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

Xiaofeng Chi,Faqi Zhang,Shilong Chen,Qi Dong

doi:10.3390/plants9111605

Xiaofeng Chi, Faqi Zhang + Show 2 more

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https://doi.org/10.3390/plants9111605

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Abstract

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 (Biebersteinia heterostemon, Peganum harmala, Nitraria roborowskii, Nitraria sibirica, and Nitraria tangutorum) 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 clpP. The effective number of codons (ENC), 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.

Highlights

Biebersteiniaceae and Nitrariaceae are two small families
The length of the chloroplast genomes of the five species ranges from 158,795 bp (B. heterostemon) to 160,038 bp (P. harmala)
The genomes have a typical structure with an large-single copy (LSC) region (86,887–88,278 bp), an small-single copy (SSC) region (18,309–18,852 bp) and two inverted repeat (IR) regions (26,469–26,779 bp; Table 1)

Summary

Introduction

Biebersteiniaceae and Nitrariaceae are two small families. Biebersteiniaceae consists of only one genus Biebersteinia, which comprises 4–5 species, and is mainly distributed in the easternMediterranean, Central, and Western Asia, northwest of China, and the Himalayas [1,2]. Biebersteiniaceae consists of only one genus Biebersteinia, which comprises 4–5 species, and is mainly distributed in the eastern. Some species of Biebersteinia was used as traditional folk medicines in Iran and China with the activities of anti-inflammatory, analgesic, antibacterial, antioxidant, antihypertensive, and hypoglycemic effects [3]. Nitrariaceae consists of four genera, namely Nitraria, Tetradiclis, Malacocarpus, and Peganum, which comprise about 20 species, and are native to arid and semi-arid regions of Mexico, North Africa, Europe, Australia, and Asia [1,4]. The plants of Nitraria genus are highly adaptable to high salinity, arid, or semi-arid environments. They can effectively alleviate the salinization degree of soil, improve the utilization rate of saline-alkali land and prevent soil desertification [5]

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