Chloroplast phylogenomic analyses maternal relationships among sections in the genus Populus. (February 2017)

• Record Type: Journal Article
• Authors: Zhang, Limei; Shang, Ce; Du, Fang K.; Zhao, Fengbin; Xiong, Biao; Zhang, Zhixiang
• Is Part Of: Biochemical systematics and ecology. Volume 70(2017)
• Page Start: 132
• Page End: 140
• Publication Date: 2017-02
• Subjects: Complete chloroplast genome -- Populus -- Phylogeny -- Incomplete lineage sorting; Chemotaxonomy -- Periodicals; Biochemical variation -- Periodicals; Ecology -- Periodicals; Biochemistry -- Periodicals; Ecology -- Periodicals; Chimiotaxinomie -- Périodiques; Variation biochimique -- Périodiques; Écologie -- Périodiques; 578.012
• DOI: 10.1016/j.bse.2016.11.008
• Languages: English
• ISSNs: 0305-1978

Abstract

Abstract: The genus Populus L. has been divided into five sections based on morphological characters, but the phylogenetic relationships among sections remain uncertain. Topological discrepancies have been reported between trees obtained using nuclear and plastid sequences. We selected nine chloroplast genomes from all five sections, including two new sequenced species in this study for analyses of maternal phylogenetic relationships in the genus Populus at the sectional level. Phylogenetic analyses were performed using various subsets of data, coding sequences, noncoding sequences, and different districts of the genome, yielding contradictory outcomes for various subsets. According to our phylogenetic analyses, (1) a robust maternal phylogenetic relationship among sections based on complete chloroplast genomes was obtained; (2) Sect. Tacamahaca can be divided into two clades based on maternally inherited loci, i.e. cladeⅠ, distributed in North America and northeast China, and cladeⅡ, distributed in southwest China; (3) SSC-noncoding regions revealed an inconsistent topology compared with all other subsets; (4) this discrepancy may be resulted from incomplete lineage sorting between species of Populus . We tested multiple partitioning schemes to resolve deep-level phylogenetic relationships in Populus, and complete noncoding subset is most recommended. Highlights: We obtained a robust maternal topology among different sections of genus Populus based on complete chloroplast genomes, and confirmed the phylogenetic position of different sections in maternal inherited. We found out incomplete lineage sorting existed in chloroplast genomes, and discovered that Sect. Tacamahaca can be divided into two clades. Chloroplast complete noncoding subsets are recommended to analyses the deep-level of phylogenetic relationships among taxa in the genus Populus .