- The overall gene content and organization across the six Hosta were nearly identical with a few exceptions. - Conclusions: Our study provides detailed information on the chloroplast genome of the Hosta taxa. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article. - The genus Hosta is placed in the family Asparagaceae since it was moved to the family from Liliaceae in the 1930s based on the cytological characteristics (2n = 60) [5]. - There are approximately 22–25 species in the genus [1, 4], although the number of species (43 in Schmid) [5]. - The CP genomes are usually transmitted from one of the parents (supposedly no recombination occurring), mostly the mother in angiosperms [13]. - The sequences of the CP genomes are conserved among taxa,. - Also, despite the wide utilities of CP markers for taxo- nomic studies, the taxonomy of the most closely related taxa based on those markers often remains unresolved in many taxa due to the limited variation [15]. - 2) to compare se- quence variation and molecular evolution among the six Korean Hosta. - 3) to infer the phylogenetic rela- tionship among the six Korean Hosta and reconstruct the phylogeny of the six species within the subfamily Agavoideae.. - The average number of reads after quality-based trim- ming was about 10 million and the mean coverage of the four plastome sequences is ~ 222 (Table 1). - The complete CP genome size of the four Hosta ranged from 156,624 bp (H. - As shown in most CP genomes, the four Hosta assembled in the study exhibited the typical quadripar- tite structure comprising of the four regions, a pair of inverted repeats (IRs bp), LSC (85,004–. - Except for the one tRNA gene, all remaining genes and the com- position found in the H. - jonesii plastome was identical to those of the other five species. - About 42% of plastome sequences of the six Korean Hosta species came out as the coding region encoding tRNAs, rRNAs, and proteins. - The comparative sequence analysis of the six Korean Hosta revealed that the plastome sequences were fairly conserved across the six taxa with a few regions with variation (Fig. - Overall the sequences were more con- served in the coding regions, whereas, most of variation detected were found in non-coding sequence (CNS in Fig. - We further examined sequence variability by com- puting nucleotide polymorphism (pi) among the six taxa.. - We compared the IR and SC boundaries of the six Ko- rean Hosta. - Although the rps19 genes of all six taxa were placed in the IR region, Table 1 Sample information and summary of chloroplast genome characteristics for four Hosta species in Korea. - the location of the gene in H. - capitata indicating expansion of IR in the species. - The border across IRb and SSC was placed in the region of ycf1 gene with 926–928 bp tail section of the gene located in the IRb for most of the Korean Hosta (Fig. - However, the size of the tail section was reduced. - venusta suggest- ing contraction of the IR section in the two taxa (Fig. - According to the codon usage analysis, overall 64 codons were present across of the six Korean Hosta species en- coding 20 amino acids (AAs). - Alanine was the least frequent AA in the Korean Hosta, which is encoded only by 309 codons (1.2. - The codon usage based on relative synonymous codon usage values (RSCU) did not vary among the six Korean Hosta species except for some de- creases found in three AAs of H. - Of the six Hosta species, H. - Codons with A and/or U in the third position take up ~ 30% and ~ 24% of all codons respectively. - Over 60% of di-nucleotide SSRs were shown in the form of “AT” and the repeat number Table 2 List of genes within chloroplast genomes of six Hosta species in Korea. - ×2 refers to genes duplicated in the IR regions. - ψ Pseudogenes are presented in the species indicated with parentheses. - 2 Plots of percent sequence identity of the chloroplast genomes of six Korean Hosta species with H. - We found four types of tetra-nucleotide SSRs in four of the six taxa, whereas H.. - There was no tri- and hexa- nucleotide SSRs in the six Korean Hosta. - The type of compound SSRs differ across the six Hosta taxa. - The smallest unit size of the repeat was 18 while the largest unit size was 46. - The majority of the repeats (ca. - 88%) were size of less than 30 and nearly half of the repeats (ca. - We examined the phylogenetic relationships among 20 taxa in subfamily Agavoideae including the six Korean Hosta species using the whole plastome sequences. - The overall topology of the phylogeny computed from both Maximum likelihood (ML) and Neighbor joining (NJ) was identical (Fig. - In the phylogeny, all seven Hosta taxa (see Table 1 and Additional file 1: Table S2 for the taxa names and GenBank accessions) formed a monophy- letic group that is a sister to the group of most taxa in Agavoideae (Fig. - Hosta clausa was place in the basal node in the monophyly of Hosta (Fig. - Species in the genus Hosta are economically well recog- nized plants endemic to eastern Asia with taxonomic disputes due to the high morphological variabilities in Korea, China and Japan [1–3]. - In the present study, we newly sequenced whole CP genomes for four Korean Hosta taxa and conducted comparative analyses on all six Korean Hosta CP genomes to understand the archi- tecture of CP genomes in the taxa. - The Hosta plastomes that we analyzed revealed the typical quadri- partite structure and fell in the expected size range. - It is be- lieved that the most common gene losses in angiosperm, infA might have derived from transferring of the gene to the nucleus [22]. - 5 Phylogenetic relationships among the six Hosta species and 15 species in Agavoideae (Asparagaceae) inferred using Neighbor joining (NJ) and Maximum likelihood (ML) methods based on the whole chloroplast genomes. - In the mVISTA result, there was 278 bp sequence deletion on H. - capitata in the intergenic region around the trnK-UUU gene (Fig. - Our amplification result of the region indicates that the deletion is a unique feature of H. - Despite the lowered sequence variation, we identified four hyper-variable sites located in the SSC region (Fig. - clausa samples from two different collection sites was 18, which is surprisingly high consid- ering the limited number of variable sites (0–2) observed in the other genes and species (Additional file 1: Table S3 and Table S4). - With the finding that our study discovered, some might further investigate diversity pattern of ndhD gene with larger sample size to determine the evolutionary his- tory of the gene in the light of the species and population diversification.. - It is hypothesized that the structural integrity of the whole plastomes is highly linked to the IR structure and the changes in plastome structure are often associated with IR expansions and contractions [28]. - six Korean Hosta plastome structures and compared the sizes and the borders of the three components, LSC, SSC and IRs. - In the CP genome, the compositional bias associated with A/U rich positions is the primary cause of codon usage bias [32, 33]. - The six Hosta CP genomes are low in GC content. - In the six Korean Hosta taxa, we found a slight bias toward the nucleotide pair A/U. - 55% of total codons were with A/U at third position of the co- dons. - We found inter- specific polymorphism in about 30 to 40% of the total SSRs (Table 3). - Of the six Hosta taxa, H. - Aside from the two copies of inverted repeats, ap- proximately 50 small repeats were dispersed throughout coding and non-coding regions of the six Hosta taxa.. - There was no record of plastome re- combination in Asparagaceae, however plastome studies examining the recombination in the taxa are completely lacking thus far. - We utilized the complete CP genome sequences of 21 taxa in subfamily Agavoi- deae (Asparagaceae) to infer phylogenetic relationships among the six Korean Hosta taxa and the related taxa.. - There was no difference in the tree topology between the ML and NJ phylogenies with robust supports for the most clades sug- gesting a high confidence in the relationships among the clades and taxa (Fig. - 5) were congruent to the one shown in the recent phylogenetic studies for family Aspar- agaceae [3, 43]. - gene content and organization for complete CP genomes in the six Korean Hosta species. - Inter- and intra- specific recombination events might have happened in the past are likely be one plausible explanation for the increased number. - We prepared the voucher specimen for all four sam- ples used and deposited them in the National Insti- tute of Biological Resources with the accession numbers listed in Table 1.. - Total Genomic DNA were extracted from each of the four Hosta plants using a DNeasy Plant Mini Kit (Qia- gen Co., Hilden, Germany) following the manufacturer’s protocol. - Illumina paired-end (PE) libraries (read length: 2 × 125 bp) with insert sizes of 270 to 700 bp for each of the four Hosta species were constructed and sequenced on MiSeq platform (Illumina Inc., San Diego, CA) by Macrogen Inc. - Gaps were filled by the Gapcloser fuction in the SOAP package. - The visual presentations of the plastome circular map were drawn in OGDRAW (http://ogdraw.mpimp-golm.. - The annotated CP genome sequences of the four newly sequenced Hosta species in our study were then deposited in GenBank under the accession num- bers listed in Table 1.. - The whole plastome sequences of the six Hosta plants were aligned with MAFFT (http://mafft.. - The detailed method of amplification and data analysis are provided in the supplementary information (Additional file 1: S1). - We also examined the sequence di- vergence among the six Korean Hosta species through a sliding window analysis computing pi among the chloro- plast genomes in DnaSP v. - Two to three individuals were collected from different populations for the six Korean Hosta species (in total 13 individuals;. - of amplification and the data analysis are provided in the supplementary information (Additional file 1: S2).. - We also investigated the size and type of repeats in the six Korean Hosta plastomes using REPuter [48]. - The summary of the chloroplast genome sequences downloaded from GenBank for phylogenetic analysis. - Sample list used in the level of polymorphism test for the four hypervariable sites (ndhF-rpl32 IGS, ndhD, psbA, and trnL). - Variable sites found in the six Hosta species in Korea. - UUG region amplified for the six Korean Hosta species. - The size of the PCR fragments was determined by electrophoresis using the QIAxcel Advanced System and QIAxcel ScreenGel Software (Qiagen).. - codons occurring significantly more often in highly expressed genes, encoding 20 amino acids in the six Hosta chloroplast genomes in Korea. - The method of amplification to identify intraspecific sequence polymorphism for the four hypervariable sites (psbA, ndhD, trnL, and ndhF-rpl32 IGS) in the six Koran Hosta species.. - KH performed additional experiments and analysis for verification of the analyzed assemblies. - NIBR provided the fund required for the project and evaluated the process of running fund and overall performance of the project.. - in the USA. - A taxonomic study of the genus Hosta in Korea. - Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. - Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants. - The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. - Comparative analysis of the complete chloroplast genomes of four Aconitum medicinal species.. - Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
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