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— Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis) and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

Phalaenopsis zhejiangensis is a rare and endangered plant species with extremely small populations. The complete chloroplast (cp) genome of P. zhejiangensis was assembled, its structural organization was described and comparative genomic analyses was carried out. The cp genome of P. zhejiangensis is 143,547 bp in length, with a GC content of 37.2%, which includes a pair of inverted repeats (IRs) of 24,464 bp separated by a small single-copy region of 10,764 bp and a large single-copy region of 83,856 bp. The cp genome contains 126 genes, consisting of 80 protein-coding genes, 38 transfer RNAs, and eight ribosomal RNAs. Six protein-coding genes, including ψndhB (two copies), ψndhD, ψndhG, ψndhK, and ψndhI, are identified as pseudogenes. Another six ndh genes, ndhA, ndhC, ndhE, ndhF, ndhH, and ndhJ, are missing from the plastid genome. A total of 41 cp simple sequence repeats (SSRs) were identified, including 40 mono-nucleotides and one di-nucleotides. Phylogenic analysis revealed P. zhejiangensis was nested inside the Phalaenopsis species and sister to P. wilsonii. The assembly and analysis of P. zhejiangensis cp genome will provide essential data for further study of taxonomy and systematics of Orchidaceae.

— Lasiocarpus is a genus of bisexual, dioecious, or trioecious shrubs or small trees of Malpighiaceae endemic to the seasonally dry tropical forests of the Pacific slopes of Mexico. In this paper the monophyly of this genus is tested using a molecular phylogeny based on three plastid (ndhF, matK, rbcL) and a single nuclear (PHYC) markers that were newly sequenced for the three currently accepted species in this genus, along with representative taxa from the main phylogenetic groups previously recognized in Malpighiaceae. The three species of Lasiocarpus were retrieved in a well supported clade corroborating the monophyly of this genus. A taxonomic treatment of this genus is presented. Lasiocarpus ovalifolius is synonymized with L. salicifolius, and a new species, Lasiocarpus andersoniorum, endemic to Southern Mexico, is proposed. It is morphologically distinguished by characters such as axillary inflorescences, reflexed sepals, petals with crenate margin and strigose indumentum, large styles, and 2-lobed stigmas. The taxonomic revision includes morphological descriptions and distribution maps for the three accepted species of Lasiocarpus.

Evolvulus alsinoides, belonging to the family Convolvulaceae, is an important medicinal plant widely used as a nootropic in the Indian traditional medicine system. In the genus Evolvulus, no research on the chloroplast genome has been published. Hence, the present study focuses on annotation, characterization, identification of mutational hotspots, and phylogenetic analysis in the complete chloroplast genome (cp) of E. alsinoides. Genome comparison and evolutionary dynamics were performed with the species of Solanales. The cp genome has 114 genes (80 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes) that were unique with total genome size of 157,015 bp. The cp genome possesses 69 RNA editing sites and 44 simple sequence repeats (SSRs). Predicted SSRs were randomly selected and validated experimentally. Six divergent hotspots such as trnQ-UUG, trnF-GAA, psaI, clpP, ndhF, and ycf1 were discovered from the cp genome. These microsatellites and divergent hot spot sequences of the Taxa ‘Evolvulus’ could be employed as molecular markers for species identification and genetic divergence investigations. The LSC area was found to be more conserved than the SSC and IR region in genome comparison. The IR contraction and expansion studies show that nine genes rpl2, rpl23, ycf1, ycf2, ycf1, ndhF, ndhA, matK, and psbK were present in the IR-LSC and IR-SSC boundaries of the cp genome. Fifty-four protein-coding genes in the cp genome were under negative selection pressure, indicating that they were well conserved and were undergoing purifying selection. The phylogenetic analysis reveals that E. alsinoides is closely related to the genus Cressa with some divergence from the genus Ipomoea. This is the first time the chloroplast genome of the genus Evolvulus has been published. The findings of the present study and chloroplast genome data could be a valuable resource for future studies in population genetics, genetic diversity, and evolutionary relationship of the family Convolvulaceae.

In this study, whole chloroplast genomes of five Salix species (S. argyracea, S. dasyclados, S. eriocephala, S. integra 'Hakuro Nishiki', and S. suchowensis) were sequenced. These chloroplast genomes were 155 ,605, 155, 763, 155, 552, 155, 538, and 155 ,550 bp in length, harboring 131 genes (77 unigenes), 37 tRNA genes, 8 rRNA genes, and 86 mRNA genes, respectively. The genes ycf1, psaI, ycf2-2, rpoC2, rpl22, atpF, and ndhF were under positive selection among the 21 Salix species. psaI, ycf2-2, atpF, and ycf1-2 were under positive selection between the tree willow and shrub willow, and rpoC2, rpl22, and ycf1-2 were positively selected among the shrub genomes. The gene rps7 was most variable among the genomes. Phylogenetic analysis of 21 Salix species and Chosenia arbutifolia provide evidence that the cp genome data partially support the relationship with traditional taxonomic concepts in the Flora of China. This chloroplast genome elucidates Salix taxonomy and provides evidence for evolutionary research.

The genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus.

PREMISE Fruit type and morphology are tightly connected with angiosperm diversification. In Boraginales, the first-branching families, including Hydrophyllaceae, have one- to many-seeded capsules, whereas most of the remaining families have four-seeded indehiscent fruits. This fact argues for many-seeded capsules as the ancestral condition. However, little is known about the evolution of fruit dehiscence and seed number. The present study investigated the gynoecium and fruit development and morphology and the evolution of seed-numbers in Hydrophyllaceae. METHODS Gynoecium and fruit development and morphology were studied using scanning electron microscopy and x-ray microcomputed tomography. Ancestral character state reconstruction of seed number was performed using a broadly sampled phylogeny of Boraginales (ndhF and ITS) with an emphasis on Hydrophyllaceae. RESULTS Our ontogenetic studies not only demonstrate parallel developmental trajectories across Hydrophyllaceae, but also a striking diversity regarding the internal organization of the gynoecium. Ovule number appears to determine ovary structure. Many-seeded capsules are retrieved as the ancestral state of Hydrophyllaceae. At least seven transitions to fruits with (one to) four seeds and four reversals (i.e., from four- to many-seeded fruits) were reconstructed in Hydrophyllaceae. CONCLUSIONS Several shifts in seed number from "many" to "four" and back to "many" have taken place in capsular-fruited Hydrophyllaceae, a strikingly high number considering that seed number is virtually conserved across the rest of the order. The groups with a conserved seed number of four are characterized by indehiscent schizocarps or drupes and by seeds that are integrated into mericarps. This functional integration probably acts as an evolutionary constraint to shifts in seed number.

The taxonomy of Neurachninane has been unstable, with its member genera consisting of Ancistrachne, Calyptochloa, Cleistochloa, Dimorphochloa, Neurachne, Paraneurachne and Thyridolepis, changing since its original circumscription that comprised only the latter three genera. Recent studies on the phylogeny of Neurachninae have focused primarily on molecular data. We analysed the phylogeny of Neurachninae on the basis of molecular data from seven molecular loci (plastid markers: matK, ndhF, rbcL, rpl16, rpoC2 and trnLF, and ribosomal internal transcribed spacer, ITS) and morphological data from 104 morphological characters, including new taxonomically informative micromorphology of upper paleas. We devised an impact assessment scoring (IAS) protocol to aid selection of a tree for inferring the phylogeny of Neurachninae. Combining morphological and molecular data resulted in a well resolved phylogeny with the highest IAS value. Our findings support reinstatement of subtribe Neurachninae in its original sense, Neurachne muelleri and Dimorphochloa rigida. We show that Ancistrachne, Cleistochloa and Dimorphochloa are not monophyletic and Ancistrachne maidenii, Calyptochloa, Cleistochloa and Dimorphochloa form a new group, the cleistogamy group, united by having unique morphology associated with reproductive dimorphism.

The processing of chloroplast RNA requires a large number of nuclear-encoded RNA-binding proteins (RBPs) that are imported post-translationally into the organelle. The chloroplast ribonucleoprotein 31A (CP31A) supports RNA editing at 13 sites and also supports the accumulation of multiple chloroplast mRNAs. In cp31a mutants it is the ndhF mRNA (coding for a subunit of the NDH complex) that is most strongly affected. CP31A becomes particularly important at low temperatures, where it is essential for chloroplast development in young tissue. Next to two RNA-recognition motifs (RRMs), CP31A has an N-terminal acidic domain that is phosphorylated at several sites. We investigated the function of the acidic domain in the role of CP31A in RNA metabolism and cold resistance. Using point mutagenesis, we demonstrate that the known phosphorylation sites within the acidic domain are irrelevant for any of the known functions of CP31A, both at normal and at low temperatures. Even when the entire acidic domain is removed, no effects on RNA editing were observed. By contrast, loss of the acidic domain reduced the ability of CP31A to stabilize the ndhF mRNA, which was associated with reduced NDH complex activity. Most importantly, acidic domain-less CP31A lines displayed bleached young tissue in the cold. Together, these data show that the different functions of CP31A can be assigned to different regions of the protein: the RRMs are sufficient to maintain RNA editing and to allow the accumulation of basal amounts of ndhF mRNA, while chloroplast development under cold conditions critically depends on the acidic domain.

Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

—The tribe Crescentieae includesAmphitecna(21 species),Crescentia(six species), andParmentiera(10 species), three genera of understory trees with a center of diversity in Central America and a small number of species in the Antilles and northern South America. Species in Crescentieae are united by their fleshy, indehiscent fruit and cauliflorous, bat-pollinated flowers. To lay a foundation for examining morphological, ecological, and biogeographic patterns within the tribe, we inferred the phylogeny for Crescentieae using both chloroplast (ndhF,trnL-F) and nuclear markers (PepC, ITS). The most recent circumscription of Crescentieae, containingAmphitecna,Crescentia, andParmentierais supported by our phylogenetic results. Likewise, the sister relationship between Crescentieae and the Antillean-endemicSpirotecomais also corroborated by our findings. This relationship implies the evolution of fleshy and indehiscent fruits from dry and dehiscent ones, as well as the evolution of bat pollination from insect pollination. Fruits and seeds from species in Crescentieae are consumed by humans, ungulates, birds, and fish.

The increasingly wide application of chloroplast (cp) genome super‐barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. Corydalis is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, there currently are few reports about cp genomes of the genus Corydalis. In this study, we sequenced four complete cp genomes of two endangered lithophytes Corydalis saxicola and Corydalis tomentella in Corydalis, conducted a comparison of these cp genomes among each other as well as with others of Papaveraceae. The cp genomes have a large genome size of 189,029–190,247 bp, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955–42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola, and Papaveraceae species, five NADH dehydrogenase‐like genes (ndhF, ndhD, ndhL, ndhG, and ndhE) with psaC, rpl32, ccsA, and trnL‐UAG normally located in the SSC region have migrated to IRs, resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI‐CAU, and trnL‐CAA) was found within IR regions. The accD gene was found to be absent and the ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis based on the sequences of common CDS showed that the genus Corydalis is quite distantly related to the other genera of Papaveraceae, it provided a new clue for recent advocacy to establish a separate Fumariaceae family. Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships., Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships.

Background Lima bean (Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important economic value and great diversity. However, our knowledge of the chloroplast genome level of lima beans is limited. Results The chloroplast genome of lima bean was obtained by Illumina sequencing technology for the first time. The Cp genome with a length of 150,902 bp, including a pair of inverted repeats (IRA and IRB 26543 bp each), a large single-copy (LSC 80218 bp) and a small single-copy region (SSC 17598 bp). In total, 124 unique genes including 82 protein-coding genes, 34 tRNA genes, and 8 rRNA genes were identified in the P. lunatus Cp genome. A total of 61 long repeats and 290 SSRs were detected in the lima bean Cp genome. It has a typical 50 kb inversion of the Leguminosae family and an 70 kb inversion to subtribe Phaseolinae. rpl16, accD, petB, rsp16, clpP, ndhA, ndhF and ycf1 genes in coding regions was found significant variation, the intergenic regions of trnk-rbcL, rbcL-atpB, ndhJ-rps4, psbD-rpoB, atpI-atpA, atpA-accD, accD-psbJ, psbE-psbB, rsp11-rsp19, ndhF-ccsA was found in a high degree of divergence. A phylogenetic analysis showed that P. lunatus appears to be more closely related to P. vulgaris, V.unguiculata and V. radiata. Conclusions The characteristics of the lima bean Cp genome was identified for the first time, these results will provide useful insights for species identification, evolutionary studies and molecular biology research.

Mahonia lancasteri (Berberidaceae) is described from cultivation as a new species from west-central Sichuan, China. A detailed description, distributional data and ecological information along with color photographs are provided. In addition, a comparison of M. lancasteri with morphologically similar species, as well as information about its introduction and history in cultivation, is presented. We also performed a phylogenetic analysis using five molecular loci (nuclear ITS, accD, ndhF, rbcL and psbA-trnH) to further determine the close affinities of M. lancasteri. The new species naturally occurs in sympatry with several other Mahonia species.

Quercus L. has significant societal, ecological and economic benefits in the Northern Hemisphere. However, species identification among oaks is notoriously difficult. China harbours highly diverse oaks, of which the diversity of white oaks is the most extensive; however, to date, the evolution of chloroplast (cp) genomes in white oaks in China has not been comprehensively studied. Thus, we sequenced the complete cp genomes (161,254 bp, 161,229 bp and 161,254 bp in size) of three white oak species (Quercus serrata Thunb. var. brevipetiolata A. DC. Nakai, Quercus wutaishansea Mary and Quercus mongolica Fischer ex Ledebour, respectively). Six white oak species (Quercus aliena Blume, Quercus dentata Thunb., Quercus aliena Blume var. acutiserrata Maximowicz ex Wenzig, Q. serrata var. brevipetiolata, Q. wutaishanica and Q. mongolica) and five other Fagaceae species (Quercus rubra L., Quercus variabilis Bl., Quercus aquifolioides Rehd. et Wils., Fagus engleriana Seem. and Castanea henryi Skan Rehd. et Wils.) were retrieved for comparative analyses. We detected 11 highly divergent regions (psbA, matK/rps16, rps16, trnS-GCU/trnG-GCC, trnR-UCU/atpA, trnT-GGU/psbD, ndhJ, ndhJ/ndhK, accD, ndhF and ycfI) through comparative analyses and these regions might be used as molecular markers. The ω ratio of the rps12, rpoC2 and ycf1 genes was greater than 1 in several comparison groups between white oaks and the petA gene was subjected to significant positive selection between the comparison of six white oaks and Q. variabilis. Phylogenetic analyses revealed that six white oaks were grouped with Q. rubra, forming a single clade.

Seasonally Dry Tropical Forests (SDTFs) are found scattered throughout the Neotropics, from northwestern Mexico to northern Argentina, and southwestern and eastern Brazil, with eastern Brazil having the largest and most isolated fragment of SDTF, known as Caatinga. Growing knowledge from dated phylogenies and ancestral reconstruction studies suggests that SDTF lineages are nested in geographically structured phylogenies with clades highly restricted to each disjunct patch. To address these hypotheses, we investigated the biogeographic history of Euphorbia sect. Brasilienses, a group of succulent spurges from eastern Brazil's SDTF. To this aim, we assembled a concatenated matrix from 126 accessions with four markers (302 sequences from previous studies and 19 newly generated): one nuclear (ITS1) and three plastid (matK, ndhF, trnL‐trnF) loci. Our results showed that clade Brasilienses and its sister group Stachydium diverged from a common ancestor during the Miocene around 16.5 Ma. Clade Stachydium was recovered with a mean crown age of 7.7 Ma, while clade Brasilienses was recovered as a relatively young group that started diversifying about 3.1 Ma. Biogeographic results showed that the ancestral range of the clade Stachydium + Brasilienses comprised the Andes and eastern Brazil's SDTF, therefore suggesting past connections between western and eastern South America. The ancestral range of clade Brasilienses was restricted to eastern Brazil SDTF, which contrasts with clade Stachydium, which was recovered with a broader ancestral range around Late Miocene. Our results suggest limited dispersal abilities, niche conservatisms and an origin for E. sect. Brasilienses pre‐dating the Pleistocene. By contributing to the understanding of the origin and diversification of this group of endemic spurges, our study provides insights into the history of this SDTF in eastern South America.

In spite of availability of several plastomes representing different tribes of Plantaginaceae, sparse attempts have been made to understand the plastome structure, evolution, and phylogenomics. In the present study, we have made an effort to understand the gene content and plastome evolution in the family Plantaginaceae using the newly generated plastome sequence of Veronica ovata subsp. kiusiana, a taxon native to SE Asia. In the first-ever attempt, plastomes of seven out of 10 tribes of Plantaginaceae have been compared to understand the evolution across the tribes of Plantaginaceae. The size of the plastome of V. ovata subsp. kiusiana is 152,249 bp, showing a typical quadripartite structure containing LSC, SSC, and two IRs with the sizes of 83,187, 17,704, and 25,679 respectively. The plastome comparison revealed the unique deletions in ycf2 and ndhF genes of members of different tribes, and also revealed high nucleotide variable hotspots. The study also revealed six highly variable genes and intergenic spacer viz. rps16, rps15-ycf1, ccsA-ndhD, ndhC-trnV, petN-psbM, and ycf1-trnN as potential DNA barcodes for the genus Veronica. The phylogenomic study revealed the sister relationship between V. ovata subsp. kiusiana and V. persica and also suggested the tentative placement of seven tribes in the family Plantaginaceae.

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

A new species Althenia tzvelevii is described from south western Australia. This is the second species after A. bilocularis described with bilocular anthers. Illustrations of plant morphology are provided by means of SEM images and habitat photographs are included. The phylogenetic relationships of the new species were investigated using five plastid DNA markers (matK, ndhF, rbcL, rpoB, and rpoC1), with published sequences augmented by several new sequences resulting in coverage of all described species in the genus. Althenia tzvelevii forms a clade with A. patentifolia and A. bilocularis and other relationships within the genus are clarified. The Western Australian Althenia hearnii is strongly supported as sister to the Eurasian-African clade composed by A. filiformis and A. orientalis.

We found an unrecorded species, Carex molestiformis Reznicek & Rothrock, in Byeokparyeong, Daehwa-myeon, Pyeongchang-gun, Gangwon-do, South Korea. This species is native to southern parts of the United States (ca. 11 states, including Arkansas, Missouri, and Oklahoma). These plants are usually distributed densely in stream flood plains, bottomlands, stream banks, and along roadsides. Belonging to section Ovales Kunth, perennial herbs with gynecandrous spikes, C. molestiformis is closely related to C. maackii Maxim. and C. scoparia Willd. and is distinguished from them by the number (2-4) of spikes in each inflorescence and the width (2.6-3.4 mm) and number (6-9) of veins of perigynia. A new Korean name of C. molestiformis ‘Ga- Neun-Ta-Rae-Sa-Cho’ was given, as it has slender overall appearance compared with C. maackii (Ta-Rae-Sa- Cho). We also provide a description, illustrations, photographs and a key of related taxa in Korea. We compared three DNA barcode region (chloroplast DNA matK, ndhF and nuclear ribosomal DNA internal transcribed spacer) sequences from C. molestiformis with those of C. maackii and C. scoparia, determining eight speciesspecific single nucleotide polymorphism sites for C. molestiformis.

—We present a phylogenetic classification for Plukenetia (Euphorbiaceae, Acalyphoideae) based on morphology and molecular phylogenetic studies using nuclear (ETS, ITS, KEA1 introns 11 and 17, TEB exon 17) and plastid (matK, ndhF, psbA-trnH) DNA data. Plukenetia comprises 25 species divided into six sections, with three new sections and four new species described here. The circumscription of Plukenetia is unaltered from recent treatments and we continue to recognize Romanoa as distinct. The sections of Plukenetia correspond with the subclade system proposed by Cardinal-McTeague and Gillespie (2016): P1 = P. sect. Fragariopsis comb. et stat. nov.; P2 = P. sect. Penninerviae sect. nov.; P3 = P. sect. Plukenetia; P4 = P. sect. Angostylidium; and P5 = P. sect. Hedraiostylus + P. sect. Madagascarienses sect. nov. The sections are distinguished by a combination of leaf venation, staminate flower morphology, pistillate flower number, style morphology, fruit type, and seed size. Additionally, we describe three new species from South America belonging to sect. Penninerviae: Plukenetia brevistyla and Plukenetia megastyla from the Amazon basin and Plukenetia chocoensis from the Chocó Biogeographic Region of Colombia. The new Amazonian species are morphologically similar to P. brachybotrya but distinguished by their style shape and size. The new Colombian species is morphologically similar to P. penninervia but distinguished by its elongate basilaminar extrafloral nectaries, presence of abaxial laminar extrafloral nectaries, and longer inflorescences. We also describe a new species from sect. Plukenetia, Plukenetia sylvestris, which is found in central and southern Peru. This species is suggested to be the wild progenitor of the cultivated P. carolis-vegae, differing by its smaller seeds/fruits and fewer stamens. Molecular data, including a new ETS phylogeny sampling P. brevistyla, support our new taxa as distinct. Keys to the sections and species of Plukenetia are provided and we designate 12 new lectotypes for Plukenetia and Romanoa.

Several genera in the Melastomataceae mostly endemic to southeastern Brazil have not been assessed for their tribal placement in a phylogenetic context. Most workers have placed the monotypic diminutive herb Lithobium in the Microlicieae, but some classifications have assigned it to either the Sonerileae or Bertolonieae. Another monotypic genus, Eriocnema, has been included in the Bertolonieae, Sonerileae, or Microlicieae. Physeterostemon contains five species, and has not previously been assigned to any tribe. Ochthephilus, a monotypic genus endemic to Guyana, was assigned to the Merianieae, but lack of fruit and seed data, and a paucity of collections, have impeded phylogenetic assessment. To assess the placement of these genera, we conducted a phylogenetic analysis of 91 species representing 73 genera from across the Melastomataceae, including 24 of the 27 putative close relatives of Lithobium, Eriocnema, Ochthephilus, and Physeterostemon and seven gene regions, i.e., the nuclear ribosomal external and internal transcribed spacer regions, and the plastid regions accD-psaI, ndhF, psbK-psbL, rbcL, and rpl16. Lithobium groups as sister to a clade comprising all non-Olisbeoideae, Pternandreae, Henrietteeae, and Astronieae tribes. A new tribe, Lithobieae, is thus created to accommodate this placement. The capsular-fruited Eriocnema, Ochthephilus, and Physeterostemon form a clade that is sister to the berry-fruited Miconieae and widely separated from tribes with which they have been associated in historical classifications. Thus another new tribe, Eriocnemeae, is created. Lectotypes are designated for E. acaulis and L. cordatum.

An extended molecular phylogeny of the genus Dasymaschalon (Annonaceae) has been reconstructed using up to six plastid DNA regions (matK, ndhF, rbcL exons; trnL intron; psbA-trnH, trnL-trnF intergenic spacers). The results unraveled the non-monophyly of a widely distributed D. dasymaschalum. A lineage of D. dasymaschalum native to Java and cultivated at Bogor Botanical Garden represents the true D. dasymaschalum, whereas the name Pelticalyx argentea is applicable to a distantly related clade of D. dasymaschalum from mainland Asia. Dasymaschalon argenteum comb. nov. is accordingly made. Additionally, the true D. dasymaschalum has been retrieved as the sister group of D. halabalanum, a new species from Narathiwat Province, southern Thailand herein described. Pedicel length, petal size and color, and the number of stamens per flower principally distinguish the new species from its sister group.

Background Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group. Results The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution, where ndhF and trnS-G were able to distinguish the highest proportion of Calligonum species (56%). Conclusions The entire plastid genome was the most effective barcode for the genus Calligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum.

The genus Polyalthiopsis Chaowasku (Annonaceae) was a poorly known monotypic genus from Vietnam that was recently segregated from the highly polyphyletic genus Polyalthia s.l. The sister clade relationship between Polyalthiopsis and Miliusa was not well established in previous study. The phylogenetic position of two Polyalthia spp. from China, P. chinensis S.K.Wu ex P.T.Li and P. verrucipes C.Y.Wu ex P.T.Li, remains unresolved and is shown here to be phylogenetically affiliated with Polyalthiopsis. Phylogenetic analyses of six chloroplast regions (matK, ndhF, psbA-trnH, rbcL, trnL-F and ycf1; ca.7.3 kb, 60 accessions) unambiguously placed Polyalthia chinensis and P. verrucipes in the same clade with Polyalthiopsis floribunda (PP = 1, MPBS = 97%); the entire clade is sister to Miliusa with weak to strong support (PP = 1, MPBS = 54%). Polyalthia chinensis and P. verrucipes share several diagnostic characters with Polyalthiopsis floribunda, including the raised midrib on the upper surface of the leaf in vivo, conspicuous foliar glands when dried, petiole with transverse striations when dried and axillary inflorescences. The two species differ from Polyalthiopsis floribunda in having fewer flowers per inflorescence, longer linear petals and two ovules per carpel. On the basis of the combined molecular phylogenetic and morphological data, we propose two new combinations, Polyalthiopsis chinensis (S.K.Wu ex P.T.Li) B.Xue & Y.H.Tan and Polyalthiopsis verrucipes (C.Y.Wu ex P.T.Li) B.Xue & Y.H.Tan. The protologue of Polyalthia verrucipes did not include a description of the flowers, which we provide here. An updated description for the genus Polyalthiopsis and a key to species in the genus Polyalthiopsis is also provided.

—The Amazon houses a large proportion of the overall biodiversity currently found on Earth. Despite that, our knowledge of Amazonian biodiversity is still limited. In this study, we reconstruct the phylogeny of Pachyptera (Bignoniaceae), a genus of neotropical lianas that is centered in the Amazon. We then use this phylogenetic framework to re-evaluate species limits and study the biogeographic history of the genus. We sampled three molecular markers (i.e. ndhF, rpl32-trnL, and PepC) and 51 individuals representing the breadth of morphological variation and geographic distribution of all species recognized in the genus. We used this information to reconstruct phylogenetic relationships among individuals of Pachyptera using Bayesian and maximum likelihood approaches. The resulting molecular phylogeny was used as a basis to test species limits within the P. kerere species complex using a cpDNA coalescent approach (GMYC). GMYC identified five potential species within the P. kerere species complex that were subsequently evaluated in the light of morphology. Morphological data supported the recognition of four of the five potential species suggested by GMYC, all of which were also supported by a multispecies coalescent model in a Bayesian framework. The phylogeny of Pachyptera was time-calibrated and used to reconstruct the biogeographical history of the genus. We identified historically important migration pathways using our comprehensive cpDNA dataset and a Bayesian stochastic search variable selection (BSSVS) framework. Our results indicate that the genus originated in lowland Amazonia during the Middle Eocene, and subsequently occupied Central America and the Andes. Most of the diversification of Pachyptera occurred in the Miocene, a period of intense perturbations in South America.

During ongoing taxonomic studies with Tanaecium, we identified some morphological disparities between Tanaecium mutabile and the remaining species of the genus. Here, we reconstruct a molecular phylogeny of Tanaecium based on two molecular markers (i.e., the chloroplast ndhF and the nuclear pepC), and a broad sampling of members of the Arrabidaea and allies clade, where Tanaecium is included. In the newly constructed phylogeny, T. mutabile is nested within Fridericia, indicating the need for taxonomic arrangements. These findings are further supported by new morphological data (e.g., venation angle, domatia type, and corolla curvature). Based on these results, we formally transfer T. mutabile into Fridericia, and propose the necessary new combination. We further designate a new lectotype for Arrabidaea muehlbergiana, a synonym of T. mutabile. Morphological comparisons between T. mutabile and other morphologically similar species are presented.

BackgroundMany species of the genusRosahave been used as ornamental plants and traditional medicines. However, industrial development of roses is hampered due to highly divergent characteristics.MethodsWe analyzed the chloroplast (cp) genomes ofRosa laevigata, R. rugosaandR. canina, including the repeat sequences, inverted-repeat (IR) contractions and expansions, and mutation sites.ResultsThe size of the cp genome ofR. laevigata, R. rugosaandR. caninawas between 156 333 bp and 156 533 bp, and contained 113 genes (30 tRNA genes, 4 rRNA genes and 79 protein-coding genes). The regions with a higher degree of variation were screened out (trnH-GUU,trnS-GCU,trnG-GCC,psbA-trnH,trnC-GCA,petN,trnT-GGU,psbD,petA,psbJ,ndhF,rpl32,psaCandndhE). Such higher-resolution loci lay the foundation of barcode-based identification of cp genomes inRosagenus. A phylogenetic tree of the genusRosawas reconstructed using the full sequences of the cp genome. These results were largely in accordance with the current taxonomic status ofRosa.ConclusionsOur data: (i) reveal that cp genomes can be used for the identification and classification ofRosaspecies; (ii) can aid studies on molecular identification, genetic transformation, expression of secondary metabolic pathways and resistant proteins; (iii) can lay a theoretical foundation for the discovery of disease-resistance genes and cultivation ofRosaspecies.

Phylogenetic relationships in Inuleae subtribe Inulinae (Asteraceae) were investigated. DNA sequence data from three chloroplast regions (ndhF, trnL-F and psbA-trnH) and the nuclear ribosomal internal transcribed spacer (ITS) region were analysed separately and in combination using parsimony and Bayesian inference. A total of 163 ingroup taxa were included, of which 60 were sampled for all four markers. Conflicts between chloroplast and nuclear data were assessed using partitioned Bremer support (PBS). Rather than averaging PBS over several trees from constrained searches, individual trees were considered by evaluating PBS ranges. Criteria to be used in the detection of a significant conflict between data partitions are proposed. Three nodes in the total data tree were found to encompass significant conflict that could result from ancient hybridization. Neither of the large, heterogeneous and widespread genera Inula and Pulicaria is monophyletic. A monophyletic group ("the Inula complex") that comprises all species of Inula includes also Telekia, Carpesium, Chrysophthalmum, Rhanteriopsis, Amblyocarpum, and Pentanema sensu stricto. Two species of Pentanema were found to be closer to Blumea (including Blumeopsis and Merrittia) and Caesulia. The monophyletic "Pulicaria complex" includes all taxa with heteromorphic pappus. Within this group, Francoeuria is distinct from Pulicaria and merits recognition as a separate genus. © The Willi Hennig Society 2009.

A phylogenetic analysis of the monocot order Liliales was performed using sequence data from three mitochondrial (atp1, cob, nad5) and two plastid genes (rbcL, ndhF). The complete data matrix includes 46 terminals representing all 10 families currently included in Liliales. The two major partitions, mitochondrial and plastid data, were congruent, and parsimony analysis resulted in 50 equally parsimonious trees and a well resolved consensus tree confirming monophyly of all families. Mitochondrial genes are known to include RNA edited sites, and in some cases unprocessed genes are replaced by retro-processed gene copies, that is processed paralogs. To test the effects on phylogeny reconstruction of predicted edited sites and potentially unintentionally sampled processed paralogs, a number of analyses were performed using subsets of the complete data matrix. In general, predicted edited sites were more homoplasious than the other characters and increased incongruence among most data partitions. The predicted edited sites have a non-random phylogenetic signal in conflict with the signal of the non-edited sites. The potentially misleading signal was caused partially by the apparent presence of processed paralogs in Galanthus (Amaryllidaceae), part of the outgroup, but also by a deviating evolutionary pattern of predicted edited sites in Liliaceae compared with the remainder of the Liliales. Despite the problems that processed paralogs may cause, we argue that they should not a priori be excluded from phylogenetic analysis.

Bruguiera is a genus of true mangroves that are mostly distributed in the Indo-West Pacific region. However, the number of published whole chloroplast genome sequences of Bruguiera species are limited. Here, the complete chloroplast sequences of five Bruguiera species were sequenced and assembled using Illumina data. The chloroplast genomes of B. gymnorhiza, B. hainesii, B. cylindrica, B. parviflora and B. sexangula were assembled into 161,195, 164,295, 164,297, 163,228 and 164,170 bp, respectively. All chloroplast genomes contain 37 tRNA and eight rRNA genes, with either 84 or 85 protein-coding genes. A comparative analysis of these genomes revealed high similarity in gene structure, gene order and boundary position of the LSC, SSC and two IR regions. Interestingly, B. gymnorhiza lost a rpl32 gene in the SSC region. In addition, a ndhF gene in B. parviflora straddles both the SSC and IRB boundary regions. These genes reveal differences in chloroplast evolution among Bruguiera species. Repeats and SSRs in the chloroplast genome sequences were found to be highly conserved between B. cylindrica and B. hainesii as well as B. gymnorhiza and B. sexangula indicating close genetic relationships based on maternal inheritance. Notably, B. hainesii, which is considered a hybrid between B. gymnorhiza and B. cylindrica, appears to have inherited the chloroplast from B. cylindrica. Investigating the effects of selection events on shared protein-coding genes showed a positive selection in rps7 and rpl36 genes in all species compared to land-plant species. A phylogenetic analysis, based on 59 conserved chloroplast protein-coding genes, showed strong support that all Bruguiera species are in the clade Rhizophoraceae. This study provides valuable genetic information for the study of evolutionary relationships and population genetics in Bruguiera and other mangrove species.

Hawthorns (Crataegus L.) are one of the most important processing and table fruits in China, due to their medicinal properties and health benefits. However, the interspecific relationships and evolution history of cultivated Crataegus in China remain unclear. Our previously published data showed C. bretschneideri may be derived from the hybridization of C. pinnatifida with C. maximowiczii, and that introgression occurs between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. In the present study, chloroplast sequences were used to further elucidate the phylogenetic relationships of cultivated Crataegus native to China. The chloroplast genomes of three cultivated species and one related species of Crataegus were sequenced for comparative and phylogenetic analyses. The four chloroplast genomes of Crataegus exhibited typical quadripartite structures and ranged from 159,607 bp (C. bretschneideri) to 159,875 bp (C. maximowiczii) in length. The plastomes of the four species contained 113 genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Six hypervariable regions (ndhC-trnV(UAC)-trnM(CAU), ndhA, atpH-atpI, ndhF, trnR(UCU)-atpA, and ndhF-rpl32), 196 repeats, and a total of 386 simple sequence repeats were detected as potential variability makers for species identification and population genetic studies. In the phylogenomic analyses, we also compared the entire chloroplast genomes of three published Crataegus species: C. hupehensis (MW201730.1), C. pinnatifida (MN102356.1), and C. marshallii (MK920293.1). Our phylogenetic analyses grouped the seven Crataegus taxa into two main clusters. One cluster included C. bretschneideri, C. maximowiczii, and C. marshallii, whereas the other included C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. Taken together, our findings indicate that C. maximowiczii is the maternal origin of C. bretschneideri. This work provides further evidence of introgression between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major, and suggests that C. pinnatifida var. major might have been artificially selected and domesticated from hybrid populations, rather than evolved from C. pinnatifida.