Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae

Abstract

The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion.

Sequencing, de novo assembly ofLudwigiaplastomes, and comparative analysis within the Onagraceae family

“…ranged from 159,496 bp to 160,416 bp, and Epilobium sp. ranged from 160,748 bp to 161,144 bp [78]. Our study revealed that the size of the complete chloroplast of Ludwigia (Onagraceae subfamily Ludwigioideae) ranged from 159,369 bp to 159,584 bp, which is remarkably similar to other Onagraceae plants (average length of 162,030 bp).…”

“…and Epilobium sp. (38.1 to 38.2%, [77]) and more generally for the order Myrtales (36.9-38.9%, with the average GC content being 37%, [78]).…”

“…and Epilobium sp. (38.1 to 38.2%, [77]) and more generally for the order Myrtales (36.9–38.9%, with the average GC content being 37%, [78]). Higher GC content of the IR regions (43.5%) found in Ludwigia sp.…”

Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris

“…The cp has its genetic material separate from the nucleus and its genome, generally 120 to 170 kb in size, and encodes for 120 to 130 genes 13 . The cp genome usually has a quadripartite structure with a large single copy, a small single copy, and two inverted repeat (IRa and IRb) regions 14 . Homologous recombination occurs between these two inverted regions 15 , 16 .…”

Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes of Clematis nannophylla

“…However, the in uence of replication mechanisms on base bias differs in the AT and CG asymmetries. Replication is generally strong for GC skew, whereas AT skew is caused by coding sequence-related mechanisms [42,43].…”