Abstract
BackgroundThe genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia. Due to considerable morphological variability, the genus has been well recognized as a group with taxonomic problems. Chloroplast is a cytoplasmic organelle with its own genome, which is the most commonly used for phylogenetic and genetic diversity analyses for land plants. To understand the genomic architecture of Hosta chloroplasts and examine the level of nucleotide and size variation, we newly sequenced four (H. clausa, H. jonesii, H. minor, and H. venusta) and analyzed six Hosta species (including the four, H. capitata and H. yingeri) distributed throughout South Korea.ResultsThe average size of complete chloroplast genomes for the Hosta taxa was 156,642 bp with a maximum size difference of ~ 300 bp. The overall gene content and organization across the six Hosta were nearly identical with a few exceptions. There was a single tRNA gene deletion in H. jonesii and four genes were pseudogenized in three taxa (H. capitata, H. minor, and H. jonesii). We did not find major structural variation, but there were a minor expansion and contractions in IR region for three species (H. capitata, H. minor, and H. venusta). Sequence variations were higher in non-coding regions than in coding regions. Four genic and intergenic regions including two coding genes (psbA and ndhD) exhibited the largest sequence divergence showing potential as phylogenetic markers. We found compositional codon usage bias toward A/T at the third position. The Hosta plastomes had a comparable number of dispersed and tandem repeats (simple sequence repeats) to the ones identified in other angiosperm taxa. The phylogeny of 20 Agavoideae (Asparagaceae) taxa including the six Hosta species inferred from complete plastome data showed well resolved monophyletic clades for closely related taxa with high node supports.ConclusionsOur study provides detailed information on the chloroplast genome of the Hosta taxa. We identified nucleotide diversity hotspots and characterized types of repeats, which can be used for developing molecular markers applicable in various research area.
Highlights
The genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia
Chloroplast genome assembly The genomic libraries from the four Korean Hosta species sequenced in our study produced ~ 7.8 to 13GB
As shown in most CP genomes, the four Hosta assembled in the study exhibited the typical quadripartite structure comprising of the four regions, a pair of inverted repeats (IRs 26,676–26,698 bp), large single-copy region (LSC) (85,004– 85,099 bp) and small single-copy region (SSC) (18,225–18,244 bp; Fig. 1; Table 1)
Summary
The genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia. (Asparagaceae) is a group of economically important perennial herbs and distributed exclusively in eastern Asia [1,2,3]. The plants in Hosta are commonly called as plantain lily (bibichu in Korean) and have grown the popularity in gardens due to the advantages in cultivating due to the tolerance to shade and high soil moisture contents [5, 6]. The Hosta plants have been used as a folk medicine for treating multiple symptoms including multiple inflammatory diseases such as urethritis and pharyngolaryngitis in China and Japan [8]
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