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Background  The 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.    Results  The 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.    Conclusions  Our 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.

Complete chloroplast genomes of all six Hosta species occurring in Korea: molecular structures, comparative, and phylogenetic analyses