Characterization and phylogenetic analysis of the chloroplast genome of Iris lactea var. chinensis

The chloroplast genome of the Iris japonica Thunberg (Butterfly flower) reveals the genomic and evolutionary characteristics of Iris species

Iris japonica Thunberg is one of the horticultural species belonging to the Iris genus and Iridaceae family. Previous studies have revealed its hepatoprotective activity and ornamental values. However, little genetic and genomic information about this species is available. Here, to decipher the chloroplast genome and reveal its evolutionary characteristics, we sequenced, de novo assembled, and comprehensively analyzed the chloroplast genome of I. japonica. The genome was 152,453 bp in length and displayed a circular structure with a large single-copy region, a small single-copy region, and two inverted repeat regions. It contained 131 genes, including 85 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. We also identified 23 microsatellite repeat sequences, 34 tandem repeat sequences, and 60 dispersed repeat sequences in the chloroplast genome of I. japonica. Sequence divergence analyses of the chloroplast genomes of 20 Iris species revealed that the top four most highly variable regions were ndhC-trnV-UAC, rpl22-rps19, rps16-trnQ-UUG, and trnG-UCC-trnR-UCU. Phylogenetic analysis showed that I. japonica was most closely related to I. tectorum. This study reported a new chloroplast genome of I. japonica and performed comparative analyses of 20 Iris chloroplast genomes. The results would facilitate the evolutionary research and development of molecular markers for Iris species.

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.