Complete Plastid Genome Sequence Research Articles

Comparative analyses of eight complete plastid genomes of two hemiparasitic Cassytha vines in the family Lauraceae.

Cassytha is the sole genus of hemiparasitic vines (ca. 20 spp.) belonging to the Cassytheae tribe of the Lauraceae family. It is extensively distributed in tropical and subtropical regions. In this study, we determined the complete plastid genome sequences of C. filiformis and C. larsenii, which do not possess the typical quadripartite structure. The length of C. filiformis plastomes ranged from 114,215 to 114,618bp, whereas that of C. larsenii plastomes ranged from 114,900 to 114,988bp. Comparative genomic analysis revealed 1,013 mutation sites, four large intragenomic deletions, and five highly variable regions in the eight plastome sequences. Phylogenetic analyses based on 61 complete plastomes of Laurales species, 19 ITS sequences, and trnK barcodes from 91 individuals of Cassytha spp. confirmed a non-basal group comprising individuals of C. filiformis, C. larsenii, and C. pubescens in the family Lauraceae and proposed a sister relationship between C. filiformis and C. larsenii. Further morphological comparisons indicated that the presence or absence of hairs on the haustoria and the shape or size of fruits were useful traits for differentiating C. filiformis and C. larsenii.

Phylogenetic and comparative analyses of Hydnora abyssinica plastomes provide evidence for hidden diversity within Hydnoraceae

BackgroundTo date, plastid genomes have been published for all but two holoparasitic angiosperm families. However, only a single or a few plastomes represent most of these families. Of the approximately 40 genera of holoparasitic angiosperms, a complete plastid genome sequence is available for only about half. In addition, less than 15 species are currently represented with more than one published plastid genome, most of which belong to the Orobanchaceae. Therefore, a significant portion of the holoparasitic plant plastome diversity remains unexplored. This limited information could hinder potential evolutionary pattern recognition as well as the exploration of inter- and intra-species plastid genome diversity in the most extreme holoparasitic angiosperms.ResultsHere, we report the first plastomes of Kenyan Hydnora abyssinica accessions. The plastomes have a typical quadripartite structure and encode 24 unique genes. Phylogenetic tree reconstruction recovers the Kenyan accessions as monophyletic and together in a clade with the Namibian H. abyssinica accession and the recently published H. arabica from Oman. Hydnora abyssinica as a whole however is recovered as non-monophyletic, with H. arabica nested within. This result is supported by distinct structural plastome synapomorphies as well as pairwise distance estimates that reveal hidden diversity within the Hydnora species in Africa.ConclusionWe propose to increase efforts to sample widespread holoparasitic species for their plastid genomes, as is the case with H. abyssinica, which is widely distributed in Africa. Morphological reinvestigation and further molecular data are needed to fully investigate the diversity of H. abyssinica along the entire range of distribution, as well as the diversity of currently synonymized taxa.

A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences.

The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies-Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae-which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated (de novo) the plastid genomes of 24 taxa together with seven published species representing all the seven subfamilies of Iridaceae and performed comparative genomics using the Illumina MiSeq platform. The plastomes of the autotrophic Iridaceae represent 79 protein-coding, 30 tRNA, and four rRNA genes, with lengths ranging from 150,062 to 164,622 bp. The phylogenetic analysis of the plastome sequences based on maximum parsimony, maximum likelihood, and Bayesian inference analyses suggested that Watsonia and Gladiolus were closely related, supported by strong support values, which differed considerably from recent phylogenetic studies. In addition, we identified genomic events, such as sequence inversions, deletions, mutations, and pseudogenization, in some species. Furthermore, the largest nucleotide variability was found in the seven plastome regions, which can be used in future phylogenetic studies. Notably, three subfamilies-Crocoideae, Nivenioideae, and Aristeoideae-shared a common ycf2 gene locus deletion. Our study is a preliminary report of a comparative study of the complete plastid genomes of 7/7 subfamilies and 9/10 tribes, elucidating the structural characteristics and shedding light on plastome evolution and phylogenetic relationships within Iridaceae. Additionally, further research is required to update the relative position of Watsonia within the tribal classification of the subfamily Crocoideae.

Characterization of the complete plastid genome of Korean endemic, Ajuga spectabilis Nakai (Lamiaceae)

Ajuga spectabilis Nakai is a Korean endemic species in Lamiaceae. In spite of its importance, genomic studies are not performed on this species. Here, we report the complete plastid genome sequences of A. spectabilis, which will provide valuable information for its natural conservation and future studies for the plastid genome evolution. The plastid genome is 150,417 bp in length, containing a large single-copy region (LSC) of 82,140 bp and a small single-copy (SSC) region of 17,165 bp which are separated by a pair of inverted repeats (IR) of 25,556 bp. It encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The overall GC content is 38.3%, and those in the LSC, SSC, and IR regions are 36.4%, 32.2%, and 43.3%, respectively, which is consistent with other Ajuga species. Our phylogenetic analysis revealed that A. spectabilis formed a close relationship with A. ciliata and A. decumbens.

Plastid Phylogenomics Provide Evidence to Accept Two New Members of Ligusticopsis (Apiaceae, Angiosperms).

Peucedanum nanum and P. violaceum are recognized as members of the genus Peucedanum because of their dorsally compressed mericarps with slightly prominent dorsal ribs and narrowly winged lateral ribs. However, these species are not similar to other Peucedanum taxa but resemble Ligusticopsis in overall morphology. To check the taxonomic positions of P. nanum and P. violaceum, we sequenced their complete plastid genome (plastome) sequences and, together with eleven previously published Ligusticopsis plastomes, performed comprehensively comparative analyses. The thirteen plastomes were highly conserved and similar in structure, size, GC content, gene content and order, IR borders, and the patterns of codon bias, RNA editing, and simple sequence repeats (SSRs). Nevertheless, twelve mutation hotspots (matK, ndhC, rps15, rps8, ycf2, ccsA-ndhD, petN-psbM, psbA-trnK, rps2-rpoC2, rps4-trnT, trnH-psbA, and ycf2-trnL) were selected. Moreover, both the phylogenetic analyses based on plastomes and on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences robustly supported that P. nanum and P. violaceum nested in Ligusticopsis, and this was further confirmed by the morphological evidence. Hence, transferring P. nanum and P. violaceum into Ligusticopsis genus is reasonable and convincing, and two new combinations are presented.

The complete plastome of Cynanchum rostellatum (Apocynaceae), an indigenous plant in Korea

The climbing plant Cynanchum rostellatum (Turcz.) Liede & Khanum is widely distributed throughout Korea and Northeast Asia as a member of the Apocynaceae family. Although this plant has a high value in medicinal and industrial purposes, genetic research on this plant is insufficient. This study announces the complete plastid genome (plastome) sequence of C. rostellatum with 663× mean coverage, which was assembled using 763 Mbp short-read data generated by the Illumina HiSeq X platform. The C. rostellatum plastome was 158,018 bp in length and displayed the typical quadripartite structure composed of the large single-copy (LSC) region (89,058 bp), the small single-copy (SSC) region (18,718 bp), and a pair of inverted repeat (IR) regions (25,116 bp). A total of 129 genes have been annotated, including 84 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis indicated the genus Cynanchum including 12 Cynanchum plastome sequences, was monophyletic and was located within the sub-family Asclepiadoideae. Two C. rostellatum plastomes, including the plastome assembled in this study, formed a subclade and were sister to the C. thesioides plastome, whereas the other C. rostellatum, which was previously reported one, was located within the clade of C. wilfordii and C. bungei.

Characteristics of the Complete Plastid Genome Sequences of the Monotypic Genus Dodecadenia (Family: Lauraceae) and Its Phylogenomic Implications

As one of a dozen monotypic genera in the family Lauraceae, the systematic position of Dodecadenia Nees remains controversial. Here, two complete plastomes of Dodecadenia grandiflora Nees were sequenced. The two plastid genomes, with the length of 152,659 bp and 152,773 bp, had similar quadripartite structure. Both consisted of one large single-copy (LSC) region with 93,740 bp and 93,791 bp, one small single-copy region (SSC) with 18,805 bp and 18,846 bp, and a pair of inverted repeats (IR) regions with 20,057 bp and 20,068 bp. A total of 128 genes were annotated for the D. grandiflora plastid genomes (plastomes), which included 84 protein-coding genes (PCGs), 36 tRNA genes and eight rRNA genes. Codon usage analysis of the D. grandiflora plastomes showed a bias toward A/U at the third codon. A total of 122 RNA editing events were predicted, and all codon conversions were cytosine to thymine. There were 30/36 oligonucleotide repeats and 89/94 simple sequence repeats in these two plastomes of D. grandiflora. Based on 71 plastomes, both Bayesian and maximum likelihood phylogenetic analyses showed that D. grandiflora are nested among the species of Litsea Lam. together with Litsea auriculata Chien et Cheng and suggested that the monotypic genus Dodecadenia Nees should be revised. In addition, the highly variable loci trnG intron and ycf3-trnS could be used as excellent candidate markers for population genetic and phylogenetic analyses of D. grandiflora.

The complete plastid genome of a medicinal tree Lindera chienii Cheng 1934 (Lauraceae: Laureae)

Lindera chienii Cheng 1934 is an important medicine plant. The first complete plastid genome sequence of L. chienii was assembled and analyzed in this study. The plastid genome is 152,744 bp in length with a GC content of 39.15%, contains a large single-copy region of 93,767 bp and a small single-copy region of 18,843 bp, which were separated by a pair of inverted repeat regions of 20,067 bp. A total of 128 genes were detected in the plastid genome, including eight ribosomal RNA genes, 36 transfer RNA genes, and 81 protein-coding genes. The phylogenomic analysis based on plastid genomes supports the close relationships among Lindera chienii, L. megaphylla and Litsea acutivena.

Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology.

Iris ruthenica Ker Gawl. and I. uniflora Pall. ex Link, which are rare and endangered species in Korea, possess considerable horticultural and medicinal value among Korean irises. However, discrimination of the species is hindered by extensive morphological similarity. Thus, the aim of the present study was to identify discriminating features by comparing the species’ complete plastid genome (i.e., plastome) sequences and micromorphological features, including leaf margins, stomatal complex distribution (hypostomatic vs. amphistomatic leaves), anther stomata density, and tepal epidermal cell patterns. Plastome comparison revealed slightly divergent regions within intergenic spacer regions, and the most variable sequences, which were distributed in non-coding regions, could be used as molecular markers for the discrimination of I. ruthenica and I. uniflora. Phylogenetic analysis of the Iris species revealed that I. ruthenica and I. uniflora formed a well-supported clade. The comparison of plastomes and micromorphological features performed in this study provides useful information for elucidating taxonomic, phylogenetic, and evolutionary relationships in Iridaceae. Further studies, including those based on molecular cytogenetic approaches using species specific markers, will offer insights into species delimitation of the two closely related Iris species.

The complete plastid genome sequence of Peucedanum hakuunense Nakai (Apiaceae), an endemic and rare species in Korea

Peucedanum hakuunense Nakai is one of the rare species in the Korean Peninsula. This study characterized the complete plastid genome (plastome) sequence of P. hakuunense by de novo assembly with next-generation sequencing data. The complete plastome of P. hakuunense is 147,426 bp in length with a typical quadripartite structure comprising a large single-copy region of 91,915 bp, a small single-copy region of 17,425 bp, and two inverted repeat regions of 19,043 bp in length. The plastome of P. hakuunense is composed of 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic analysis revealed that two Peucedanum species formed an independent subclade, sister to the subclade of Angelica species within the tribe Selineae.

Phylogenetic relationships of Aquilaria and Gyrinops (Thymelaeaceae) revisited: evidence from complete plastid genomes

Abstract The agarwood-producing genera, Aquilaria and Gyrinops, have been treated as sister genera in Thymelaeaceae (Aquilarieae, Malvales). However, there are differing opinions about their taxonomic positions. Using new evidence from complete plastid genome (plastome) sequences of 12 Aquilaria spp. and seven Gyrinops spp., corresponding to more than half the total number of species recognized in each genus, we reconstructed a phylogenetic tree of Aquilarieae. Members of both genera shared similar sequence variations at the plastome level. The phylogenetic relationships of the two genera were completely resolved using the complete plastome sequences. Gyrinops was paraphyletic to Aquilaria, i.e. Aquilaria nested in Gyrinops. Overlapping clustering patterns were observed from topology-clustering analysis using the complete plastome and the protein-coding gene sequences, which further reinforced the paraphyletic link. The maximum-likelihood-based RelTime analysis suggested that Aquilarieae and Daphneae diverged c. 44 Mya during the Eocene, followed by a rapid divergence event in Aquilarieae, with the split between G. vidalii and G. walla c. 1.24 Mya during the Pleistocene. Our new phylogenetic estimation demonstrates the relationship between the two genera, which will aid in future taxonomic revisions involving members of Aquilarieae.

The complete plastid genome of an Antarctic moss Chorisodontium aciphyllum (Hook. f. & Wilson) Broth (Dicranaceae, Dicranales)

Plastid genomes are useful markers in resolving plant phylogenetic relationships for various taxonomic groups. Here, we sequenced and de novo assembled the complete plastid genome sequence of an Antarctic moss Chorisodontium aciphyllum (Hook. f. & Wilson) Broth using genome skimming data. The newly generated plastid genome is conserved in structure and gene content compared with that of other Bryopsida. Plastid phylogenetic analysis of mosses recovered a robust phylogeny in which Chorisodontium aciphyllum clustered with Fissidens nobilis from the Dicranales. The plastid genome sequence of C. aciphyllum will aid future evolution and diversification studies of land plants.

Genome structure and diversity among Cynanchum wilfordii accessions

BackgroundCynanchum wilfordii (Cw) and Cynanchum auriculatum (Ca) have long been used in traditional medicine and as functional food in Korea and China, respectively. They have diverse medicinal functions, and many studies have been conducted, including pharmaceutical efficiency and metabolites. Especially, Cw is regarded as the most famous medicinal herb in Korea due to its menopausal symptoms relieving effect. Despite the high demand for Cw in the market, both species are cultivated using wild resources with rare genomic information.ResultsWe collected 160 Cw germplasm from local areas of Korea and analyzed their morphological diversity. Five Cw and one Ca of them, which were morphologically diverse, were sequenced, and nuclear ribosomal DNA (nrDNA) and complete plastid genome (plastome) sequences were assembled and annotated. We investigated the genomic characteristics of Cw as well as the genetic diversity of plastomes and nrDNA of Cw and Ca. The Cw haploid nuclear genome was approximately 178 Mbp. Karyotyping revealed the juxtaposition of 45S and 5S nrDNA on one of 11 chromosomes. Plastome sequences revealed 1226 interspecies polymorphisms and 11 Cw intraspecies polymorphisms. The 160 Cw accessions were grouped into 21 haplotypes based on seven plastome markers and into 108 haplotypes based on seven nuclear markers. Nuclear genotypes did not coincide with plastome haplotypes that reflect the frequent natural outcrossing events.ConclusionsCw germplasm had a huge morphological diversity, and their wide range of genetic diversity was revealed through the investigation with 14 molecular markers. The morphological and genomic diversity, chromosome structure, and genome size provide fundamental genomic information for breeding of undomesticated Cw plants.

The complete plastid genome of Cheniella didyma (H.Y.Chen) R.Clark & Mackinder (Leguminosae)

We report here for the first time the complete plastid genome of Cheniella didyma of the legume family. The plastid genome has a typical circular structure with a total length of 157,186 bp and contains two inverted repeat regions (IRs, 24,455 bp), a large single-copy region (LSC, 89,410 bp), and a small single-copy region (SSC, 18,866 bp). This is the first report of the complete plastid genome sequence of Cheniella, a genus recently segregated from Bauhinia s.l. The phylogenetic analysis based on 77 coding regions of the plastome of this species and those of the related species strongly suggested that C. didyma is sister to Lysiphyllum and is not directly related to Bauhinia s.s.

Structural and evolutive features of the Plinia phitrantha and P. cauliflora plastid genomes and evolutionary relationships within tribe Myrteae (Myrtaceae).

Plinia phitrantha and P. cauliflora are Myrtaceae species with recognized horticultural and pharmacological potential. Nevertheless, studies on molecular genetics and the evolution of these species are absent in the literature. In this study, we report the complete plastid genome sequence of these species and an analysis of structural and evolutive features of the plastid genome within the tribe Myrteae. The two plastid genomes present the conserved quadripartite structure and are similar to already reported plastid genomes of Myrteae species concerning the size, number, and order of the genes. A total of 69-70 SSR loci, 353 single nucleotide polymorphisms, and 574 indels were identified in P. phitrantha and P. caulifora. Observed evolutive features of the plastid genomes support the development of programs for the conservation and breeding of Plinia. The phylogenomic analysis based on the complete plastid genome sequence of 15 Myrteae species presented a robust phylogenetic signal and evolutive traits of the tribe. Ten hotspots of nucleotide diversity were identified, evidence of purifying selection was observed in 27 genes, and relative conservation of the plastid genomes was confirmed for Myrteae. Altogether, the outcomes of the present study provide support for planning conservation, breeding, and biotechnological programs for Plinia species.

The complete plastid genome of Kelloggia chinensis Franch. (Rubiaceae), an endemic species from East Asia

Kelloggia chinensis Franch. is an herbal plant species endemic to East Asia. Its complete plastid genome sequence is 155, 665 bp in length, with a large single-copy (LSC) region of 85, 788 bp, a small single-copy (SSC) region of 16, 977 bp, and a pair of inverted repeat regions (IRs) of 26, 450 bp. The whole plastid genome contains 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of K. chinensis plastid genome is 37.1%. K. chinesis is evolutionarily close to tribe Rubieae according to the Maximum likelihood phylogenetic analysis based on 12 taxa.

The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing.

Complete chloroplast genome sequence of a moss, Takakia lepidozioides (Takakiopsida) is reported. The largest collection of genes in mosses and the intensive RNA editing were discussed from evolutionary perspectives. We assembled the entire plastid genome sequence of Takakia lepidozioides (Takakiopsida), emerging from the first phylogenetic split among extant mosses. The genome sequences were assembled into a circular molecule 149,016bp in length, with a quadripartite structure comprising a large and a small single-copy region separated by inverted repeats. It contained 88 genes coding for proteins, 32 for tRNA, four for rRNA, two open reading frames, and at least one pseudogene (tufA). This is the largest number of genes of all sequenced plastid genomes in mosses and Takakia is the only moss that retains the seven coding genes ccsA, cysA, cysT, petN rpoA, rps16 and trnPGGG. Parsimonious interpretation of gene loss suggests that the last common ancestor of bryophytes had all seven genes and that mosses lost at least three of them during their diversification. Analyses of the plastid transcriptome identified the extraordinary frequency of RNA editing with more than 1100 sites. We indicated a close correlation between the monoplastidy of vegetative tissue and the intensive RNA editing sites in the plastid genome in land plant lineages. Here, we proposed a hypothesis that the small population size of plastids in each vegetative cell of some early diverging land plants, including Takakia, might cause the frequent fixation of mutations in plastid genome through the intracellular genetic drift and that deleterious mutations might be continuously compensated by RNA editing during or following transcription.

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron.

Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3-4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.

Complete plastid genome sequence of Neolitsea aciculata (Laurales: Lauraceae), an evergreen broad-leaved tree endemic to East Asia

In this study, we sequenced the complete plastid genome (plastome) of Neolitsea aciculata, an evergreen broad-leaved tree endemic to East Asia, a woody component of East Asian warm-temperate and subtropical forests across China, Korea, and Japan. The plastome of N. aciculata is assembled as a single contig (152,722 bp). A large and a small single copy (93,785 and 18,795 bp, respectively) of the genome are separated by a pair of inverted repeats (20,071 bp). The genome consists of 126 genes, including 80 protein-coding, eight ribosomal RNA, and 36 transfer RNA genes. Two genes in the IR region (ycf1 and ycf2) are pseudogenized. Our phylogenetic analysis revealed the phylogenetic position of N. aciculata in a highly supported clade of the genus Neolitsea along with other two congeners, N. pallens and N. sericea.

The complete plastid genome sequence of Vaccinium japonicum (Ericales: Ericaceae), a deciduous broad-leaved shrub endemic to East Asia

We here sequenced the complete plastid genome (plastome) of Vaccinium japonicum (Ericaceae), a deciduous broad-leaved shrub endemic to East Asia. This species has considerable practical economic value. The plastome of V. japonicum is assembled as a single contig (187,213 bp). A large single copy (104,637 bp) and a small single copy (3,000 bp) of the genome are separated by a pair of inverted repeats (39,788 bp). The genome consists of 135 genes, which include 88 protein coding, eight ribosomal RNA, and 39 transfer RNA genes. The plastome of V. japonicum is similar to that of Vaccinium macrocarpon in gene content and order. Our phylogenetic analysis revealed the phylogenetic position of V. japonicum in a highly supported clade of the genus Vaccinium together with other four congeners, V. bracteatum, V. vitis-idaea, V. uliginosum and V. macrocarpon.