspecific relationships of Crataegus bretschneideri C. K. Schneid. and related species in China.

Crataegus bretschneideri C. K. Schneid. is one of the species cultivated in China. Due to its unclear taxonomic classification status, the conservation and utilization of this germplasm resource have been limited. In this study, we analyzed the chloroplast genomes and nuclear sequences to reveal the taxonomic relationships among C. bretschneideri and related species. We assembled the chloroplast genomes of C. bretschneider and related species and varieties, including C. maximowiczii C. K. Schneid., C. maximowiczii var. ninganensis S. Q. Nie & B. J. Jen., C. pinnatifida Bunge, and C. pinnatifida var. major N. E. Br. The lengths of the chloroplast genomes ranged from 159,644 bp (C. bretschneideri) to 159,947 bp (C. pinnatifida var. major). The five Crataegus chloroplast genomes had similar features and possessed 86 to 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes which were arranged in the same order. Eight mutation hotspot regions, including matk, psaB, accD, petA, clpP, trnD-GUC, psbH-petB, and trnN-GUU-trnR-ACG could be used as potential molecular markers for further studies of Crataegus genetic diversity. Phylogenetic analyses based on 17 chloroplast genomes of Crataegus and Amelanchier indicated that C. bretschneideri was related to C. maximowiczii and C. maximowiczii var. ninganensis. However, the phylogenetic trees constructed by nuclear sequences of 36 Crataegus accessions reflected a closer relationship between C. bretschneideri and C. pinnatifida. Furthermore, divergence time estimation suggested that C. bretschneideri and C. maximowiczii diverged in the late Miocene and that speciation of C. pinnatifida occurred during the middle to late Miocene. These findings revealed that C. bretschneideri is an independent species and may be of hybrid origin. [ABSTRACT FROM AUTHOR]