Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes

• Main Authors: Xiaofeng Chi, Faqi Zhang, Qi Dong, Shilong Chen
• Format: Article
• Language: English
• Published: MDPI AG 2020-11-01
• Series: Plants
• Subjects: Biebersteiniaceae; Nitrariaceae; chloroplast genome; codon usage bias; phylogenetic analysis
• Online Access: https://www.mdpi.com/2223-7747/9/11/1605

Biebersteiniaceae and Nitrariaceae, two small families, were classified in Sapindales recently. Taxonomic and phylogenetic relationships within Sapindales are still poorly resolved and controversial. In current study, we compared the chloroplast genomes of five species (<i>Biebersteinia heterostemon, Peganum harmala, Nitraria roborowskii, Nitraria sibirica, </i>and<i> Nitraria tangutorum</i>) from Biebersteiniaceae and Nitrariaceae. High similarity was detected in the gene order, content and orientation of the five chloroplast genomes; 13 highly variable regions were identified among the five species. An accelerated substitution rate was found in the protein-coding genes, especially <i>clpP</i>. The effective number of codons (EN_C), parity rule 2 (PR2), and neutrality plots together revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported (Nitrariaceae (Biebersteiniaceae + The Rest)) relationships in Sapindales. Our findings can provide useful information for analyzing phylogeny and molecular evolution within Biebersteiniaceae and Nitrariaceae.