**Gene Losses and Variations in Chloroplast Genome of Parasitic Plant** *Macrosolen* **and Phylogenetic Relationships within Santalales**

**Liping Nie 1,2, Yingxian Cui 1,2, Liwei Wu 1,2, Jianguo Zhou 1,2, Zhichao Xu 1,2, Yonghua Li 3,\*, Xiwen Li 4, Yu Wang 1,2 and Hui Yao 1,2,\***


Received: 17 October 2019; Accepted: 17 November 2019; Published: 19 November 2019

**Abstract:** *Macrosolen* plants are parasitic shrubs, several of which are important medicinal plants, that are used as folk medicine in some provinces of China. However, reports on *Macrosolen* are limited. In this study, the complete chloroplast genome sequences of *Macrosolen cochinchinensis*, *Macrosolen tricolor* and *Macrosolen bibracteolatus* are reported. The chloroplast genomes were sequenced by Illumina HiSeq X. The length of the chloroplast genomes ranged from 129,570 bp (*M. cochinchinensis*) to 126,621 bp (*M. tricolor*), with a total of 113 genes, including 35 tRNA, eight rRNA, 68 protein-coding genes, and two pseudogenes (*ycf1* and *rpl2*). The simple sequence repeats are mainly comprised of A/T mononucleotide repeats. Comparative genome analyses of the three species detected the most divergent regions in the non-coding spacers. Phylogenetic analyses using maximum parsimony and maximum likelihood strongly supported the idea that Loranthaceae and Viscaceae are monophyletic clades. The data obtained in this study are beneficial for further investigations of *Macrosolen* in respect to evolution and molecular identification.

**Keywords:** *Macrosolen*; *Macrosolen cochinchinensis*; *Macrosolen tricolor*; *Macrosolen bibracteolatus*; Santalales; gene loss; chloroplast genome; phylogenetic relationship
