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

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.

Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

“…9), the result is consistent with previous studies [93,96]. In the LSC analysis, Sapindaceae was sister to the Burseraceae + Anacardiaceae + Nitrariaceae clade (BS = 49, PP = 0.99, Figure S1), In the SSC analysis, Sapindaceae was sister to the Rutaceae + Simaroubaceae + Meliaceae clade (BS = 52, PP = 1, Figure S2), which is similar to the previous work [95,97]. Overall, as the sister group of Sapindaceae, most results exhibited weak support in maximum likelihood analysis.…”

“…However, the present analyses could not demonstrate the paraphyly of the Aesculus because of lacking su cient samples. In this study, we found Eurycorymbus cavaleriei as sister to Dodonaea viscosa with strong support (PP = 1.00, BS = 100), which similar to previous studies[45,47, 48,74,95]. Buerki et al[17, 18] conducted molecular phylogenetic studies of Sapindaceae s. lat.…”

The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses

“…Analyzing codon usage is essential to evaluate the evolution of the chloroplast genome (Chi et al, 2020; Sun et al, 2021). RSCU values were computed for the C .…”

“…Analyzing codon usage is essential to evaluate the evolution of the chloroplast genome (Chi et al, 2020;Sun et al, 2021). RSCU values were computed for the C. glandulifera, C. velutina, and L. chinense chloroplast genomes based on the protein-coding sequences.…”

Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species

“…Codon usage bias in evolution research has been reported on model organisms, including E. coli ( Krisko et al, 2014 ), Dengue virus ( Manokaran et al, 2019 ), S. cerevisiae , Drosophila melanogaster ( Kliman et al, 2003 ), and humans ( Sauna and Kimchi-Sarfaty, 2011 ), as well as studies assessing codon usage in plant evolution research ( Rensing et al, 2005 ; Liu et al, 2010 ; Sahoo et al, 2019 ; Chi et al, 2020 ). Plant species are broadly diverse in their gene expression, physiology, and stress response in varied environments.…”