The complete plastid genome sequence of Chloranthus fortunei (A. Gray) Solms-Laub. in Chloranthaceae.

Chloranthus fortunei (A. Gray) Solms-Laub. is a perennial herb in a basal angiosperm family Chloranthaceae. Here, we reported the complete plastid genome of C. fortunei using Illumina short-read data. The total genome size was 157,063 bp in length, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The gene content and order were consistent with previously reported Chloranthus plastid genomes. The overall GC content of the C. fortunei plastid genome was 39.0%. In the phylogenetic result, genus Chloranthus was monophyletic and divided into two subclades: C. japonicus+C. angustifolius+C. fortunei, and C. henryi+C. spicatus+C. erectus. Our phylogenetic result was consistent with previous phylogenetic studies, and was supported by a previously proposed infrageneric classification of the genus Chloranthus.

The complete plastid genome sequence of Viola selkirkii Pursh ex Goldie (Violaceae).

Viola selkirkii, belonging to the genus Viola, has heart-shaped leaves and pale purple flowers, and it is widely distributed in the Northern Hemisphere, including Europe, North America, and Asia. In this study, the plastid genome of V. selkirkii was sequenced and phylogenetic analysis was performed on 11 Viola plastid genomes. The length of the plastid genome length of V. selkirkii was 156,774 bp, and it was identified as having a typical quadripartite structure with a large single-copy region (85,930 bp), a small single-copy region (17,982 bp), and two inverted repeat regions (26,431 bp each). A phylogenetic analysis was conducted with 77 protein-coding genes from the complete plastid genomes of 11 Viola and nine Salicaceae species; the complete plastid genome of Erythroxylum novogranatense was used as an outgroup. Viola formed a monophyletic clade, and V. selkirkii was closely related to V. ulleungdoensis. These results contribute to the clear identification of the phylogenetic position of V. selkirkii in Viola.

The complete chloroplast genome sequence of Campanula zangezura (Campanulaceae).

The complete chloroplast genome sequence of Campanula zangezura was determined by Illumina pair-end sequencing. The complete cp genome was 166,331 bp in length, containing a large single-copy (LSC) region of 100,034 bp and a small single-copy (SSC) region of 7781 bp, which were separated by a pair of 29,258 bp inverted repeats (IRs). A total of 113 unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among these genes, 17 genes contained one or two introns. The ML tree based on 74 protein-coding genes showed that C. zangezura formed a sister to the Campanula punctata and Campanula takesimana clade.

The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species.

We report the complete chloroplast genomes of four Viola species (V. mirabilis, V. phalacrocarpa, V. raddeana, and V. websteri) and the results of a comparative analysis between these species and the published plastid genome of the congeneric species V. seoulensis. The total genome length of the five Viola species, including the four species analyzed in this study and the species analyzed in the previous study, ranged from 156,507 (V. seoulensis) to 158,162 bp (V. mirabilis). The overall GC contents of the genomes were almost identical (36.2-36.3%). The five Viola plastomes each contained 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Among the annotated genes, 16 contained one or two introns. Based on the results of a chloroplast genome structure comparison using MAUVE, all five Viola plastomes were almost identical. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved among the Viola species. A total of 259 exon, intron, and intergenic spacer (IGS) fragments were compared to verify the divergence hotspot regions. The nucleotide diversity (Pi) values ranged from 0 to 0.7544. The IR region was relatively more conserved than the LSC and SSC regions. The Pi values in ten noncoding regions were relatively high (>0.03). Among these regions, all but rps19-trnH, petG-trnW, rpl16-rps3, and rpl2-rpl23 represent useful molecular markers for phylogenetic studies and will be helpful to resolve the phylogenetic relationships of Viola. The phylogenetic tree, which used 76 protein-coding genes from 21 Malpighiales species and one outgroup species (Averrhoa carambola), revealed that Malpighiales is divided into five clades at the family level: Erythroxylaceae, Chrysobalanaceae, Euphorbiaceae, Salicaceae, and Violaceae. Additionally, Violaceae was monophyletic, with a bootstrap value of 100% and was divided into two subclades.

Origins of East Asian Campanuloideae (Campanulaceae) diversity.

The Campanulaceae comprises approximately 2300 species that are distributed among five major lineages: Campanuloideae, Cyphioideae, Cyphocarpoideae, Lobelioideae, and Nemacladoideae. Of these, the Campanuloideae, a primarily Old World clade, has the largest diversity in East Asia. In this study, we reconstruct the phylogeny of East Asian Campanuloideae based on one nuclear gene (i.e., PPR70) and five plastid markers (i.e., atpB, matK, petD, rbcL, and trnL-trnF). We then use this phylogenetic framework to reconstruct the biogeographical history of the genus. Our molecular dataset includes 376 of the 1045 currently recognized species in the Campanuloideae. Of the 376 sampled species, 116 are from East Asia, representing ca. 60% of the East Asian Campanuloideae. Our PPR dataset included sequences for 156 accessions, representing 54 species, while our plastid dataset included sequences for 305 accessions, representing 354 species. Phylogenetic analyses recovered three large clades containing East Asian taxa: Campanulinae, Platycodinae, and Wahlenberginae. The historical assembly of Campanuloideae diversity in East Asia appears to have resulted from numerous, independent movements from Africa, Europe/W. Asia, and North America. Africa was inferred as the ancestral range for the Campanuloideae. Movement of the largest East Asian clade (Platycodinae) occurred at approximately 53.1 Ma (46.6-58.73 95% HPD) from Africa, with much of the current diversity found in East Asia having resulted from in situ diversification. Thirteen additional movements into East Asia, primarily from Europe/Western Asia, occurred subsequently. One dispersal event from western North America was also inferred. In contrast, only six movements out of East Asia were found. Our results suggest that East Asia has acted primarily as a sink for Campanuloideae diversity, with Europe, Western Asia, and Africa representing major source areas.

The complete chloroplast genome sequence of Berchemia berchemiifolia (Rhamnaceae).

The complete chloroplast genome sequence of Berchemia berchemiifolia, rare plant to Korea, was determined in this study. The total genome size was 160,410 bp in length, containing a pair of inverted repeats (IRs) of 26,514 bp, which were separated by a large single copy (LSC) and small single copy (SSC) of 88,627 bp and 18,755 bp, respectively. The overall GC contents of the chloroplast genome were 37.2%. One hundred twenty nine genes were annotated, including 84 protein coding genes, 37 tRNA genes, and 8 rRNA genes. In these genes, 18 genes contained one or two introns. The phylogenetic tree showed that Berchemia berchemiifolia was most closely related to Berchemiella wilsonii.

Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album.

The Chenopodium genus comprises ~150 species, including Chenopodium quinoa and Chenopodium album, two important crops with high nutritional value. To elucidate the phylogenetic relationship between the two species, the complete chloroplast (cp) genomes of these species were obtained by next generation sequencing. We performed comparative analysis of the sequences and, using InDel markers, inferred phylogeny and genetic diversity of the Chenopodium genus. The cp genome is 152,099 bp (C. quinoa) and 152,167 bp (C. album) long. In total, 119 genes (78 protein-coding, 37 tRNA, and 4 rRNA) were identified. We found 14 (C. quinoa) and 15 (C. album) tandem repeats (TRs); 14 TRs were present in both species and C. album and C. quinoa each had one species-specific TR. The trnI-GAU intron sequences contained one (C. quinoa) or two (C. album) copies of TRs (66 bp); the InDel marker was designed based on the copy number variation in TRs. Using the InDel markers, we detected this variation in the TR copy number in four species, Chenopodium hybridum, Chenopodium pumilio, Chenopodium ficifolium, and Chenopodium koraiense, but not in Chenopodium glaucum. A comparison of coding and non-coding regions between C. quinoa and C. album revealed divergent sites. Nucleotide diversity >0.025 was found in 17 regions-14 were located in the large single copy region (LSC), one in the inverted repeats, and two in the small single copy region (SSC). A phylogenetic analysis based on 59 protein-coding genes from 25 taxa resolved Chenopodioideae monophyletic and sister to Betoideae. The complete plastid genome sequences and molecular markers based on divergence hotspot regions in the two Chenopodium taxa will help to resolve the phylogenetic relationships of Chenopodium.

Authentication of Zanthoxylum Species Based on Integrated Analysis of Complete Chloroplast Genome Sequences and Metabolite Profiles.

We performed chloroplast genome sequencing and comparative analysis of two Rutaceae species, Zanthoxylum schinifolium (Korean pepper tree) and Z. piperitum (Japanese pepper tree), which are medicinal and culinary crops in Asia. We identified more than 837 single nucleotide polymorphisms and 103 insertions/deletions (InDels) based on a comparison of the two chloroplast genomes and developed seven DNA markers derived from five tandem repeats and two InDel variations that discriminated between Korean Zanthoxylum species. Metabolite profile analysis pointed to three metabolic groups, one with Korean Z. piperitum samples, one with Korean Z. schinifolium samples, and the last containing all the tested Chinese Zanthoxylum species samples, which are considered to be Z. bungeanum based on our results. Two markers were capable of distinguishing among these three groups. The chloroplast genome sequences identified in this study represent a valuable genomics resource for exploring diversity in Rutaceae, and the molecular markers will be useful for authenticating dried Zanthoxylum berries in the marketplace.

The complete chloroplast genome sequences of three Adenophora species and comparative analysis with Campanuloid species (Campanulaceae).

We report the complete chloroplast genomes of three Adenophora species, and analyzed these compared them to five published Campanuloid plastomes. The total genome length of Adenophora divaricata, Adenophora erecta, and Adenophora stricta ranged from 159,759 to 176,331 bp. Among the eight Campanuloid species, many inversions were found to be only in the LSC region. IR contraction was also identified in the plastid genome of Adenophora stricta. Phylogenetic analyses based on 76 protein coding genes showed that Campanuloids are monophyletic, and are composed of two major groups: Campanula s. str. and Rapunculus. When we compared each homologous locus among the four Adenophora species, ten regions showed high nucleotide divergence value (>0.03). Among these, nine loci, excepting ycf3-rpoB, are considered to be useful molecular markers for phylogenetic studies and will be helpful to resolve phylogenetic relationships of Adenophora.

The first complete chloroplast genome sequence from Violaceae (Viola seoulensis).

The complete chloroplast genome of Viola seoulensis, an endemic species to Korea, was determined in this study. The total genome size was 156 507 bp in length, containing a pair of inverted repeats (IRs) of 26 404 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 85 691 and 18 008 bp, respectively. The overall GC contents of the plastid genome were 36.3%. One hundred and thirty genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. In these genes, 17 genes contained one or two introns. A phylogenetic tree showed that Violaceae was closely related to Salicaceae.

Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets (Viola).

Cyclotides are a family of plant proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK) motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. By disrupting cell membranes, the cyclotides function as host defense peptides by exhibiting insecticidal, anthelmintic, antifouling, and molluscicidal activities. In this work, we provide the first insight into the evolution of this family of plant proteins by studying the Violaceae, in particular species of the genus Viola. We discovered 157 novel precursor sequences by the transcriptomic analysis of six Viola species: V. albida var. takahashii, V. mandshurica, V. orientalis, V. verecunda, V. acuminata, and V. canadensis. By combining these precursor sequences with the phylogenetic classification of Viola, we infer the distribution of cyclotides across 63% of the species in the genus (i.e., ~380 species). Using full precursor sequences from transcriptomes, we show an evolutionary link to the structural diversity of the cyclotides, and further classify the cyclotides by sequence signatures from the non-cyclotide domain. Also, transcriptomes were compared to cyclotide expression on a peptide level determined using liquid chromatography-mass spectrometry. Furthermore, the novel cyclotides discovered were associated with the emergence of new biological functions.

Complete chloroplast genome sequence of Hanabusaya asiatica (Campanulaceae), an endemic genus to Korea.

The complete chloroplast genome of Hanabusaya asiatica, an endemic genus to Korea, was determined in this study. The total genome size was 167,287 bp in length, containing a pair of inverted repeats (IRs) of 26,877 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 104,955 and 8578, respectively. The overall GC contents of the plastid genome were 38.8%. One hundred and twelve unique genes were annotated, including 78 protein coding genes, 30 tRNA genes and 4 rRNA genes. In these genes, 17 genes contained 1 intron, and 2 genes comprised of 2 introns.

Complete chloroplast genome sequence of Campanula takesimana (Campanulaceae), an endemic to Korea.

The complete chloroplast genome of Campanula takesimana, an endemic species to Korea, was determined in this study. The total genome size was 169,551 bp in length, containing a pair of inverted repeats (IRs) of 29,742 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 102,320 and 7747, respectively. The overall GC contents of the plastid genome were 38.8%. 131 genes were annotated, including 87 protein-coding genes, 36 tRNA genes and 8 rRNA genes. In these genes, 17 genes contained one or two introns.

Complete chloroplast genome sequence of Campanula punctata Lam. (Campanulaceae).

The complete chloroplast genome of Campanula punctata Lam. was determined in this study. The total genome size was 169 341 bp in length, containing a pair of inverted repeats (IRs) of 29 637 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 102 323 bp and 7744 bp, respectively. The overall GC contents of the plastid genome were 38.8%. One hundred thirteen unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. In these genes, 15 genes contained one intron and 2 genes had two introns. A phylogenetic tree showed that Campanula punctata was closely related to Campanula takesimana.

Complete chloroplast genome sequence of Adenophora remotiflora (Campanulaceae).

The complete chloroplast genome of Adenophora remotiflora was determined in this study. The total genome size was 171 724 bp in length, containing a pair of inverted repeats of 27 437 bp, which were separated by large single copy and small single copy of 105 555 bp and 11 295 bp, respectively. The overall GC contents of the plastid genome were 38.8%. One hundred and twelve unique genes were annotated, including 78 protein coding genes, 30 tRNA genes and 4 rRNA genes. In these genes, 15 genes contained one intron and 2 genes had two introns. A phylogenetic tree showed that Adenophora remotiflora was closely related to Hanabusaya asiatica.

Discordance of chloroplast and nuclear ribosomal DNA data in Osmorhiza (Apiaceae).

Phylogenetic studies were conducted to evaluate interspecific relationships in Osmorhiza (Apiaceae: Apioideae) using sequences of the ITS regions of nuclear ribosomal DNA, the chloroplast ndhF gene, and two noncoding regions (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer). All data sets suggest the monophyly of the New World taxa and showed that Osmorhiza aristata from Asia is relatively divergent from other members of the genus, even though it is morphologically similar to the eastern North American O. claytonii and O. longistylis. The ITS and chloroplast DNA trees differ in the relationships among the New World taxa, especially the phylogenetic position of O. occidentalis, O. glabrata, and O. depauperata. The lack of congruence between the two data sets may be a result of hybridization or introgression. Although there is high discordance between nrITS and two chloroplast DNA data sets, the latter two show similar topologies.