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Background: Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point., Results: A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214-171,315 bp and exhibit a typical four part structure. The IR region is between 23,901-36,747 bp, with the large single copy region spanning 83,691-91,249 bp and the small single copy region spanning 11,150-19,703 bp. In total, 123-133 genes are present in the chloroplasts including 77-81 protein coding genes, four rRNA genes and 30-31 tRNA genes. The GC content was 36.9-38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7-37.3%, 30.6-36.8% and 39.7-43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88-114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50-118.62 Ma)., Conclusions: The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.

Background and Aims: The genetic and morphological consequences of natural selection and selective breeding are explored in the genus Abelia . The genus consists of ornamental shrubs endemic to China, which have been bred to create attractive and diverse cultivars., Methods: DNA fingerprinting (AFLP) and DNA sequence data are used to investigate the genetic diversity among 46 accessions of Abelia (22 natural taxa and 24 horticultural breeds). In the cultivated varieties these data are used to explore taxon boundaries, hybridisation and backcrossing. The genetic analysis dataset is also used to investigate morphological variation within natural species complexes and subsequently to inform a taxonomic treatment., Key Results: Abelia comprises five species: A. forrestii , A. schumannii , A. macrotera , A. uniflora and A. chinensis and has a total of 11 varieties. Abelia uniflora and A. macrotera do not occur in sympatry and are disjunctly distributed to the east and west of the A. chinensis distribution range. Abelia chinensis is widespread in eastern China and creates hybrids and introgressive taxa, including A. uniflora , along the contact zones with the previous taxa. Abelia `Maurice Foster' is a horticultural variety collected from wild stocks in Sichuan (China). Bayesian clustering methods (inferred in STRUCTURE based on AFLP data) indicate admixture between A. macrotera and A. schumannii in this variety. Hybridization probably occurred in the wild where these progenitor taxa co-occur and naturally form hybrids. AFLP results also reveal that a few diagnostic morphological characters such as sepal number or inflorescence structure were transferred between natural species and this is mirrored by taxa such as in Abelia `Saxon Gold' and A. forrestii ., Conclusions: Studying both natural and cultivated species from the same group has helped understanding both differentiation mechanisms and how to improve cultivated plants in the future by studying which morphological characters are transferred between species and which taxa may already have arisen through hybridisation., (© The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com)

The discontinuous geographic distribution pattern of plants in the north temperate zone has been a focus of biogeographic research, especially concerning the mechanisms behind the formation of such a pattern and the spatial and temporal evolution of this intermittent distribution pattern. Hypotheses of boreotropical origin, land bridge migration, and out‐of‐Tibet have been proposed to explain the formation of the discontinuous distribution pattern. The distribution of Lonicera shows a typical Europe–Asia–North America discontinuous distribution, which makes for a good case study to investigate the above three hypotheses. In this study, we inferred the phylogeny based on plastid genomes and a nuclear data set with broad taxon sampling, covering 83 species representing two subgenera and four sections. Both nuclear and plastid phylogenetic analyses found section Isika polyphyletic, while sections Nintooa, Isoxylosteum, and Coelxylosteum were monophyletic in subgenus Chamaecerasus. Based on the nuclear and chloroplast phylogeny, we suggest transferring Lonicera maximowiczii and Lonicera tangutica into section Nintooa. Reconstruction of ancestral areas suggests that Lonicera originated in the Qinghai–Tibetan Plateau (QTP) and/or Asia, and subsequently dispersed to other regions. The aridification of the Asian interior may have facilitated the rapid radiation of Lonicera in the region. At the same time, the uplifts of the Tibetan Plateau appear to have triggered the spread and recent rapid diversification of the genus on the QTP and adjacent areas. Overall, our results deepen the understanding of the evolutionary diversification history of Lonicera. [ABSTRACT FROM AUTHOR]

The use of diverse data sets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we used target enrichment data, species tree, and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 complete plastome sequence data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the family using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggested putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 66.65 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we here recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity of using a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and plastid genomes to reconstruct deep and shallow phylogenies of plants. [ABSTRACT FROM AUTHOR]

To better identify biodiversity hotspots for conservation on Hainan Island, a tropical island in southern China, we assessed spatial variation in phylogenetic diversity and species richness using 18,976 georeferenced specimen records and a newly reconstructed molecular phylogeny of 957 native woody plants. Within this framework, we delineated bioregions based on vegetation composition and mapped areas of neoendemism and paleoendemism to identify areas of priority for conservation. Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range‐weighted turnover metrics, we delineated three major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old‐growth forests and natural secondary growth forest at the margins of Hainan, and nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves). Our study helps to elucidate potential botanical conservation priorities for Hainan within an evolutionary, phylogenetic framework. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships in Dipsacales have long been a major challenge. Although considerable progress has been made during the past two decades, questions remain; the uncertain systematic positions of Heptacodium, Triplostegia, and Zabelia, in particular, impede our understanding of Dipsacales evolution. Here we use 75 complete plastomic sequences to reconstruct the phylogeny of Dipsacales, of which 28 were newly generated. Two primary clades were recovered that form the phylogenetic backbone of Dipsacales. Seven of the primary clades correspond to the recognized families Adoxaceae, Caprifoliaceae s. str., Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae, and Valerianaceae, and one corresponds to Zabelia, which was found to be the closest relative of Morinaceae in all analyses. Additionally, our results, with greatly increased confidence in most branches, show that Heptacodium and Triplostegia are members of Caprifoliaceae s. str. and Dipsacaceae, respectively. The results of our study indicate that the complete plastomic sequences provide a fully‐resolved and well‐supported representation of the phylogenetic relationships within Dipsacales. [ABSTRACT FROM AUTHOR]

Diospyros is the largest genus (about 485 species) in Ebenaceae. It is a deciduous or evergreen tree or shrub. It grows in pantropical and extending into temperate regions. Here, we report and characterize the complete plastid genome sequences of D. maclurei Merr. and D. hainanensis Merr. in an effort to provide genomic resources useful for promoting their systematics research and potential economic development. The complete plastome of D. maclurei is 157,946 bp in length, including two Inverted Repeat (IR) regions of 26,081 bp, a Large Single-Copy (LSC) region of 87,387 bp, and a Small Single-Copy (SSC) region of 18,397 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of D. maclurei is 62.60%. The complete plastome of D. hainanensis is 157,999 bp in length, including two Inverted Repeat (IR) regions of 26,077 bp, a Large Single-Copy (LSC) region of 87,523 bp, and a Small Single-Copy (SSC) region of 18,322 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of D. hainanensis is 62.60%. The complete plastome sequences of D. Maclurei and D. hainanensis will provide a useful resource for the conservation genetics of the two species as well as for the phylogenetic studies of Diospyros. [ABSTRACT FROM AUTHOR]

Mallotus peltatus is a tropical plant of the Euphorbiaceae family, which could be used as a beverage and medicine in Hainan, China. Here, we report and characterize the complete plastome of M. peltatus. The complete plastome is 163,304 bp in length and contains a typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,112 bp, a large single-copy (LSC) region of 89,886 bp and a small single-copy (SSC) region of 18,840 bp. The plastome contains 131 genes, consisting of 78 unique protein-coding genes, 30 unique tRNA gene, four unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA), and eight pseudogenes. The overall A/T content in the plastome of M. peltatus is 64.02%. The complete plastome sequence of M. peltatus will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Euphorbiaceae. [ABSTRACT FROM AUTHOR]

Croton laevigatus grows as an evergreen tree or shrub with 15 meters height. It is distributed in the dense or open forests of Hainan province, China. Here, we report and characterize the complete plastome of C. laevigatus in an effort to provide genomic resources useful for promoting its systematics research. The plastome of C. laevigatus is found to possess a total length 162,515 bp with the typical quadripartite structure of angiosperms, contains two Inverted Repeats (IRs) of 26,866 bp, a Large Single-Copy (LSC) region of 90,234 bp and a Small Single-Copy (SSC) region of 18,549 bp. The plastome contains 113 genes, consisting of 79 unique protein-coding genes, 30 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of C. laevigatus is 64.10%. The phylogenetic analysis indicated that C. laevigatus is close to C. tiglium within Euphorbiaceae in this study. The complete plastome sequence of C. laevigatus will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Euphorbiaceae. [ABSTRACT FROM AUTHOR]

Euphorbia milii (Euphorbiaceae) grows as a scrambling shrub with many branches. Here, we report and characterize the complete plastome of E. milii in an effort to provide genomic resources useful for promoting its systematic research. The plastome of E. milii is found to possess a total length of 160,806 bp with the typical quadripartite structure of angiosperms, contains two Inverted Repeats (IRs) of 26,695 bp, a Large Single-Copy (LSC) region of 90,211 bp and a Small Single-Copy (SSC) region of 17,205 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of E. milii is of 64.10%. The phylogenetic analysis indicated that E. milii is close to E. tirucalli within Euphorbiaceae in this study. The complete plastome sequence of E. milii will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Euphorbiaceae. [ABSTRACT FROM AUTHOR]

Magnolia fordiana var. hainanensis (Dandy) Noot. (Magnoliaceae) is an endemic and ornamental tree distributed in Hainan, China. In this study, we report and characterize the complete plastid genome sequence of M. fordiana var. hainanensis in order to provide genomic resources helpful for promoting its conservation and garden utilization. The complete plastome is 160,157 bp in length and contains the typical quadripartite structure of angiosperm, including two Inverted Repeat (IRs) regions of 26,573 bp, a Large Single-Copy (LSC) region of 88,255 bp and a Small Single-Copy (SSC) region of 18,756 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene and 4 unique rRNA genes. The overall A/T content in the plastome of M. fordiana var. hainanensis is 60.70%. The complete plastome sequence of M. fordiana var. hainanensis will provide a useful resource for the conservation and garden utilization of this species as well as for the phylogenetic studies of Magnoliaceae. [ABSTRACT FROM AUTHOR]

Elaeagnus glabra is an evergreen vine or climbing shrub with 5 m height. It is widespread in southern China. It grows in the sunny forests or forest margins below 1000 m a.s.l. In this paper, we report and describe the complete plastome of E. glabra in order to provide useful genomic data for its systematic research. The complete plastome of E. glabra is 152,555 bp with a typical quadripartite structure of angiosperms. It contains two Inverted Repeats (IRs) of 25,918 bp, a large single-copy (LSC) of 82,408 bp, and a small single-copy (SSC) region of 18,311 bp. The complete plastome contains 129 genes, including 83 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The overall A/T content in the chloroplast genome of E. glabra is 62.90%. The phylogenetic analysis indicated that E. glabra is close to E. loureirii within Elaeagnaceae. The complete plastome of E. glabra will provide useful resources for the development and utilization of this species and the phylogenetic study of Rosales. [ABSTRACT FROM AUTHOR]

iThe plastome of Manilkara zapota is found to be 158,386 bp long with the typical quadripartite structure of angiosperms, contains two inverted repeats (IRs) of 26,099 bp each, a large single-copy (LSC) region of 87,745 bp, and a small single-copy (SSC) region of 18,443 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of M. zapota is 63.00%. The phylogenetic analysis indicated that M. zapota is close to Sideroxylon wightianum within Sapotaceae in this study. [ABSTRACT FROM AUTHOR]

Magnolia omeiensis is an evergreen tree with 25 meters heights. It is distributed in tropical 1200–1300 m. Mount Emei. And it has been ranked as a CR (Critically Endangered) species in China. Here, we report and characterize the complete plastome of M. omeiensis in an effort to provide genomic resources useful for promoting its systematics research. The plastome of M. omeiensis is found to possess a total length 160,021 bp with the typical quadripartite structure of angiosperms, contains two Inverted Repeats (IRs) of 26,336 bp, a Large Single-Copy (LSC) region of 88,061 bp and a Small Single-Copy (SSC) region of 19,288 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes and 4 unique rRNA genes. The overall A/T content in the plastome of M. omeiensis is 60.70%. The phylogenetic analysis indicated that M. omeiensis is close to Magnolia yunnanensis within Magnoliaceae in this study. The complete plastome sequence of M. omeiensis will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Magnoliaceae. [ABSTRACT FROM AUTHOR]

Salacia amplifolia belongs to Celastraceae. The complete plastome of S.amplifolia is 163,255 bp in length, including two inverted repeat (IR) regions of 28,932 bp, a large single-copy (LSC) region of 86,856 bp, and a small single-copy (SSC) region of 18,535 bp. The plastome contains 113 genes, consisting of 79 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of S. amplifolia is 62.50%. The complete plastome sequence of S. amplifolia will provide a useful resource for the conservation genetics of this specie as well as for the phylogenetic studies of Salacia. [ABSTRACT FROM AUTHOR]

Stauntonia obovatifoliola subsp. urophylla belongs to Lardizabalaceae. It is woody vine, with fine lines on its stems, branches, and petioles. In China, they are mainly distributed in Fujian, Guangdong, Guangxi, Jiangxi, Hunan, and Zhejiang. Here, we report and characterize the complete plastid genome sequence of S. obovatifoliola subsp. urophylla in an effort to provide genomic resources useful for promoting its systematics research. The complete plastome of S. obovatifoliola subsp. urophylla is 158,944 bp in length, including two Inverted Repeat (IR) regions of 26,284 bp, a Large Single-Copy (LSC) region of 87,306 bp and a Small Single-Copy (SSC) region of 19,070 bp. The plastome contains 115 genes, consisting of 80 unique protein-coding genes, 31 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of S. obovatifoliola subsp. urophylla is 61.40%. The complete plastome sequence of S. obovatifoliola subsp. urophylla will provide a useful resource for the conservation genetics of the species as well as for the phylogenetic studies of the genus Stauntonia. [ABSTRACT FROM AUTHOR]

Heliciopsis lobata, National class II rare and Endangered plant protection, is one of the subtropical important medicinal plants. However, its complete plastome information and systematic position are still unknown. In order to enhance the development of its Chinese medicinal value and deepen the study of it, we report and characterize the complete plastid genome sequence of H. lobata in an effort to provide genomic resources useful to promoting its medicinal value and systematic research. The complete plastome is 160,961 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 26,455 bp, a large single-copy (LSC) region of 88,929 bp, and a small single-copy (SSC) region of 19,122 bp. The plastome contains 117 genes, consisting of 83 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. lobata is 62.00%. The complete plastome sequence of H. lobata will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Proteaceae. [ABSTRACT FROM AUTHOR]

Artocarpus heterophyllus is an evergreen tree with 10–20 m height. It is distributed in tropical low-altitude areas, and is a tropical fruit with great economic value. Here, we report and characterize the complete plastome of A. heterophyllus in an effort to provide genomic resources useful for promoting its systematics research. The plastome of A. heterophyllus is found to possess a total length 160,389 bp with the typical quadripartite structure of angiosperms, contains two Inverted Repeats (IRs) of 25,708 bp, a large single-copy (LSC) region of 89,077 bp, and a small single-copy (SSC) region of 19,896 bp. The plastome contains 112 genes, consisting of 78 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of A. heterophyllus is 63.90%. The phylogenetic analysis indicated that A. heterophyllus is close to Morus cathayana within Moraceae in this study. The complete plastome sequence of A. heterophyllus will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Moraceae. [ABSTRACT FROM AUTHOR]

Mussaenda hirsutula is a plant of the family Rubiaceae. So far, there is no study on the genomic information of M. hirsutula. Here, we report and characterize the complete plastid genome sequence of M. hirsutula in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 155,503 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat regions of 25,964 bp, a large single-copy region of 85,451 bp, and a small single-copy region of 18,124 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of M. hirsutula is 62.30%. The complete plastome sequence of M. hirsutula will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Rubiaceae. [ABSTRACT FROM AUTHOR]

Hedyotis ovata is a plant of the family Rubiaceae. So far, there is no study on the genome of H. ovata. Here, we report and characterize the complete plastid genome sequence of H. ovata in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 154,560 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 26,058 bp, a large single-copy (LSC) region of 84,579 bp and a small single-copy (SSC) region of 17,865 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. ovata is 61.90%. The complete plastome sequence of H. ovata will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Rubiaceae. [ABSTRACT FROM AUTHOR]

Saprosma merrillii is a plant of the family Rubiaceae. So far, there is no study on the genome of S. merrillii. Here, we report and characterize the complete plastid genome sequence of S. merrillii in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 155,820 bp in length and contains the typical structure and gene content of angiosperm plastome, including two Inverted Repeat (IR) regions of 26,228 bp, a Large Single-Copy (LSC) region of 85,625 bp and a Small Single-Copy (SSC) region of 17,739 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of S. merrillii is 62.50%. The complete plastome sequence of S. merrillii will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Rubiaceae. [ABSTRACT FROM AUTHOR]

Arisaema ringens is a dioecious herb of the family Araceae. So far, there have been no studies on the genome of A. ringens. Here we report and characterize the complete plastid genome sequence of A. ringens in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 160,792 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat regions of 25,312 bp, a large single copy region of 88,915 bp, and a small single copy region of 21,253 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of A. ringens is 63.50%. The complete plastome sequence of A. ringens will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Araceae. [ABSTRACT FROM AUTHOR]

Antirhea chinensis is a plant of the family Rubiaceae. So far, there is no study on the genome of A. chinensis. Here we report and characterize the complete plastid genome sequence of A. chinensis in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 155,616 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat regions of 25,690 bp, a large single copy region of 86,252 bp and a small single copy region of 17,984 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of A. chinensis is 62.40%. The complete plastome sequence of A. chinensis will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Rubiaceae. [ABSTRACT FROM AUTHOR]

Homalium (Salicaceae) is mainly distributed in tropical and subtropical regions. Here we report and characterize the complete plastid genome sequences of Homalium paniculiflorum, H. stenophyllum, and H. ceylanicum in an effort to provide genomic resources useful for promoting its systematics research. The plastomes of H. paniculiflorum, H. stenophyllum, and H. ceylanicum were found to possess a total length 157,206 bp, 156,395 bp, and 156,551 bp, respectively. They all have typical quadripartite structure of angiosperms, containing two Inverted Repeats (IRs) of 27,796 bp in H. paniculiflorum, 27,669 in H. stenophyllum and 27,639 bp in H. ceylanicum, a Large Single-Copy (LSC) region of 85,031 bp (H. paniculiflorum), 84,458 bp (H. stenophyllum) and 84,627 bp (H. ceylanicum), a Small Single-Copy (SSC) region of 16,584 bp (H. paniculiflorum), 16,599 bp (H. stenophyllum), and 16,646 bp (H. ceylanicum). The all plastome contains 111 genes, consisting of consisting of 77 unique protein-coding genes (seven of which are duplicated in the IR), 30 unique tRNA genes (seven of which are duplicated in the IR) and 4 unique rRNA genes. The overall A/T content in the plastomes of H. paniculiflorum, H. stenophyllum, and H. ceylanicum are 63.30, 63.20, and 63.20%. The complete plastome sequences of H. paniculiflorum, H. stenophyllum, and H. ceylanicum will provide a useful resource for the conservation genetics of the three species as well as for the phylogenetic studies of Homalium. [ABSTRACT FROM AUTHOR]

Syzygium forrestii Merr. et Perry is an evergreen broad-leaved tree, 8–15 metres tall. It is mainly distributed in the Southwest of China (Nu river valley to Xishuangbanna area), growing from 800 to 2400 metres above sea level. It grows in the evergreen broad-leaved forest and the hillside shrubbery. It is an endemic plant species in China. At present, it has not been artificially introduced and cultivated. However, its complete plastome information and systematic position is still unknown. Here we report and characterize the complete plastid genome sequence of S. forrestii in an effort to provide genomic resources useful for promoting its conservation and systematic research. The complete plastome is 159,996 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 26,414 bp, a large single-copy (LSC) region of 88,560 bp and a small single-copy (SSC) region of 18,608 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA gene and 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA). The overall A/T content in the plastome of S. forrestii is 63.10%. The complete plastome sequence of S. forrestii will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Myrtaceae. [ABSTRACT FROM AUTHOR]

Pandanus tectorius Parkinson ex Du Roi (Pandanaceae) is a tree or shrub which is widely distributed in seashores and sandy beaches in Fujian, Guangdong, Guangxi, Guizhou, Hainan, Taiwan, Yunnan Provinces of China. P. tectorius sometimes is used as a living fence, the leaves are used for weaving and the fruit is beneficial for the treatment of diabetes. Here, we report and characterize the complete plastid genome sequence of P. tectorius in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 159,362 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 26,702 bp, a large single-copy (LSC) region of 87,447 bp and a small single-copy (SSC) region of 18,511 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA, and 16S rRNA). The overall A/T content in the plastome of P. tectorius is 62.40%. The complete plastome sequence of P.tectorius will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Pandanaceae. [ABSTRACT FROM AUTHOR]

Heptacodium miconioides Rehd. is a rare and endangered plant species occurring in Anhui, Hubei, and Zhejiang Provinces of China, which is endemic to China. Here, we report and characterize the complete plastid genome sequence of H. miconioides in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 156,313 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 23,904 bp, a large single-copy (LSC) region of 89,760 bp and a small single-copy (SSC) region of 18,745 bp. The plastome contains 114 genes, comprising 79 unique protein-coding genes, 31 unique tRNA genes, and 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA, and 16S rRNA). The overall A/T content in the plastome of D. indica is 61.60%. The complete plastome sequence of H. miconioides will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Caprifoliaceae. [ABSTRACT FROM AUTHOR]

Dillenia indica Linn. is an endangered plant species occurring in southern Guangxi province and Yunnan province of China, which has been grown in gardens as an ornamental plant and is widely used in the medical field. Here, we report and characterize the complete plastid genome sequence of D. indica to provide genomic resources useful for promoting its conservation. The complete plastome is 159,266 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 26,457 bp, a large single-copy (LSC) region of 88,305 bp, and a small single-copy (SSC) region of 18,047 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA, and 16S rRNA). The overall A/T content in the plastome of D. indica is 63.40%. The complete plastome sequence of D. indica will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Dilleniaceae. [ABSTRACT FROM AUTHOR]

Clinacanthus nutans (Burm.f.) Lindau. is a medicinal species occurring in southern Guangdong province, Guangxi province, Hainan province and Yunnan province of China, which has been widely used in the medical field. However, its complete plastome information and systematic position are still unknown. In order to enhance the development of its medicinal value, we report and characterize the complete plastid genome sequence of C. nutans in an effort to provide genomic resources useful to promoting its medicinal value and systematic research. The complete plastome is 151,669 bp in length and contains the typical structure and gene content of angiosperm plastome, including two Inverted Repeat (IR) regions of 25,366 bp, a Large Single-Copy (LSC) region of 83,502 bp and a Small Single-Copy (SSC) region of 17,435 bp. The plastome contains 113 genes, consisting of 80 unique protein-coding genes, 29 unique tRNA gene and four unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA). The overall A/T content in the plastome of C. nutans is 61.60%. The complete plastome sequence of C. nutans will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Acanthaceae. [ABSTRACT FROM AUTHOR]

Hoya is the largest genus (about 350-450 species) within Apocynaceae. It is a subshrub or liana, epiphytic or epilithic. Most species grow in tropical and subtropical South and Southeast Asia. Here we report and characterize the complete plastid genome sequence of Hoya pottsii Traill and Hoya liangii Tsiang in an effort to provide genomic resources useful for promoting its systematics research. The complete plastome of H. pottsii is 161,565 bp in length, including two Inverted Repeat (IR) regions of 24,657 bp, a Large Single-Copy (LSC) region of 92,532 bp, and a Small Single-Copy (SSC) region of 19,719 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. pottsii is 62.40%. The complete plastome of H. liangii is 162,989 bp in length, including two IR regions of 24,841 bp, a LSC region of 93,292 bp, and a SSC region of 20,015 bp. The plastome contains 115 genes, consisting of 81 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of H. pottsii is 62.30%. The complete plastome sequence of H. pottsii and H. liangii will provide a useful resource for the conservation genetics of the two species as well as for the phylogenetic studies of Hoya. [ABSTRACT FROM AUTHOR]

Hydnocarpus hainanensis Merr. is an evergreen tree with a height of 6-12 m and a diameter at breast height of 50 cm. It is distributed in Guangxi, Guizhou, Hainan, South of Yunnan Province of China. Here, we report and characterize the complete plastid genome sequence of H. hainanensis in an effort to provide genomic resources useful for promoting its conservation and systematics research. The plastome of H. hainanensis is found to possess a total length 163,330 bp with the typical quadripartite structure of angiosperms, containing two inverted repeats (IRs) of 26,870 bp, a large single copy (LSC) region of 91,510 bp and a small single copy (SSC) region of 18,080 bp. The plastome contains 111 genes, consisting of 78 unique protein-coding genes (seven of which are duplicated in the IR: rps12, rps7, ndhB, ycf2, rpl23, rpl2, and rps19), 29 unique tRNA genes (seven of which are duplicated in the IR, i.e. trnNGUU, trnRACG, trnAUGC, trnlGAU, trnVGAC, trnLCAA, and trnlCAU) and four unique rRNA genes (5S rRNA, 4.55S rRNA, 23S rRNA, and 16S rRNA). The overall A/T content in the plastome of H. hainanensis is 63.70%. The phylogenetic analysis indicated that H. hainanensis is close to Salix rorida within Malpighiales. The complete plastome sequence of H. hainanensis will provide a useful resource for the conservation genetics of the one species as well as for the phylogenetic studies of Achariaceae. [ABSTRACT FROM AUTHOR]

Vatica mangachapoi is a tree up to 20 m tall with white resinous. It is distributed in China (Hainan province), Indonesia, Malaysia (N Borneo), Philippines, Thailand, and Vietnam. It grows in forests on hills and mountain slopes below 700 metres. Its durable wood is used for making boats and building bridges and houses. It has been ranked as a VU (Vulnerable) species in China. Here we report and characterize the complete plastid genome sequence of V. mangachapoi in an effort to provide genomic resources useful for promoting its conservation and phylogenetic research. The complete plastome is 151,538 bp in length and contains the typical structure and gene content of angiosperm plastome, including two Inverted Repeat (IR) regions of 23,921 bp, a Large Single-Copy (LSC) region of 83,587 bp and a Small Single-Copy (SSC) region of 20,109 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, and 4 unique rRNA genes. The overall A/T content in the plastome of V. mangachapoi is 62.80%. The phylogenetic analysis indicated that V. mangachapoi and V. odorata is closely related and as an independent branch in Malvales in our study. The complete plastome sequence of V. mangachapoi will provide a useful resource for the conservation genetics of this species and for the phylogenetic studies for Vatica. [ABSTRACT FROM AUTHOR]

Piper laetispicum is dioecious climbers woody with 10 m tall, which is an endemic species in China. It grows on trees or rocks in forests (100-600 m) in Guangdong and Hainan Province of China. Here, we report and characterize the complete plastid genome sequence of P. laetispicum in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 161,721 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,125 bp, a large single copy (LSC) region of 89,224 bp and a small single copy (SSC) region of 18,247 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, and four unique rRNA genes. The overall A/T content in the plastome of P. laetispicum is 61.70%. The complete plastome sequence of P. laetispicum will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Piper. [ABSTRACT FROM AUTHOR]

Changiostyrax dolichocarpa is a critically endangered plant species occurring in central and southeastern China. Although the systematic position of Changiostyrax was still unclear, morphological characters, plastid and nSSR evidence supported that C. dolichocarpa should be separated from Sinojackia (Styracaceae). Here, we report and characterize the complete plastid genome sequence of C. dolichocarpa in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 158,821 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 26,000 bp, a large single copy (LSC) region of 88,038 bp and a small single copy (SSC) region of 18,784 bp. The plastome contains 120 genes, consisting of 83 unique protein-coding genes, 37 unique tRNA gene, and eight unique rRNA genes. The overall A/T content in the plastome of C. dolichocarpa is 62.70%. The complete plastome sequence of C. dolichocarpa will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Changiostyrax. [ABSTRACT FROM AUTHOR]

• 15 newly created plastomes from Malvaceae s.l. and Dipterocarpaceae are reported. • The relationships among eight subfamilies within Malvaceae s.l. are strongly supported. • Inverted Repeat regions boundaries have fluctuated within the plastomes of Malvaceae s.l. • Malvaceae s.l. diversified from the late Cretaceous to early Eocene. Malvaceae s.l. is the largest family of Malvales, comprising more than 4225 species. Within Malvaceae, the phylogenetic relationships among subfamilies remain controversial. To resolve these relationships and explore plastome evolution in Malvaceae, we assembled a complete plastome data set of 39 Malvales species, including newly reported sequences for 13 Malvaceae and two Dipterocarpaceae species. All species possessed the typical quadripartite structure of angiosperm plastomes, but significant independent expansions of the Inverted Repeat regions were detected in Abelmoschus esculentus and Durio zibethinus. Nine coding sequences were identified with positively selected sites in Malvaceae. Several highly variable noncoding and coding regions were identified in the plastomes of Malvaceae that may be valuable for phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstructions based on 78 protein-coding genes strongly supported nearly all relationships among Malvaceae subfamilies. The diversification of the subfamilies of Malvaceae was dated to the late Cretaceous and early Eocene, during a time of global warmth. [ABSTRACT FROM AUTHOR]

• We assembled the complete plastomes of 50 Dipsacales accessions, including all major clades of the Caprifoliaceae s.l. • Adoxaceae plastomes were found to be characterized by the inversion of the ndhF gene. • The backbone relationships of Caprifoliaceae s.l. were clarified with strong support, including the positions of Zabelia and Heptacodium. • The generic status of several recently erected genera such as Vesalea and Diabelia was strongly supported. The family Caprifoliaceae s.l. is an asterid angiosperm clade of ca. 960 species, most of which are distributed in temperate regions of the northern hemisphere. Recent studies show that the family comprises seven major clades: Linnaeoideae, Zabelia , Morinoideae, Dipsacoideae, Valerianoideae, Caprifolioideae, and Diervilloideae. However, its phylogeny at the subfamily or genus level remains controversial, and the backbone relationships among subfamilies are incompletely resolved. In this study, we utilized complete plastome sequencing to resolve the relationships among the subfamilies of the Caprifoliaceae s.l. and clarify several long-standing controversies. We generated and analyzed plastomes of 48 accessions of Caprifoliaceae s.l. , representing 44 species, six subfamilies and one genus. Combined with available Caprifoliaceae s.l. plastomes on GenBank and 12 outgroups, we analyzed a final dataset of 68 accessions. Genome structure was strongly conserved in general, although the boundaries between the Inverted Repeat were found to have contracted across Caprifoliaceae s.l. to exclude rpl2, rps19, and ycf1 , all or parts of which are typically present in the IR of most angiosperms. The ndhF gene was found to have been inverted in all plastomes of Adoxaceae. Phylogenomic analyses of 68 complete plastomes yielded a highly supported topology that strongly supported the monophyly of Zabelia and its sister relationship to Morinoideae. Moreover, a clade of Valerianoideae + Dipsacoideae was recovered as sister to a clade of Linnaeoideae + Zabelia + Morinoideae clade, and Heptacodium was sister to remaining Caprifolioideae. The Diervilloideae and Caprifolioideae were successively sister to all other Caprifoliaceae s.l. Major lineages of Caprifoliaceae s.l. were estimated to have diverged from the Upper Cretaceous to the Eocene (50–100 Ma), whereas within-genus diversification was dated to the Oligocene and later, concomitant with global cooling and drying. Our results demonstrate the power of plastid phylogenomics in improving estimates of phylogeny among genera and subfamilies, and provide new insights into plastome evolution across Caprifoliaceae s.l. [ABSTRACT FROM AUTHOR]