Phylogenetic Resolution in Based on Complete Chloroplast Genomes and Nuclear DNA Sequences.

Walnuts ( of the Juglandaceae) are well-known economically important resource plants for the edible nuts, high-quality wood, and medicinal use, with a distribution from tropical to temperate zones and from Asia to Europe and Americas. There are about 21 species in . Classification of at section level is problematic, because the phylogenetic position of is disputable. Lacking morphological and DNA markers severely inhibited the development of related researches. In this study, the complete chloroplast genomes and two nuclear DNA regions (the internal transcribed spacer and ubiquitin ligase gene) of 10 representative taxa of were used for comparative genomic analyses in order to deepen the understanding on the application value of genetic information for inferring the phylogenetic relationship of the genus. The chloroplast genomes possessed the typical quadripartite structure of angiosperms, consisting of a pair of inverted repeat regions separated by a large single-copy region and a small single-copy region. All the 10 chloroplast genomes possessed 112 unique genes arranged in the same order, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A combined sequence data set from two nuclear DNA regions revealed that plants could be classified into three branches: (1) section , (2) section including which is closer to , and (3) section . However, three branches with a different phylogenetic topology were recognized in using the complete chloroplast genome sequences: (1) section , (2) section , and (3) section plus . The molecular taxonomy of is almost compatible to the morphological taxonomy except (section ). Based on the complete chloroplast genome sequence data, the divergence time between section and section was 44.77 Mya, while section diverged from other sections in the genus was 47.61 Mya. Eleven of the 12 small inversions in the chloroplast genomes provided valuable phylogenetic information for classification of walnut plants at section and species levels. Our results are valuable for future studies on genetic diversity and will enhance the understanding on the phylogenetic evolution of Juglandaceae.