Characterization of the complete chloroplast genome sequence of Conyza canadensis and its phylogenetic implications

We have determined the complete chloroplast genome of Erigeron canadensis isolated in Korea. The circular chloroplast genome of E. canadensis is 152,767 bp long and has four subregions: 84,317 bp of large single-copy and 18,446 bp of small single-copy regions are separated by 25,004 bp of inverted repeat regions including 133 genes (88 protein-coding genes, eight rRNAs, and 37 tRNAs). The chloroplast genome isolated in Korea differs from the Chinese isolate by 103 single-nucleotide polymorphisms (SNPs) and 47 insertions and deletion (INDEL) regions, suggesting different invasion sources of E. canadensis in Korea and China. A nucleotide diversity analysis revealed that the trend of the nucleotide diversity of E. canadensis followed that of 11 Erigeron chloroplasts, except for three peaks. The phylogenetic tree showed that our E. canadensis chloroplast is clustered with E. canadensis reported from China. Erigeron canadensis can be a good target when attempting to understand genetic diversity of invasive species.

Section: Resultsmentioning

confidence: 99%

“…Genome annotation was conducted based on another E. canadensis chloroplast (NC_046789) (Zhang et al, 2019) with Geneious R11 v11.0.5 (Biomatters Ltd., Auckland, New Zealand). A circular map of the Korean E. canadensis chloroplast genome was drawn using OGDRAW v1.31 (Greiner et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome of Erigeron canadensis isolated in Korea (Asteraceae): Insight into the genetic diversity of the invasive species

Park

2023

The complete chloroplast genome of Campsis grandiflora (Bignoniaceae)

Park¹,

Xi²

2022

Campsis grandiflora (Thunb.) K. Schum is an ornamental species with various useful biological effects. The chloroplast genome of C. grandiflora isolated in Korea is 154,293 bp long (GC ratio: 38.1%) and has four subregions: 84,121 bp of large single-copy (36.2%) and 18,521 bp of small single-copy (30.0%) regions are separated by 24,332 bp of inverted repeat (42.9%) regions including 132 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). One single-nucleotide polymorphism and five insertion and deletion (INDEL) regions (40-bp in total) were identified, indicating a low level of intraspecific variation in the chloroplast genome. All five INDEL regions were linked to the repetitive sequences. Seventy-two normal simple sequence repeats (SSRs) and 47 extended SSRs were identified to develop molecular markers. The phylogenetic trees of 29 representative Bignoniaceae chloroplast genomes indicate that the tribe-level phylogenic relationship is congruent with the findings of previous studies.

Comparative analyses of Agrimonia complete chloroplast genomes with newly assembled chloroplast genomes of A. coreana and A. nipponica (Rosaceae)

PARK,

SUH,

2024

The genus Agrimonia L. (1753) is a small group consisting of 19 species and three varieties. We completed two Agrimonia chloroplast genomes, Agrimonia coreana Nakai and Agrimonia nipponica Koidz, collected in Korea and conducted comprehensive analyses of six Agrimonia chloroplast genomes. Two of the Agrimonia chloroplasts genomes have a typical quadripartite structure with lengths ranging from 155,161 bp to 151,362 bp, similar to the remaining AAgrimonia chloroplast genomes. High nucleotide diversity was detected in the ycf1 gene, which can serve as a molecular marker. Intraspecific variations of four A. pilosa chloroplast genomes and interspecific variations of three Agrimonia species revealed that KY419942 is distinct to the other three A. pilosa chloroplast genomes. A phylogenetic analysis demonstrated that KY419942 was clustered with A. nipponica, requiring further analyses to understand Agrimonia species in East Asia. A comparison of simple sequence repeats identified from the six Agrimonia chloroplast genomes suggests potential molecular markers to distinguish species or populations of the same species. Our results define the phylogenetic relationship of three Agrimonia species and provide insight into the intraspecific features of Agrimonia chloroplast genomes with which to gain a better understanding of the genetic structure of Agrimonia species.