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In this study we aimed to delimit the boundaries of the Sibbaldia procumbens species complex, integrating morphological, geographical and molecular data at the population level. In total, 246 individuals were tested with simple sequence repeat (SSR) markers, and individuals were classified into three clusters. Stable variation in the morphology of leaflets, episepal and achenes was found between individuals from eastern and western Tibet, and this corresponds to the observed genetic structure when K = 2. The combined analysis of morphology and SSRs suggests three species should be recognized in the complex in China (S. procumbens, S. cuneata and S. aphanopetala). The ranges of these three species are mostly geographically separate from each other. Sibbaldia aphanopetala has often been treated as a variety of S. procumbens, but here we restore it to species rank.

Myripnois is a monotypic shrub genus in the daisy family constricted to northern China. Although wild populations of Myripnois dioica are relatively rare, this plant may potentially be cultured as a fine ornamental. In the present study, we sequenced the complete plastome of M. dioica, generating the first plastome sequences of the subfamily Pertyoideae. The plastome of M. dioica has a typical quadripartite circular structure. A large ∼20-kb and a small ∼3-kb inversion were detected in the large single copy (LSC) region and shared by other Asteraceae species. Plastome phylogenomic analyses based on 78 Asteraceae species and three outgroups revealed four groups, corresponding to four Asteraceae subfamilies: Asteroideae, Cichorioideae, Pertyoideae and Carduoideae. Among these four subfamilies, Pertyoideae is sister to Asteroideae + Cichorioideae; Carduoideae is the most basal clade. In addition, we characterized 13 simple sequence repeats (SSRs) that may be useful in future studies on population genetics. Keywords: Myripnois, Asteraceae, Plastomes, Large inversion, Phylogenomic analyses

Torreya Arn., a small genus of Taxaceae, consists of six species occurring in North America and eastern Asia. Several phylogenetic studies have previously been undertaken to reveal relationships within this genus, although only a few DNA segments or species were used. In the present study, we sequenced five Torreya plastomes and combined these with two existing plastomes from the genus to investigate plastome evolution and phylogenetic relationships within Torreya. All sequenced Torreya plastomes shared the same complement of 82 protein‐coding genes, 4 ribosomal RNA genes, and 31 transfer RNA genes. Phylogenetic inference using a maximum likelihood framework consisted of an 82‐gene, 17‐taxon dataset, including all species of Torreya, resolved Torreya as a monophyletic clade. Strongly supported relationships within the genus include the position of the early diverging T. jackii Chun, the two sister pairs T. fargesii Franch.–T. nucifera (L.) Siebold & Zucc. and T. grandis Fortune ex Lindl.–T. californica Torr., and the monophyly of the clade including T. fargesii var. yunnanensis, T. fargesii, and T. nucifera. In addition to the inference of species relationships, divergence time estimation and biogeographical analysis were carried out. The diversification of Torreya was estimated to be approximately 8.9 Ma. Ancestral state reconstruction of the geographical area suggested China/eastern North America as the most likely ancestral region for the six extant Torreya species.

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja.

The relationships among the genera of the early-diverging eudicot family Berberidaceae have long been controversial. To resolve these relationships and to better understand plastome evolution within the family, we sequenced the complete plastome sequences of ten Berberidaceae genera, combined these with six existing plastomes for the family, and conducted a series of phylogenomic analyses on the resulting data set. Five of the newly sequenced plastomes were found to possess the typical angiosperm plastome complement of 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. The infA gene was found to be pseudogenized in Bongardia, Diphylleia, Dysosma and Vancouveria; rps7 was found to be severely truncated in Diphylleia, Dysosma and Podophyllum; clpP was found to be highly divergent in Vancouveria; and a ∼19 kb inversion was detected in Bongardia. Maximum likelihood phylogenetic analyses of a 79-gene, 24-taxon data set including nearly all genera of Berberidaceae recovered four chromosome groups (x = 6, 7, 8, 10), resolved the x = 8 group as the sister to the x = 10 group, and supported the monophyly of the clade comprising x = 7, 8, 10. The generic relationships within each group were all resolved with high support. Based on gene presence within the Inverted Repeat (IR), a total of seven plastome IR types were identified within Berberidaceae. Biogeographical analysis indicated the origin and diversification of Berberidaceae has likely been strongly influenced by the distribution of its favored habitat: temperate forests.

Background Among the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae. Results Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora. Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses. Conclusion The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3956-3) contains supplementary material, which is available to authorized users.

Potentilleae, one of ten tribes of the Rosaceae, are mainly distributed in alpine regions of the northern hemisphere. The taxonomy of Potentilleae has been challenging due to extensive hybridization, polyploidization and/or apomixis characterizing several genera of Potentilleae, such as Alchemilla, Argentina and Potentilla. To help clarify relationships within Potentilleae, a phylogenetic analysis of the tribe with an emphasis on the polyphyletic genus Sibbaldia was conducted using nuclear ribosomal ITS and ETS and the plastid trnL-F and trnS-G spacer regions. In agreement with previous phylogenetic analyses, three major clades were identified in the present study–the subtribe Fragariinae, the genera Argentina and Potentilla. The 15 species of Sibbaldia were recovered in five distinct clades: three in subtribe Fragariinae, one in Argentina and the last in Potentilla. The recently established genus Chamaecallis, comprising a single species formerly treated in Sibbaldia that has intermediate floral character states with respect to Fragariinae and Potentilla, was recovered as sister to Drymocallis. Morphological character state reconstruction indicated that a reduction in the number of stamens (≤10) is a derived character state that has arisen multiple times in Potentilleae. Molecular dating analyses agreed with previously published estimates and suggested that crown group Potentilleae arose in the Middle to Late Eocene, with most generic-level divergences occurring in the Oligocene and Miocene.

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja.

Myripnois is a monotypic shrub genus in the daisy family constricted to northern China. Although wild populations of Myripnois dioica are relatively rare, this plant may potentially be cultured as a fine ornamental. In the present study, we sequenced the complete plastome of M. dioica, generating the first plastome sequences of the subfamily Pertyoideae. The plastome of M. dioica has a typical quadripartite circular structure. A large ∼20-kb and a small ∼3-kb inversion were detected in the large single copy (LSC) region and shared by other Asteraceae species. Plastome phylogenomic analyses based on 78 Asteraceae species and three outgroups revealed four groups, corresponding to four Asteraceae subfamilies: Asteroideae, Cichorioideae, Pertyoideae and Carduoideae. Among these four subfamilies, Pertyoideae is sister to Asteroideae + Cichorioideae; Carduoideae is the most basal clade. In addition, we characterized 13 simple sequence repeats (SSRs) that may be useful in future studies on population genetics.

Background Saussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine plastome evolution and resolve backbone relationships within Saussurea, we sequenced the complete plastomes of 17 species representing all four subgenera. Results All Saussurea plastomes shared the gene content and structure of most Asteraceae plastomes. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection. Phylogenomic analyses of 20 Saussurea plastomes that alternatively included nucleotide or amino acid sequences of all protein-coding genes, vs. the nucleotide sequence of the entire plastome, supported the monophyly of Saussurea and identified three clades within it. Three of the four traditional subgenera were recovered as paraphyletic. Seven plastome regions were identified as containing the highest nucleotide variability. Conclusions Our analyses reveal both the structural conservatism and power of the plastome for resolving relationships in congeneric taxa. It is very likely that differences in topology among data sets is due primarily to differences in numbers of parsimony-informative characters. Our study demonstrates that the current taxonomy of Saussurea is likely based at least partly on convergent morphological character states. Greater taxon sampling will be necessary to explore character evolution and biogeography in the genus. Our results here provide helpful insight into which loci will provide the most phylogenetic signal in Saussurea and Cardueae. Electronic supplementary material The online version of this article (10.1186/s12870-019-1896-6) contains supplementary material, which is available to authorized users.

Figure S2. Inferred molecular phylogeny from ML (maximum likelihood) and BI (Bayesian inference) analyses for the amino acid sequence of (79 CDS; data set 2). Maximum likelihood bootstrap values (BS) and posterior probabilities (PP) are shown at nodes. Branches with * have 100% bootstrap support and 1.0 posterior probability. (PDF 272 kb)

Table S1. Taxa included in present study. Collection locality and voucher information are provided for newly sequenced Table S2. The sequencing and assembly information of newly sequenced plastomes. Q30: the percentage of bases with Phred quality score greater than 30 in the total base.plastomes. (DOCX 27 kb)

Figure S3. Estimated species tree from 79 CDS alignment by coalescent-based approach. Local posterior probabilities are labeled at nodes. Branches with * have 1.0 posterior probability. The clade of S. kingii is colored in red. (PDF 548 kb)

Figure S1. The ratio of nonsynonymous and synonymous substitutions (ω, dN/dS) within each protein coding gene, as calculated by CodeML in PAML. Genes with ω > 1 are colored in red. (PDF 1045 kb)

Plastome sequences are rich sources of information for resolving difficult phylogenetic relationships and provide genomic data for conservation studies. Here, the complete plastome sequence of Alniphyllum eberhardtii Guillaumin is reported, representing the first plastome of the basal asterid family Styracaceae (Ericales). The plastome is 155,384 bp in length and contains 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes, totaling 113 unique genes with 19 genes in the inverted repeat region. Unusual features of the plastome include the presence a large 20-kb inversion in the Large Single-Copy region, the pseudogenization of the accD gene, and the loss of the second intron from clpP. The 20-kb inversion includes 14 genes and has not been previously reported in other Ericales plastomes. Thirty-nine plastid simple sequence repeats (SSRs) that may provide genetic resources for the conservation of this economically import timber plant are characterized. Phylogenetic results inferred from ML and MP analyses of 66 plastid genes and 26 taxa reveal that the Styracaceae are sister to a clade including Actinidiaceae and Ericaceae and suggest that complete plastomes are likely to be very helpful in resolving the basal relationships among Ericales families, which have resisted resolution in smaller phylogenetic data sets.

Relationships among the genera of the small, woody family Styracaceae and among families of the large, diverse order Ericales have resisted complete resolution with sequences from one or a few genes. We used plastome sequencing to attempt to resolve the backbone relationships of Styracaceae and Ericales and to explore plastome structural evolution. Complete plastomes for 23 species are newly reported here, including 18 taxa of Styracaceae and five of Ericales (including species of Sapotaceae, Clethraceae, Symplocaceae, and Diapensiaceae). Combined with publicly available complete plastome data, this resulted in a data set of 60 plastomes, including 11 of the 12 genera of Styracaceae and 12 of 22 families of Ericales. Styracaceae plastomes were found to possess the quadripartite structure typical of angiosperms, with sizes ranging from 155 to 159 kb. Most of the plastomes were found to possess the full complement of typical angiosperm plastome genes. Unusual structural features were detected in plastomes of Alniphyllum and Bruinsmia, including the presence of a large 20-kb inversion (14 genes) in the Large Single-Copy region, the loss or pseudogenization of the clpP and accD genes in Bruinsmia, and the loss of the first exon of rps16 in B. styracoides. Likewise, the second intron from clpP was found to be lost in Alniphyllum and Huodendron. Phylogenomic analyses including all 79 plastid protein-coding genes provided improved resolution for relationships among the genera of Styracaceae and families of Ericales. Styracaceae was strongly supported as monophyletic, with Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia successively sister to the remainder of the family, all with strong support. All genera of Styracaceae were recovered as monophyletic, except for Halesia and Pterostyrax, which were each recovered as polyphyletic with strong support. Within Ericales, all families were recovered as monophyletic with strong support, with Balsaminaceae sister to remaining Ericales. Most relationships recovered in plastome analyses are congruent with previous analyses based on smaller data sets. Our results demonstrate the power of plastid phylogenomics to improve phylogenetic hypotheses among genera and families, and provide new insight into plastome evolution across Ericales.

Ks values calculation of five pseudogenes in Kingdonia. (DOC 29 kb)

Repeats â Ľ30Â bp in the plastome of Kingdonia. F, forward; P, palindromic. (DOC 42 kb)

Repeats â Ľ30Â bp in the plastome of Circaeaster. F, forward; P, palindromic. (DOC 51 kb)

Primers designed for verifying endpoints of plastome structural rearrangements. (DOC 54 kb)

Repeats â Ľ30Â bp in the plastomes of seven other Ranunculales species. (DOC 30 kb)

List of taxa included in phylogenetic analyses. (DOC 67 kb)

Phylogram of the best tree determined by RAxML for the 79-gene, 99-taxon data set with no data partitions. Numbers associated with branches are ML bootstrap support values. Branches with no bootstrap values listed have 100% bootstrap support. (PDF 204 kb)