Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales

Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the 'woody clade' in Saxifragales

BACKGROUND

The "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence.

RESULTS

Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected.

CONCLUSIONS

Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.

The complete plastome sequence of Heuchera micrantha Douglas ex Lindl. (Saxifragaceae), an ornamental plant

The perennial herb Heuchera micrantha (Saxifragaceae) is a popular ornamental plant. However, the plastome sequence of H. micrantha has not been reported yet. Here, we assembled the complete plastome of H. micrantha using Illumina high-throughput pair-end sequencing. The plastome is a circular DNA molecule of 155,469 bp, comprising a pair of inverted repeat (IR, 25,654 bp) regions, a small single copy (SSC, 18,050 bp) region, and a large single copy (LSC, 86,111 bp) region. It encodes 129 genes, of which 84 are protein-coding genes, 37 are transfer RNAs, and eight are rRNAs. The total GC content is 37.8%. Phylogenetic analysis shows that H. micrantha, together with three other Heuchera species is clustered with Tiarella cordifolia. This complete plastome is beneficial for future genetic research on the Heuchera group.

Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant (Ribes nigrum), red and white currant (Ribes rubrum), and gooseberry (Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae

Background

Blackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding.

Methods

The complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five Ribes cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the Ribes were revealed.

Results

The four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species.

Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids

Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an "expanded" malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.

Characterization of the complete plastid genome and phylogenetic implication of Micranthes octopetala (Nakai) Y.I.Kim & Y.D.Kim (Saxifragaceae), endemic to Korea

Micranthes octopetala (Nakai) Y.I.Kim & Y.D. Kim et al. 2015, which belongs to the family Saxifragaceae, is a perennial herb endemic to Korea. M. octopetala was originally treated as a synonym of M. manchuriensis. However, in 2015, molecular phylogenetic analysis confirmed that M. octopetala is an independent species. In this study, the plastid genome of M. octopetala was sequenced for the first time, and the taxonomic position of this species was identified. The complete plastid genome of M. octopetala has a total length of 149 751 bp (large single copy: 83 083 bp; small single copy: 17 196 bp; inverted repeat: 24 736 bp), containing 130 genes, including 79 CDS, 30 tRNAs, and 4 rRNAs. Moreover, the absence of intron in the rpl2 gene, which is a common feature of Saxifragaceae, was confirmed. Phylogenetic analysis based on 79 protein-coding genes from 21 species revealed that M. octopetala belongs to the genus Micranthes, being a sister to other Micranthes species. The plastid genome of M. octopetala obtained in this study provides fundamental information for future studies on the genus Micranthes.

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Saxifragales is a 15-family order of early-divergent Eudicots with a rich morphological diversity and an ancient rapid radiation. Codon usage bias (CUB) analyses have emerged as an essential tool for understanding the evolutionary dynamics in genes. Thus far, the codon utilization patterns had only been reported in four separate genera within Saxifragales. This study provides a comprehensive assessment of the codon manipulation based on 50 plastid genes, covering 11 constituent families at a larger sampling scale. Our results first showed a high preference for AT bases and AT-ending codons. We then used effective number of codons (ENC) to assess a range of codon bias levels in the plastid genes. We also detected high-informative intrafamilial differences of ENC in three families. Subsequently, parity rule 2 (PR2) plot analyses revealed both family-unique and order-shared bias patterns. Most importantly, the ENC plots and neutrality analyses collectively supported the dominant roles of selection in the CUB of Saxifragales plastid genes. Notably, the phylogenetic affinities inferred by both ML and BI methods were consistent with each other, and they all comprised two primary clades and four subclades. These findings significantly enhance our understanding of the evolutionary processes of the Saxifrage order, and could potentially inspire more CUB analyses at higher taxonomic levels.

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

BACKGROUND

Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to the high intraspecific diversity and low interspecific variation in the morphological characters of species within this genus. In this study, 22 samples representing 15 Eriocaulon species from China, were sequenced and combined with published samples of Eriocaulon to test the phylogenetic resolution using the complete chloroplast genome. Furthermore, comparative analyses of the chloroplast genomes were performed to investigate the chloroplast genome evolution of Eriocaulon.

RESULTS

The 22 Eriocaulon chloroplast genomes and the nine published samples were proved highly similar in genome size, gene content, and order. The Eriocaulon chloroplast genomes exhibited typical quadripartite structures with lengths from 150,222 bp to 151,584 bp. Comparative analyses revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification of Eriocaulon species. Phylogenetic results supported Eriocaulon as a monophyletic group. The identified relationships supported the taxonomic treatment of section Heterochiton and Leucantherae, and the section Heterochiton was the first divergent group. Phylogenetic tree supported Eriocaulon was divided into five clades. The divergence times indicated that all the sections diverged in the later Miocene and most of the extant Eriocaulon species diverged in the Quaternary. The phylogeny and divergence times supported rapid radiation occurred in the evolution history of Eriocaulon.

CONCLUSION

Our study mostly supported the taxonomic treatment at the section level for Eriocaulon species in China and demonstrated the power of phylogenetic resolution using whole chloroplast genome sequences. Comparative analyses of the Eriocaulon chloroplast genome developed molecular markers that can help us better identify and understand the evolutionary history of Eriocaulon species in the future.

Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)

Comprising ca. 200 species, Saxifraga sect. Ciliatae is the most species-rich section of Saxifraga s.str., whose center of diversity is in the Tibeto-Himalayan region. The infra-sectional classification of sect. Ciliatae is still in debate due to the high level of species richness, as well as remarkable variations of habitat, morphology, physiology and life cycles. Subdivisions of this section proposed in various taxonomic systems have not been adequately tested in previous phylogenetic studies, partly due to low taxonomic sampling density, but also to the use of few DNA markers. In order to achieve a more robust infra-sectional classification of sect. Ciliatae, complete chloroplast genomes of 94 taxa from this section were analyzed, of which 93 were newly sequenced, assembled and annotated. The length of the 94 plastomes of sect. Ciliatae taxa range from 143,479 to 159,938 bp, encoding 75 to 79 unique protein-coding genes (PCGs). Analyses of the 94 plastomes revealed high conservation in structural organization, gene arrangement, and gene content. Gene loss and changes of IR boundaries were detected but in extremely low frequency. The molecular phylogenetic tree from concatenated PCGs and complete chloroplast genome sequences exhibited high resolution and support values and confirms that sect. Ciliatae is monophyletic. Three well-supported clades were revealed within the section that agree relatively well with the subsectional taxonomy of Gornall (1987), but some minor modifications should be made. Firstly, the monotypic subsection Cinerascentes should be abandoned and its constituent species, S. cinerascens, assigned to subsect. Gemmiparae. Secondly, subsections Rosulares and Serpyllifoliae should be merged and become subsect. Rosulares. Section Ciliatae thus comprises: subsect. Hirculoideae Engl. & Irmsch.; subsect. Rosulares Gornall; subsect. Gemmiparae Engl. & Irmsch.; subsect. Flagellares (C. B. Clarke) Engl. & Irmsch. and subsect. Hemisphaericae (Engl. & Irmsch.) Gornall.

Insights into chloroplast genome structure, intraspecific variation, and phylogeny of Cyclamen species (Myrsinoideae)

Species from the flowering plant genus Cyclamen are popular amongst consumers. In particular Cyclamen persicum Mill. has been significantly used commercially, and certain small flowering species such as Cyclamen hederifolium and Cyclamen coum are gradually growing in popularity in the potted flower market. Here, the chloroplast genomes of nine Cyclamen samples including four Cyclamen species and five varieties of C. hederifolium were sequenced for genome structure comparison, White green septal striped leaves related gene screening and DNA molecular markers were developed for phylogenetic analysis. In comparing Cyclamen species' chloroplast genomes, gene content and gene order were found to be highly similar with the length of genomes ranging from 151,626 to 153,058 bp. The chloroplast genome of Cyclamen has 128 genes, including 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Based on intraspecific variation, seven hotspots, including three genes and four intergenic regions, were identified as variable markers for downstream species delimitation and interspecific relationship analyses. Moreover, a phylogenetic tree constructed with complete chloroplast genomes, revealed that Cyclamen are monophyletic with Lysimachia as the closest neighbor. Phylogenetic analyses of the 14 Cyclamen species with the seven variable regions showed five distinct clades within this genus. The highly supported topologies showed these seven regions may be used as candidate DNA barcode sequences to distinguish Cyclamen species. White green septal striped leaves is common in C. hederifolium, however the molecular mechanism of this has not yet been described. Here, we find that the intergenic region rps4-trnT-UGU seems related to white green septal striped leaves.

Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species

Artemisia Linn. is a large genus within the family Asteraceae that includes several important medicinal plants. Because of their similar morphology and chemical composition, traditional identification methods often fail to distinguish them. Therefore, developing an effective identification method for Artemisia species is an urgent requirement. In this study, we analyzed 15 chloroplast (cp) genomes, including 12 newly sequenced genomes, from 5 Artemisia species. The cp genomes from the five Artemisia species had a typical quadripartite structure and were highly conserved across species. They had varying lengths of 151,132-151,178 bp, and their gene content and codon preferences were similar. Mutation hotspot analysis identified four highly variable regions, which can potentially be used as molecular markers to identify Artemisia species. Phylogenetic analysis showed that the five Artemisia species investigated in this study were sister branches to each other, and individuals of each species formed a monophyletic clade. This study shows that the cp genome can provide distinguishing features to help identify closely related Artemisia species and has the potential to serve as a universal super barcode for plant identification.

Variations in genetic diversity in cultivated Pistacia chinensis

Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.

Application of Analytical Technologies in the Discrimination and Authentication of Herbs from Fritillaria: A Review

Medicinal plants of Fritillaria are widely distributed in numerous countries around the world and possess excellent antitussive and expectorant effects. In particular, Fritillariae Bulbus (FB) as a precious traditional medicine has thousands of years of medical history in China. Herbs of Fritillaria have a high market value and demand while limited by harsh growing circumstances and scarce wild resources. As a consequence, fraudulent behaviors are regularly engaged by the unscrupulous merchants in an attempt to reap greater profits. It is of an urgent need to evaluate the quality of Fritillaria herbs and their products using various analytical instruments and techniques. This review has scrutinized approximately 160 articles from 1995 to 2022 published on the investigation of Fritillaria herbs and related herbal products. The botanical classification of genus Fritillaria, types of counterfeits, technologies applied for differentiating Fritillaria species were comprehensively summarized and discussed in the current review. Molecular and chromatographic identification were the dominant technologies in the authentication of Fritillaria herbs. Additionally, we brought some potential and promising technologies and analytical strategies into attention, which are worthy attempting in the future researches. This review could conduce to excellent reference value for further investigations of the authenticity assessment of Fritillaria species.

Plastome evolution of Aeonium and Monanthes (Crassulaceae): insights into the variation of plastomic tRNAs, and the patterns of codon usage and aversion

This study reported 13 new plastomes from Aeonium and Monanthes, and observed new markers for phylogeny and DNA barcoding, such as novel tRNA structures and codon usage bias and aversion. The Macaronesian clade of Crassulaceae consists of three genera: Aichryson, with about 15 species; Monanthes, with about 10 species; Aeonium, with about 40 species. Within this clade, Aeonium, known as "the botanical equivalent of Darwin's finches", is regarded as an excellent model plant for researching adaptive evolution. Differing from the well-resolved relationships among three genera of the Macaronesian clade, the internal branching patterns within the genus Aeonium are largely unclear. In this study, we first reported 13 new plastomes from genus Aeonium and the closely related genus Monanthes. We further performed comprehensive analyses of the plastomes, with focuses on the secondary structures of pttRNAs and the patterns of codon usage and aversion. With a typical circular and quadripartite structure, the 13 plastomes ranged from 149,900 to 151,030 bp in size, and the unique pattern in IR junctions might become a family-specific marker for Crassulaceae species. Surprisingly, the π values of plastomes from Monanthes were almost twice those from Aeonium. Most importantly, we strongly recommend that highly polymorphic regions, novel putative pttRNA structures, patterns of codon usage bias and aversion derived from plastomes might have phylogenetic implications, and could act as new markers for DNA barcoding of plants. The results of phylogenetic analyses strongly supported a clear internal branching pattern in Macaronesian clade (represented by Aeonium and Monanthes), with higher nodal support values. The findings reported here will provide new insights into the variation of pttRNAs, and the patterns of codon usage and aversion of the family Crassulaceae.

Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia, Boraginaceae) in China

Arnebiae Radix is a traditional medicine with pleiotropic properties that has been used for several 100 years. There are five species of Arnebia in China, and the two species Arnebia euchroma and Arnebia guttata are the source plants of Arnebiae Radix according to the Chinese Pharmacopoeia. Molecular markers that permit species identification and facilitate studies of the genetic diversity and divergence of the wild populations of these two source plants have not yet been developed. Here, we sequenced the chloroplast genomes of 56 samples of five Arnebia species using genome skimming methods. The Arnebia chloroplast genomes exhibited quadripartite structures with lengths from 149,539 and 152,040 bp. Three variable markers (rps16-trnQ, ndhF-rpl32, and ycf1b) were identified, and these markers exhibited more variable sites than universal chloroplast markers. The phylogenetic relationships among the five Arnebia species were completely resolved using the whole chloroplast genome sequences. Arnebia arose during the Oligocene and diversified in the middle Miocene; this coincided with two geological events during the late Oligocene and early Miocene: warming and the progressive uplift of Tianshan and the Himalayas. Our analyses revealed that A. euchroma and A. guttata have high levels of genetic diversity and comprise two and three subclades, respectively. The two clades of A. euchroma exhibited significant genetic differences and diverged at 10.18 Ma in the middle Miocene. Three clades of A. guttata diverged in the Pleistocene. The results provided new insight into evolutionary history of Arnebia species and promoted the conservation and exploitation of A. euchroma and A. guttata.

Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

BACKGROUND

Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, and incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. The olive family (Oleaceae) is composed of 25 genera classified into five tribes with tribe Oleeae consisting of four subtribes. Previous phylogenetic analyses showed that ILS and/or hybridization led to phylogenetic incongruence in the family. It was essential to distinguish phylogenetic signal conflicts, and explore mechanisms for the uncertainties concerning relationships of the olive family, especially at the deep-branching nodes.

RESULTS

We used the whole plastid genome and nuclear single nucleotide polymorphism (SNP) data to infer the phylogenetic relationships and to assess the variation and rates among the main clades of the olive family. We also used 2608 and 1865 orthologous nuclear genes to infer the deep-branching relationships among tribes of Oleaceae and subtribes of tribe Oleeae, respectively. Concatenated and coalescence trees based on the plastid genome, nuclear SNPs and multiple nuclear genes suggest events of ILS and/or ancient introgression during the diversification of Oleaceae. Additionally, there was extreme heterogeneity in the substitution rates across the tribes. Furthermore, our results supported that introgression/hybridization, rather than ILS, is the main factor for phylogenetic discordance among the five tribes of Oleaceae. The tribe Oleeae is supported to have originated via ancient hybridization and polyploidy, and its most likely parentages are the ancestral lineage of Jasmineae or its sister group, which is a "ghost lineage," and Forsythieae. However, ILS and ancient introgression are mainly responsible for the phylogenetic discordance among the four subtribes of tribe Oleeae.

CONCLUSIONS

This study showcases that using multiple sequence datasets (plastid genomes, nuclear SNPs and thousands of nuclear genes) and diverse phylogenomic methods such as data partition, heterogeneous models, quantifying introgression via branch lengths (QuIBL) analysis, and species network analysis can facilitate untangling long and complex evolutionary processes of ancient introgression, paleopolyploidization, and ILS.

Reassessment of the Phylogeny and Systematics of Chinese Parnassia (Celastraceae): A Thorough Investigation Using Whole Plastomes and Nuclear Ribosomal DNA

Parnassia L., a perennial herbaceous genus in the family Celastraceae, consists of about 60 species and is mainly distributed in the Pan-Himalayan and surrounding mountainous regions. The taxonomic position and phylogenetic relationships of the genus are still controversial. Herein, we reassessed the taxonomic status of Parnassia and its intra- and inter-generic phylogeny within Celastraceae. To that end, we sequenced and assembled the whole plastid genomes and nuclear ribosomal DNA (nrDNA) of 48 species (74 individuals), including 25 species of Parnassia and 23 species from other genera of Celastraceae. We integrated high throughput sequence data with advanced statistical toolkits and performed the analyses. Our results supported the Angiosperm Phylogeny Group IV (APG IV) taxonomy which kept the genus to the family Celastraceae. Although there were topological conflicts between plastid and nrDNA phylogenetic trees, Parnassia was fully supported as a monophyletic group in all cases. We presented a first attempt to estimate the divergence of Parnassia, and molecular clock analysis indicated that the diversification occurred during the Eocene. The molecular phylogenetic results confirmed numerous taxonomic revisions, revealing that the morphological characters used in Parnassia taxonomy and systematics might have evolved multiple times. In addition, we speculated that hybridization/introgression might exist during genus evolution, which needs to be further studied. Similarly, more in-depth studies will clarify the diversification of characters and species evolution models of this genus.

The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses

Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.‐Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single‐copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single‐copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132–133 genes, including 85–87 protein‐coding genes, 37–38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37–43 long repeats and 175–178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.

The complete chloroplast genome of Callianthe picta (Malvaceae)

Callianthe picta likes a warm and humid climate, is resistant to barrenness, and is easy to reproduce. Its petals and leaves can promote blood circulation and remove blood stasis, and can also be used to relax the muscles and collaterals. In this study, we sequenced the complete chloroplast genome sequence of C. picta to investigate its phylogenetic relationship in the family Abutilon. The complete chloroplast size of C. picta is 160,398 bp, including a large single-copy (LSC) region of 89,088 bp, a small single-copy (SSC) region of 20,138 bp, a pair of invert repeats (IRs) regions of 25,586 bp. The GC content of the whole complete chloroplast genome is 37.0%. We annotated 128 genes in the genome in detail, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that C. picta was closely related to Abutilon theophrati.

Plastid phylogenomic insights into relationships of all flowering plant families

BACKGROUND

Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades.

RESULTS

Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation.

CONCLUSIONS

We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

Phylogenomics and biogeography of Catalpa (Bignoniaceae) reveal incomplete lineage sorting and three dispersal events

Catalpa Scop. (Bignoniaceae) is a small genus (8 spp.) of trees that is disjunctly distributed among eastern Asia, eastern United States, and the West Indies. Catalpa bears beautiful inflorescences and have been cultivated as important ornamental trees for landscaping, gardening, and timber. However, the phylogenetic relationships and biogeographic history of the genus have remained unresolved. In this study, we used a large genomic dataset that includes data from the chloroplast (plastomes), and nuclear genomes (ITS and 5,759 single-copy nuclear genes) to reconstruct phylogenetic relationship within Catalpa, test interspecific gene flow events within the genus, and infer its biogeographic history. Our phylogenetic results indicate that Catalpa is monophyletic containing two main clades, section Catalpa and section Macrocatalpa. Section Catalpa is further divided into three subclades. While most relationships are congruent between the chloroplast and nuclear datasets, the position of C. ovata differs, likely due to incomplete lineage sorting. Interspecific gene flow events include C. bungei s.s. with vectors of inheritance from C. duclouxii and C. fargesii, supporting a combination of these three species and recognizing a broadly circumscribed C. bungei s.l. Our biogeographic study suggests three main dispersal events, two of which occurred during the Oligocene. The first dispersal event occurred from southwestern North America and Mexico into the Greater Antilles giving rise to the ancestor of the section of Macrocatalpa. The second dispersal event also occurred from southwestern North America and Mexico, but led to central and northern North America, subsequently reaching China through the Bering land bridge, and also reaching Europe through the North Atlantic land bridge. The third dispersal event took place in the Miocene from China to North America and gave rise to a clade composed of C. bignonioides and C. speciosa. This study uses a phylogenomic approach and biogeographical methods to infer the evolutionary history of Catalpa, highlighting issues associated with gene tree discordance, and suggesting that incomplete lineage sorting likely played an important role in the evolutionary history of Catalpa.

Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources

Leonurus cardiaca has a long history of use in western herbal medicine and is applied for the treatment of gynaecological conditions, anxiety, and heart diseases. Because of its botanical relationship to the primary Chinese species, L. japonicus, and extensive medical indications that go beyond the traditional indications for the Chinese species, it is a promising medicinal resource. Therefore, the features of genetic diversity and variability in the species have been prioritized. To explore these issues, we sequenced the chloroplast genomes of 22 accessions of L. cardiaca from different geographical locations worldwide using high-throughput sequencing. The results indicate that L. cardiaca has a typical quadripartite structure and range from 1,51,236 bp to 1,51,831 bp in size, forming eight haplotypes. The genomes all contain 114 distinct genes, including 80 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Comparative analysis showed abundant diversity of single nucleotide polymorphisms (SNPs), indels, simple sequence repeats (SSRs) in 22 accessions. Codon usage showed highly similar results for L. cardiaca species. The phylogenetic and network analysis indicated 22 accessions forming four clades that were partly related to the geographical distribution. In summary, our study highlights the advantage of chloroplast genome with large data sets in intraspecific diversity evaluation and provides a new tool to facilitate medicinal plant conservation and domestication.

Complete chloroplast genome sequence of Adenostemma lavenia (Asteraceae) and phylogenetic analysis with related species

Adenostemma lavenia is a perennial medical herb in the family Asteraceae. Here, we sequenced and analyzed the complete chloroplast genome of A. lavenia. The complete chloroplast genome size is 150,063 bp with a GC content of 37.63%. The A. lavenia chloroplast genome is a typical quadripartite structure, including a large single-copy region (LSC) of 82,017 bp and a small single-copy region (SSC) of 18,142 bp separated by a pair of inverted repeats (IRs) of 24,952 bp each. A total of 114 unique genes, including 29 tRNA genes, four rRNA genes, and 81 protein-coding genes were found in the chloroplast genome. Phylogenetic analysis revealed that A. lavenia is more closely related with Chromolaena odorata.

Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria

Background

Although molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species.

Methods

We here compared 26 complete cp genomes of ten Fritillaria species including 18 new sequences sequenced in this study. Each species had repeats and the cp genomes were used as a whole DNA barcode to test whether they can distinguish Fritillaria species.

Results

The cp genomes of Fritillaria medicinal plants were conserved in genome structure, gene type, and gene content. Comparison analysis of the Fritillaria cp genomes revealed that the intergenic spacer regions were highly divergent compared with other regions. By constructing the phylogenetic tree by the maximum likelihood and maximum parsimony methods, we found that the entire cp genome showed a high discrimination power for Fritillaria species with individuals of each species in a monophyletic clade. These results indicate that cp genome can be used to effectively differentiate medicinal plants from the genus Fritillaria at the species level.

Conclusions

This study implies that cp genome can provide distinguishing differences to help identify closely related Fritillaria species, and has the potential to be served as a universal super-barcode for plant identification.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13020-021-00460-z.

Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae)

Background

Crape myrtles, belonging to the genus Lagerstroemia L., have beautiful paniculate inflorescences and are cultivated as important ornamental tree species for landscaping and gardening. However, the phylogenetic relationships within Lagerstroemia have remained unresolved likely caused by limited sampling and the insufficient number of informative sites used in previous studies.

Results

In this study, we sequenced 20 Lagerstroemia chloroplast genomes and combined with 15 existing chloroplast genomes from the genus to investigate the phylogenetic relationships and divergence times within Lagerstroemia. The phylogenetic results indicated that this genus is a monophyletic group containing four clades. Our dating analysis suggested that Lagerstroemia originated in the late Paleocene (~ 60 Ma) and started to diversify in the middle Miocene. The diversification of most species occurred during the Pleistocene. Four variable loci, trnD-trnY-trnE, rrn16-trnI, ndhF-rpl32-trnL and ycf1, were discovered in the Lagerstroemia chloroplast genomes.

Conclusions

The chloroplast genome information was successfully utilized for molecular characterization of diverse crape myrtle samples. Our results are valuable for the global genetic diversity assessment, conservation and utilization of Lagerstroemia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07769-x.

Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)

BACKGROUND

Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes.

RESULTS

The Distylium chloroplast genome size was 159,041-159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes.

CONCLUSIONS

The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately.

Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera

BACKGROUND AND AIMS

Cephalotaxus is a paleo-endemic genus in East Asia that consists of about 7-9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus.

METHODS

A total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored.

KEY RESULTS

Phylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages.

CONCLUSIONS

Our results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics.

Chloroplast genome variation and phylogenetic relationships of Atractylodes species

Background

Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing.

Results

The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT^(GGU), and trnT^(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus.

Conclusions

Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07394-8.

The characteristics of the chloroplast genome of the Michelia chartacea (Magnoliaceae)

In this study, the complete chloroplast genome of Michelia chartacea B. L. Chen & S. C. Yang was 160,138 bp in length. It includes a large single-copy (LSC) region of 88,164 bp, a small single-copy region (SSC) of 18,824 bp, and with a pair of inverted repeats (IRs) of 26,575 bp. The GC content in the chloroplast genome was 39.23%. In total, 130 genes in the chloroplast genome of Michelia chartacea were annotated, including 83 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that M. chartacea was closely related with M. martini and M. maudiae, forming a clade included in Michelia.

Climatic Refugia and Geographical Isolation Contribute to the Speciation and Genetic Divergence in Himalayan-Hengduan Tree Peonies (Paeonia delavayi and Paeonia ludlowii)

Himalaya and Hengduan Mountains (HHM) is a biodiversity hotspot, and very rich in endemic species. Previous phylogeographical studies proposed different hypotheses (vicariance and climate-driven speciation) in explaining diversification and the observed pattern of extant biodiversity, but it is likely that taxa are forming in this area in species-specific ways. Here, we reexplored the phylogenetic relationship and tested the corresponding hypotheses within Paeonia subsect. Delavayanae composed of one widespread species (Paeonia delavayi) and the other geographically confined species (Paeonia ludlowii). We gathered genetic variation data at three chloroplast DNA fragments and one nuclear gene from 335 individuals of 34 populations sampled from HHM. We performed a combination of population genetic summary statistics, isolation-with-migration divergence models, isolation by environment, and demographic history analyses. We found evidence for the current taxonomic treatment that P. ludlowii and P. delavayi are two different species with significant genetic differentiation. The significant isolation by environment was revealed within all sampled populations but genetic distances only explained by geographical distances within P. delavayi populations. The results of population divergence models and demographic history analyses indicated a progenitor–derivative relationship and the Late Quaternary divergence without gene flow between them. The coalescence of all sampled cpDNA haplotypes could date to the Late Miocene, and P. delavayi populations probably underwent a severe bottleneck in population size during the last glacial period. Genetic variation in Paeonia subsect. Delavayanae is associated with geographical and environmental distances. These findings point to the importance of geological and climatic changes as causes of the speciation event and lineage diversification within Paeonia subsect. Delavayanae.

Differentiation of Hedyotis diffusa and Common Adulterants Based on Chloroplast Genome Sequencing and DNA Barcoding Markers

Chinese herbal tea, also known as Liang Cha or cooling beverage, is popular in South China. It is regarded as a quick-fix remedy to relieve minor health problems. Hedyotis diffusa Willd. (colloquially Baihuasheshecao) is a common ingredient of cooling beverages. H. diffusa is also used to treat cancer and bacterial infections. Owing to the high demand for H. diffusa, two common adulterants, Hedyotis brachypoda (DC.) Sivar and Biju (colloquially Nidingjingcao) and Hedyotis corymbosa (L.) Lam. (colloquially Shuixiancao), are commonly encountered in the market. Owing to the close similarity of their morphological characteristics, it is difficult to differentiate them. Here, we sequenced the complete chloroplast genomes of the three species of Hedyotis using next-generation sequencing (NGS). By comparing the complete chloroplast genomes, we found that they are closely related in the subfamily Rubioideae. We also discovered that there are significant differences in the number and repeating motifs of microsatellites and complex repeats and revealed three divergent hotspots, rps16-trnQ intergenic spacer, ndhD and ycf1. By using these species-specific sequences, we propose new DNA barcoding markers for the authentication of H. diffusa and its two common adulterants.

The complete chloroplast genome of Prunus japonica thunb.(Rosaceae), an ornamental and medicinal plant

Prunus japonica is an ornamental and medicinal plant that is widely cultivated. The complete chloroplast genome of P. japonica was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 158,080 bp in length, containing two short inverted repeat (IRa and IRb) regions of 26,385 bp, which was separated by a large single copy (LSC) region of 86,270 bp and a small single copy (SSC) region of 19,040 bp. The GC content of the whole chloroplast genome was 36.8%. The chloroplast DNA of P. japonica comprised 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. Phylogenetic analysis indicated that all species of Prunus formed a monophyletic group, P. japonica was closely related to P. hulimis.

The complete chloroplast genome sequence of Sargentodoxa cuneata: genome structure and genomic resources

Sargentodoxa cuneata is used as traditional Chinese medicine. In this study, we report its complete chloroplast genome by Illumina pair-end sequencing. The total chloroplast (cp) genome size was 158,094 bp in length, containing a pair of inverted repeats of 26,132 bp, separated by large single-copy and small single-copy regions of 86,508 bp and 19,322 bp, respectively. The chloroplast genome of S. cuneata encodes 113 different genes, including 79 protein-coding genes, 30 transfer RNAs, and 4 ribosomal RNAs. A total of 84 perfect chloroplast microsatellites were analyzed in the S. cuneata. The majority of the SSRs in this chloroplast genome are mononucleotides (66.67%). The reconstructed phylogeny revealed that S. cuneata was sister to the remaining Lardizabalaceae.

The complete chloroplast genome of Euphorbia ebracteolata Hayata (Euphorbiaceae)

Euphorbia ebracteolata is a perennial medicinal plant and widely used in China for thousands of years. The complete chloroplast genome reported here is 163,090 bp in length, including two inverted repeats (IRs) of 26,699 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 91,943 and 17,749 bp, respectively. The whole chloroplast genome of E. ebracteolata contains 112 genes, including 78 protein-coding genes, 30 transfer RNA, and 4 ribosome RNA. Phylogenetic analysis result strongly indicated that E. ebracteolata is closely related to E. helioscopia.

Complete chloroplast genome of Engelhardtia fenzlii (Juglandaceae)

In this study, we successfully assembled and analyzed the chloroplast genome of Engelhardtia fenzlii. The chloroplast genome of E. fenzlii was very similar to those of other Juglandaceae species. The E. fenzlii chloroplast genome is 161,713 bp in length and displays the typical quadripartite structure, which consists of a pair of IR regions (26,016 bp) separated by an LSC region (90,478 bp) and an SSC region (19,203 bp). The chloroplast genome of E. fenzlii contained a total of 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Phylogenetic analysis based on the complete chloroplast genomes showed that Engelhardtia formed a monophyletic clade and E. fenzlii was sister to E. roxburghiana.

Sequencing and comparative analysis of the chloroplast genome of Ribes odoratum provide insights for marker development and phylogenetics in Ribes

Ribes odoratum, commonly known as clove currant, is a perennial deciduous shrub noted for its long-lasting fragrant flowers and edible fruits. Owing to its ornamental values, this species has been widely used in city gardening and urban landscaping. Here, the complete cp genome of R. odoratum was de novo assembled for the first time. The plastome is 157,152 bp in length, with a GC content of 38.2%. The cp genome featured a typical quadripartite structure, consisting of a pair of inverted repeat regions of 25,961 bp, separated by a large single copy region of 86,896 bp, and a small single copy region of 18,333 bp. A total of 131 genes were annotated in the plastome, including 86 protein coding genes, 37 tRNA genes, and 8 rRNA genes. 56 SSRs were identified, among which, 82.35% were located in the intergenic regions. A strong A/T bias in base composition was observed in these cpSSRs. In addition, 49 repeats of different sizes and types were also found in the plastome. Through comparison, seven divergence hotspots were identified between the cp genomes of R. odoratum and R. fasciculatum var. chinense. Sequences of these divergent regions could be developed as potential markers for species delimitation in further studies. We re-investigated the relationship aomong 32 Saxifragales species through plastome-based phylogenywhich revealed that R. odoratum as a sister of R. fasciculatum var. chinense. Thus, our study provides genomic resources and valuable reference for marker development and phylogenomics in Ribes.

SUPPLEMENTARY INFORMATION

The online version of this article (10.1007/s12298-021-00932-4) contains supplementary material, which is available to authorized users.

Complete chloroplast genome of Callicarpa formosana Rolfe, a famous ornamental plant and traditional medicinal herb

Callicarpa formosana is a species of beauty-berry with large medicinal value belonging to the family Verbenaceae. In this study, the complete chloroplast genome of C. formosana was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 1,54,210 bp in length, containing two short inverted repeat (IRa and IRb) regions of 25,701 bp, which was separated by a large single copy (LSC) region of 84,938 bp and a small single copy (SSC) region of 17,870 bp. The GC content of the whole chloroplast genome was 38.1%. The chloroplast DNA of C. formosana comprised 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis indicated that the genus Callicarpa L. was located in the basal position within the family Verbenaceae. The chloroplast genome (cpDNA) of C. formosana was closely related to Callicarpa nudiflora.

Characterization of the complete chloroplast genome of Arisaema erubescens (Wall.) Schott, a traditional Chinese medicinal herb

Arisaema erubescens is a well-known medicinal plant in China. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. erubescens to investigate its phylogenetic relationship in the family Araceae. The cp genome was 167,607 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 26,193 bp) separated by a large single-copy region (LSC: 93,660 bp) and a small single-copy region (SSC: 21,561 bp). The GC content of whole cp genome is 35.3%. De novo assembly and annotation showed the presence of 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis indicated that A. erubescens was closely related to A. franchetianum, and the genus Arisaema was sister to the genus Pinellia.

Complete chloroplast genome sequence of Homalium hainanense (Salicaceae)

Homalium hainanense is a large evergreen tree species belonging to Salicaceae family, and its wood is tough, fine-grained, which makes it a good source of commercial use for building construction and furniture manufacturing. In this study, we sequenced the complete chloroplast genome of H. hainanense based on next generation sequencing and used these data to assess genomic resources. The size of the H. hainanense chloroplast genome was 157,852 bp, including a large single-copy region (85,888 bp), a small single-copy region (16,592 bp), and a pair of inverted repeats regions (27,686 bp). The overall GC content of the H. hainanense chloroplast genome was 36.6%. The plastome of H. hainanense was predicted to contain 112 unique genes, including 78 protein coding genes, 30 tRNA genes and 4 rRNA genes. The reconstructed phylogeny revealed that Homalium was monophyletic and H. hainanense was sister to H. stenophyllum, H. paniculiflorum and H. racemosum.

Plastome comparative genomics in maples resolves the infrageneric backbone relationships

Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples.

Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species

Chaenomeles (family Rosaceae) is a genus of five diploid species of deciduous spiny shrubs that are native to Central Asia and Japan. It is an important horticultural crop (commonly known as flowering quinces) in Europe and Asia for its high yield in fruits that are rich in juice, aroma, and dietary fiber. Therefore, the development of effective genetic markers of Chaenomeles species is advantageous for crop improvement through breeding and selection. In this study, we successfully assembled and analyzed the chloroplast genome of five Chaenomeles species. The chloroplast genomes of the five Chaenomeles species were very similar with no structural or content rearrangements among them. The chloroplast genomes ranged from 159,436 to 160,040 bp in length and contained a total of 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Three highly variable regions, including trnR-atpA, trnL-F, and rpl32-ccsA, were identified. Phylogenetic analysis based on the complete chloroplast genome showed that Chaenomeles forms a monophyletic clade and had a close relationship with the genera Docynia and Malus. Analyses for phylogenetic relationships and the development of available genetic markers in future could provide valuable information regarding genetics and breeding mechanisms of the Chaenomeles species.

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

BACKGROUND

Plastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of pseudogenization and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context.

RESULTS

We find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the ndh complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional.

CONCLUSIONS

Saniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, perhaps related to its extreme habitat specialization, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.

Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships

BACKGROUND

Physalis L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of Physalis species are similar, and it is difficult to rapidly and accurately distinguish them based only on morphological characteristics. At present, the species classification and phylogeny of Physalis are still controversial. In this study, the complete chloroplast (cp) genomes of four Physalis species (Physalis angulata, P. alkekengi var. franchetii, P. minima and P. pubescens) were sequenced, and the first comprehensive cp genome analysis of Physalis was performed, which included the previously published cp genome sequence of Physalis peruviana.

RESULTS

The Physalis cp genomes exhibited typical quadripartite and circular structures, and were relatively conserved in their structure and gene synteny. However, the Physalis cp genomes showed obvious variations at four regional boundaries, especially those of the inverted repeat and the large single-copy regions. The cp genomes' lengths ranged from 156,578 bp to 157,007 bp. A total of 114 different genes, 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, were observed in four new sequenced Physalis cp genomes. Differences in repeat sequences and simple sequence repeats were detected among the Physalis cp genomes. Phylogenetic relationships among 36 species of 11 genera of Solanaceae based on their cp genomes placed Physalis in the middle and upper part of the phylogenetic tree, with a monophyletic evolution having a 100% bootstrap value.

CONCLUSION

Our results enrich the data on the cp genomes of the genus Physalis. The availability of these cp genomes will provide abundant information for further species identification, increase the taxonomic and phylogenetic resolution of Physalis, and assist in the investigation and utilization of Physalis plants.

Plastome Evolution in Saxifragaceae and Multiple Plastid Capture Events Involving Heuchera and Tiarella

Saxifragaceae, a family of over 600 species and approximately 30 genera of herbaceous perennials, is well-known for intergeneric hybridization. Of the main lineages in this family, the Heuchera group represents a valuable model for the analysis of plastid capture and its impact on phylogeny reconstruction. In this study, we investigated plastome evolution across the family, reconstructed the phylogeny of the Heuchera group and examined putative plastid capture between Heuchera and Tiarella. Seven species (11 individuals) representing Tiarella, as well as Mitella and Heuchera, were selected for genome skimming. We assembled the plastomes, and then compared these to six others published for Saxifragaceae; the plastomes were found to be highly similar in overall size, structure, gene order and content. Moreover, ycf15 was lost due to pseudogenization and rpl2 lost its only intron for all the analyzed plastomes. Comparative plastome analysis revealed that size variations of the plastomes are purely ascribed to the length differences of LSC, SSC, and IRs regions. Using nuclear ITS + ETS and the complete plastome, we fully resolved the species relationships of Tiarella, finding that the genus is monophyletic and the Asian species is most closely related to the western North American species. However, the position of the Heuchera species was highly incongruent between nuclear and plastid data. Comparisons of nuclear and plastid phylogenies revealed that multiple plastid capture events have occurred between Heuchera and Tiarella, through putative ancient hybridization. Moreover, we developed numerous molecular markers for Tiarella (e.g., plastid hotspot and polymorphic nuclear SSRs), which will be useful for future studies on the population genetics and phylogeography of this disjunct genus.

Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis

Ampelopsis humulifolia (A. humulifolia) and Ampelopsis japonica (A. japonica), which belong to the family Vitaceae, are valuably used as medicinal plants. The chloroplast (cp) genomes have been recognized as a convincing data for marker selection and phylogenetic studies. Therefore, in this study we reported the complete cp genome sequences of two Ampelopsis species. Results showed that the cp genomes of A. humulifolia and A. japonica were 161,724 and 161,430 bp in length, respectively, with 37.3% guanine-cytosine (GC) content. A total of 114 unique genes were identified in each cp genome, comprising 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. We determined 95 and 99 small sequence repeats (SSRs) in A. humulifolia and A. japonica, respectively. The location and distribution of long repeats in the two cp genomes were identified. A highly divergent region of psbZ (Photosystem II reaction center protein Z) -trnG (tRNA-Glycine) was found and could be treated as a potential marker for Vitaceae, and then the corresponding primers were designed. Additionally, phylogenetic analysis showed that Vitis was closer to Tetrastigma than Ampelopsis. In general, this study provides valuable genetic resources for DNA barcoding marker identification and phylogenetic analyses of Ampelopsis.

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.

Genome Comparison Reveals Mutation Hotspots in the Chloroplast Genome and Phylogenetic Relationships of Ormosia Species

The papilionoid legume genus Ormosia comprises approximately 130 species, which are distributed mostly in the Neotropics, with some species in eastern Asia and northeastern Australia. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. In this study, we determined the complete chloroplast genome sequences of five Ormosia species by Illumina sequencing. The Ormosia chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted regions separated by a large single-copy region and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined. Comparative analyses highlighted a wide spectrum of variation, with trnK-rbcL, atpE-trnS-rps4, trnC-petN, trnS-psbZ-trnG, trnP-psaJ-rpl33, and clpP intron being the most variable regions. Phylogenetic analysis revealed that Ormosia is in the Papilionoideae clade and is sister to the Lupinus clade. Overall, this study, which provides Ormosia chloroplast genomic resources and a comparative analysis of Ormosia chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus Ormosia and molecular barcoding in population genetics and will provide insight into the chloroplast genome evolution of legumes.

Comparative Chloroplast Genomes of Sorghum Species: Sequence Divergence and Phylogenetic Relationships

Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among Sorghum species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying Sorghum species. In this study, we sequenced the complete chloroplast genomes of Sorghum sudanense and S. propinquum and analyzed the published chloroplast genomes of S. bicolor and S. timorense to retrieve valuable chloroplast molecular resources for Sorghum. The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (rps16-trnQ, trnG-trnM, rbcL-psaI, and rps15-ndhF), which were suitable for phylogenetic and species identification, were detected in the Sorghum chloroplast genomes. A phylogenetic analysis strongly supported that Sorghum is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in Sorghum.