Search

The subspecies Abrus pulchellus subsp. mollis exhibits pharmacological properties akin to the traditional Chinese medicinal plant Abri Herba (A. pulchellus subsp. cantoniensis (Hance) Verdc.). In this report, we unveil the plastid genome of A. pulchellus subsp. mollis. The genome spans 156,322 base pairs (bp), comprising a large single-copy (LSC) region of 86,633 bp, a small single-copy (SSC) region of 18,219 bp, and two distinct inverted repeat regions (IRs) of 25,735 bp each. Annotation process cataloged a total of 111 genes within this genome, including 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The overall guanine-cytosine (GC) content of the plastome is 35.5%. Phylogenetic analysis utilizing maximum-likelihood (ML) based on 16 complete plastid genomes reveals a close clustering of three Abrus taxa, namely A. pulchellus subsp. mollis, A. pulchellus subsp. cantoniensis, and A. precatorius. Notably, A. pulchellus subsp. cantoniensis clusters with A. precatorius as a sister group, distinct from A. pulchellus subsp. mollis. These findings highlight significant differences between the plastid genomes of the two subspecies, laying the foundation for future research on the identification of medicinal herbs and germplasm resources related to these subspecies. [ABSTRACT FROM AUTHOR]

Background: Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer. Result: Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer. Conclusion: Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution. [ABSTRACT FROM AUTHOR]

Global environmental changes drive biodiversity loss and community compositional change. Yet whether and how both factors simultaneously impact biomass dynamics in natural ecosystems remains elusive, especially considering their multidimensional effects (e.g., taxonomic, functional, and phylogenetic) over spatial scales. To fill this knowledge gap, we generated an experimental spatial gradient using circular quadrats that vary in radius (2–30 m) in a subtropical forest on Dinghushan Mountain, China. Within each quadrat over 10 years, we calculated the changes in aboveground biomass (i.e., net Δbiomass), biodiversity (i.e., Δbiodiversity for richness, Shannon diversity, functional, phylogenetic), and community composition (i.e., β-diversity for taxonomic, functional, phylogenetic). Based on multi-model inference, we determined the most parsimonious relationships of Δbiomass as a function of Δbiodiversity and β-diversity and then quantified their standardized coefficients in response to the spatial gradient. Our results showed that Δbiomass, Δbiodiversity, and β-diversity decreased with quadrat size; the former at an accelerating rate and the latter at decelerating rates. While Δbiomass as a function of Δbiodiversity and β-diversity had low occurrences across the gradient, Δbiomass was strongly related to the change in functional dispersion (i.e., ΔFDis) and taxonomic β-diversity at larger spatial scales. Our results suggest scale-dependent influences of biodiversity loss and community compositional change on biomass dynamics in natural ecosystems. Further, our results highlight that multiple dimensions of biodiversity should be considered when predicting biomass dynamics at large spatial scales. [ABSTRACT FROM AUTHOR]

DNA barcoding is a well‐established tool for rapid species identification and biodiversity monitoring. A reliable and traceable DNA barcode reference library with extensive coverage is necessary but unavailable for many geographical regions. The arid region in northwestern China, a vast area of about 2.5 million km2, is ecologically fragile and often overlooked in biodiversity studies. In particular, DNA barcode data from the arid region in China are lacking. We develop and evaluate the efficacy of an extensive DNA barcode library for native flowering plants in the arid region of northwestern China. Plant specimens were collected, identified and vouchered for this purpose. The database utilized four DNA barcode markers, namely rbcL, matK, ITS and ITS2, for 1816 accessions (representing 890 species from 385 genera and 72 families), and consisted of 5196 barcode sequences. Individual barcodes varied in resolution rates: species‐ and genus‐level rates for rbcL, matK, ITS and ITS2 were 79.9%–51.1%/76.1%, 79.9%–67.2%/88.9%, 85.0%–72.0%/88.2% and 81.0%–67.4%/84.9%, respectively. The three‐barcode combination of rbcL + matK + ITS (RMI) revealed a higher species‐ and genus‐level resolution (75.5%/92.1%, respectively). A total of 110 plastomes were newly generated as super‐barcodes to increase species resolution for seven species‐rich genera, namely Astragalus, Caragana, Lactuca, Lappula, Lepidium, Silene and Zygophyllum. Plastomes revealed higher species resolution compared to standard DNA barcodes and their combination. We suggest future databases include super‐barcodes, especially for species‐rich and complex genera. The plant DNA barcode library in the current study provides a valuable resource for future biological investigations in the arid regions of China. [ABSTRACT FROM AUTHOR]

Background: Lysimachia L., the second largest genus within the subfamily Myrsinoideae of Primulaceae, comprises approximately 250 species worldwide. China is the species diversity center of Lysimachia, containing approximately 150 species. Despite advances in the backbone phylogeny of Lysimachia, species-level relationships remain poorly understood due to limited genomic information. This study analyzed 50 complete plastomes for 46 Lysimachia species. We aimed to identify the plastome structure features and hypervariable loci of Lysimachia. Additionally, the phylogenetic relationships and phylogenetic conflict signals in Lysimachia were examined. Results: These fifty plastomes within Lysimachia had the typical quadripartite structure, with lengths varying from 152,691 to 155,784 bp. Plastome size was positively correlated with IR and intron length. Thirteen highly variable regions in Lysimachia plastomes were identified. Additionally, ndhB, petB and ycf2 were found to be under positive selection. Plastid ML trees and species tree strongly supported that L. maritima as sister to subg. Palladia + subg. Lysimachia (Christinae clade), while the nrDNA ML tree clearly placed L. maritima and subg. Palladia as a sister group. Conclusions: The structures of these plastomes of Lysimachia were generally conserved, but potential plastid markers and signatures of positive selection were detected. These genomic data provided new insights into the interspecific relationships of Lysimachia, including the cytonuclear discordance of the position of L. maritima, which may be the result of ghost introgression in the past. Our findings have established a basis for further exploration of the taxonomy, phylogeny and evolutionary history within Lysimachia. [ABSTRACT FROM AUTHOR]

Lomas formations or "fog oases" are islands of vegetation in the desert belt of the west coast of South America, with a unique vegetation composition among the world's deserts. However, plant diversity and conservation studies have long been neglected, and there exists a severe gap in plant DNA sequence information. To address the lack of DNA information, we conducted field collections and laboratory DNA sequencing to establish a DNA barcode reference library of Lomas plants from Peru. This database provides 1,207 plant specimens and 3,129 DNA barcodes data corresponding with collections from 16 Lomas locations in Peru, during 2017 and 2018. This database will facilitate both rapid species identification and basic studies on plant diversity, thereby enhancing our understanding of Lomas flora's composition and temporal variation, and providing valuable resources for conserving plant diversity and maintaining the stability of the fragile Lomas ecosystems. [ABSTRACT FROM AUTHOR]

Background: Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales. Results: Mitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall. Conclusions: The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found. [ABSTRACT FROM AUTHOR]

Background and Aims Ongoing global warming is a challenge for humankind. A series of drastic climatic changes have been proven to have occurred throughout the Cenozoic based on a variety of geological evidence, which helps to better understand our planet's future climate. Notably, extant biomes have recorded drastic environmental shifts. The climate in southern Asia, which hosts high biodiversity, is deeply impacted by the Asian monsoon. The origins and evolutionary dynamics of biomes occurring between the tropics and sub-tropics in southern Asia have probably been deeply impacted by climatic changes; however, these aspects remain poorly studied. We tested whether the evolutionary dynamics of the above biomes have recorded the drastic, late Cenozoic environmental shifts, by focusing on Magnolia section Michelia of the family Magnoliaceae. Methods We established a fine time-calibrated phylogeny of M. section Michelia based on complete plastid genomes and inferred its ancestral ranges. Finally, we estimated the evolutionary dynamics of this section through time, determining its diversification rate and the dispersal events that occurred between tropical and sub-tropical areas. Key Results The tropical origin of M. section Michelia was dated to the late Oligocene; however, the diversification of its core group (i.e. M. section Michelia subsection Michelia) has occurred mainly from the late Miocene onward. Two key evolutionary shifts (dated approx. 8 and approx. 3 million years ago, respectively) were identified, each of them probably in response to drastic climatic changes. Conclusion Here, we inferred the underlying evolutionary dynamics of biomes in southern Asia, which probably reflect late Cenozoic climatic changes. The occurrence of modern Asian monsoons was probably fundamental for the origin of M. section Michelia ; moreover, the occurrence of asymmetric dispersal events between the tropics and sub-tropics hint at an adaptation strategy of M. section Michelia to global cooling, in agreement with the tropical conservatism hypothesis. [ABSTRACT FROM AUTHOR]

Background: Musaceae is an economically important family consisting of 70-80 species. Elucidation of the interspecific relationships of this family is essential for a more efficient conservation and utilization of genetic resources for banana improvement. However, the scarcity of herbarium specimens and quality molecular markers have limited our understanding of the phylogenetic relationships in wild species of Musaceae. Aiming at improving the phylogenetic resolution of Musaceae, we analyzed a comprehensive set of 49 plastomes for 48 species/subspecies representing all three genera of this family. Results: Musaceae plastomes have a relatively well-conserved genomic size and gene content, with a full length ranging from 166,782 bp to 172,514 bp. Variations in the IR borders were found to show phylogenetic signals to a certain extent in Musa. Codon usage bias analysis showed different preferences for the same codon between species and three genera and a common preference for A/T-ending codons. Among the two genes detected under positive selection (dN/dS > 1), ycf2 was indicated under an intensive positive selection. The divergent hotspot analysis allowed the identification of four regions (ndhF-trnL, ndhF, matK-rps16, and accD) as specific DNA barcodes for Musaceae species. Bayesian and maximum likelihood phylogenetic analyses using full plastome resulted in nearly identical tree topologies with highly supported relationships between species. The monospecies genus Musella is sister to Ensete, and the genus Musa was divided into two large clades, which corresponded well to the basic number of n = x = 11 and n = x =10/9/7, respectively. Four subclades were divided within the genus Musa. A dating analysis covering the whole Zingiberales indicated that the divergence of Musaceae family originated in the Palaeocene (59.19 Ma), and the genus Musa diverged into two clades in the Eocene (50.70 Ma) and then started to diversify from the late Oligocene (29.92 Ma) to the late Miocene. Two lineages (Rhodochlamys and Australimusa) radiated recently in the Pliocene /Pleistocene periods. Conclusions: The plastome sequences performed well in resolving the phylogenetic relationships of Musaceae and generated new insights into its evolution. Plastome sequences provided valuable resources for population genetics and phylogenetics at lower taxon. [ABSTRACT FROM AUTHOR]

Background: The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential plant groups, the tribe Perseeae (Lauraceae). Results: Our plastid tree topologies were robust to analyses based on different plastid regions and different strategies for data partitioning, nucleotide substitution saturation, and gap handling. We found that tribe Perseeae comprised six major clades and began to colonize the subtropical EBLFs of East Asia in the early Miocene. The diversification rates of tribe Perseeae accelerated twice in the late Miocene. Conclusions: Our findings suggest that the intensified precipitation in East Asia in the early Miocene may have facilitated range expansions of the subtropical EBLFs and establishment of tribe Perseeae within this biome. By the late Miocene, species assembly and diversification within the EBLFs had become rapid. [ABSTRACT FROM AUTHOR]

Lysimachia caloneura G. Hao, X.L. Yu & A. Liu sp. nova (Primulaceae) is described and illustrated from Hunan, China. In general morphology it resembles the species in subgen. Lysimachia sect. Nummularia ser. Drymarifoliae, characterized by leaves with black glandular punctuations or striations, yellow corolla, filaments being longer than anthers and basally connate into a short tube, and a dorsifixed anther opening by lateral slits. Lysimachia caloneura is to some extent similar to L. patungensis, but differs from the latter by its tiny size and by having a strikingly dark green abaxial leaf surface and narrow light green bands along the main veins on the adaxial surface. [ABSTRACT FROM AUTHOR]

Molecular studies have shown that Liparis s.l. is polyphyletic, with the epiphytic Liparis alliance well separated from the clade representing Liparis in its restricted sense and further forming a phylogenetically heterogeneous assemblage. The generic status of Cestichis, as the key member of the epiphytic Liparis alliance, remains contentious, and the relationships between Cestichis, Stichorkis and Platystyliparis are still unclear and in need of further studies. We herein employ DNA sequence data from nuclear ITS and plastid matK regions to clarify the generic boundaries of Cestichis and its relationship to the allied genera. Results from both Bayesian inference and maximum likelihood analysis congruently indicate that Cestichis as currently circumscribed is not monophyletic. The Blepharoglossum clade, corresponding to commonly recognized sect. Blepharoglossum, forms a monophyletic lineage closely related to the genus Oberonia instead of the core Cestichis clade. A re-evaluation of the diagnostic morphological characters reveals that this lineage represents a morphologically distinct group. Based on these results, Blepharoglossum is removed from Cestichis and elevated to generic status. Our study also sheds light on the homoplastic nature of some diagnostic morphological characters used traditionally in the taxonomy of the Malaxidinae. [ABSTRACT FROM AUTHOR]

Lysimachia christinae Hance is widely distributed in subtropical China at the elevational range from 500–2300 m. The species is an important medicinal herb for treating jaundice, urinary disorders, and the liver. Here, we sequenced and characterized the whole plastid genome of L. christinae. It is 154,810 bp in length, containing two copies of inverted repeat (IR) regions (26,034 bp, each), a large single-copy (LSC) region (84,809 bp), and a small single-copy (SSC) region (17,933 bp). It has 114 genes, of which 80 are protein-coding, 30 are tRNA, and 4 are rRNA genes. The ML tree indicates L. christinae is closely related to Lysimachia congestiflora Hemsl. This genome information can help us better construct a backbone phylogeny of Lysimachia in the future. [ABSTRACT FROM AUTHOR]

Summary: What causes the disparity in biodiversity among regions is a fundamental question in biogeography, ecology, and evolutionary biology. Evolutionary and biogeographic processes (speciation, extinction, dispersal) directly determine species richness patterns, and can be studied using integrative phylogenetic approaches. However, the strikingly high richness of East Asia relative to other Northern Hemisphere regions remains poorly understood from this perspective. Here, for the first time, we test two general hypotheses (older colonization time, faster diversification rate) to explain this pattern, using the plant tribe Lysimachieae (Primulaceae) as a model system. We generated a new time‐calibrated phylogeny for Lysimachieae (13 genes, 126 species), to estimate colonization times and diversification rates for each region and to test the relative importance of these two factors for explaining regional richness patterns. We find that neither time nor diversification rates alone explain richness patterns among regions in Lysimachieae. Instead, a new index that combines both factors explains global richness patterns in the group and their high East Asian biodiversity. Based on our results from Lysimachieae, we suggest that the high richness of plants in East Asia may be explained by a combination of older colonization times and faster diversification rates in this region. [ABSTRACT FROM AUTHOR]

Lysimachia sinopilosa C.M. Hu & G. Hao sp. nova (Primulaceae) is described from Yunnan, China, and illustrated. In general morphology it resembles the species in Lysimachia subgen. Idiophyton, which are characterized by a yellow corolla, and an anther longer than filament, basifixed and opening by an apical pore. Lysimachia sinopilosa is most similar to L. pilosa, but can be distinguished by its purple indumentum on stems, petioles, peduncles and adaxial surface of leaves, by its leaf blades with a sub-rounded or obtuse base, and by its smaller flowers. [ABSTRACT FROM AUTHOR]

Fortunearia sinensis Rehder & E.H.Wilson, the only species of monotypic genus Fortunearia (Hamamelidaceae), is a native rare and vulnerable deciduous tree in China. In this study, the complete plastid genome of F. sinensis was determined using the Illumina paired-end sequencing data. The complete plastid genome of F. sinensis is 1,59,441 bp in length, consisting of a pair of inverted repeats (IR) regions (26,268 bp), a large-single copy (LSC) region (88,124 bp), and a small-single copy (SSC) region (18,781 bp). The plastid genome encodes 112 unique genes, including 80 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. The phylogenetic analysis demonstrates a close relationship between F. sinensis and Sinowilsonia henryi. [ABSTRACT FROM AUTHOR]

A new species of Primulaceae, Primula persimilis G. Hao, C.M. Hu & Y. Xu, from Sichuan, China, is described and illustrated. In general morphology it is allied to the species of P. sect. Monocarpicae, characterized by the presence of multi-cellular hairs, the distinctly petiolate leaves, a campanulate calyx, and a globose or cylindrical capsule with valvate dehiscence. The new species superficially resembles P. tsiangii W.W. Smith, but can be distinguished by its white flowers, longer calyx lobes, and cylindrical capsules. [ABSTRACT FROM AUTHOR]

* Premise of the study: Microsatellite markers from Primula sikkimensis (Primulaceae) were developed for testing deep lineage divergence and speciation events. * Methods and Results: A total of 3112 microsatellites were identified from 61,755 unique reads though 454 pyrosequencing technology. Twenty-nine microsatellite loci were selected for PCR amplification and polymorphic analyses. Among the 29 tested markers, 17 microsatellite loci were further used for genotyping in three wild P. sikkimensis populations. The number of alleles varied from one to eight, and the observed heterozygosity ranged from 0.111 to 1.000. Ten simple sequence repeat loci could be successfully cross-amplified in two Primula species. The transferability values were 76.5% in P. florindae and 58.8% in P. alpicola, respectively. * Conclusions: These microsatellite markers will be valuable for testing the hypothesis of lineage divergence, genetic introgression, and cryptic speciation events between P. sikkimensis and its closely related taxa. [ABSTRACT FROM AUTHOR]

DNA barcoding of plants poses particular challenges, especially in differentiating, recently diverged taxa. The genus Gentiana (Gentianaceae) is a species-rich plant group which rapidly radiated in the Himalaya-Hengduan Mountains in China. In this study, we tested the core plant barcode (rbcL + matK) and three promising complementary barcodes (trnH-psbA, ITS and ITS2) in 30 Gentiana species across 6 sections using three methods (the genetic distance-based method, Best Close Match and tree-based method). rbcL had the highest PCR efficiency and sequencing success (100%), while the lowest sequence recoverability was from ITS (68.35%). The presence of indels and inversions in trnH-psbA in Gentiana led to difficulties in sequence alignment. When using a single region for analysis, ITS exhibited the highest discriminatory power (60%-74.42%). Of the combinations, matK + ITS provided the highest discrimination success (71.43%-88.24%) and is recommended as the DNA barcode for the genus Gentiana. DNA barcoding proved effective in assigning most species to sections, though it performed poorly in some closely related species in sect. Cruciata because of hybridization events. Our analysis suggests that the status of G. pseudosquarrosa needs to be studied further. The utility of DNA barcoding was also verified in authenticating ‘Qin-Jiao’ Gentiana medicinal plants (G. macrophylla, G. crassicaulis, G. straminea, and G. dahurica), which can help ensure safe and correct usage of these well-known Chinese traditional medicinal herbs. [ABSTRACT FROM AUTHOR]

An investigation of a questionable orchid led to the discovery of a new genus and species Thuniopsis cleistogama, endemic to Yunnan province, China. It is characterized by having a subglobose corm, a spike-like (racemose) inflorescence, half opened and spurless flowers, a collar-shaped stigma and subglobose capsules. Based on DNA sequence data from three gene regions (nuclear ribosomal ITS, chloroplast matK and trnL), we investigated its phylogenetic position within the tribe Arethuseae. Phylogenies using maximum likelihood and Bayesian inference support the recognition of Thuniopsis as a distinct genus, and suggest its close relationship to the genera Bletilla, Dilochia, and Thunia. The new genus is circumscribed and a description and illustrations of the new species are provided. The phylogenetic relationships among the genera in Arethuseae are accessed. Moreover, our phylogeny also shed light on the phylogenetic positions of several genera which, to date, remain uncertain. [ABSTRACT FROM AUTHOR]

A new species, Lysimachia huangsangensis (Primulaceae), from Hunan, China is described and illustrated. The new species is closely related to L. carinata because of the crested calyx, but differs in the leaf blades that are ovate to elliptic and (3–)4.5–9 × 2–3.4 cm, 2–5-flowered racemes, and the calyx lobes that are ovate-lanceolate and 5–6 × 3–4 mm. The systematic placement and conservation status are also discussed. [ABSTRACT FROM AUTHOR]

The genus Primula is extremely diverse in the east Himalaya-Hengduan Mountains (HHM) in China as a result of rapid radiation. In order to overcome the difficulty of morphological classification of this genus, we surveyed three plastid regions (rbcL, matK, and trnH-psbA) and two nuclear markers (ITS and ITS2) from 227 accessions representing 66 Primula species across 18 sections, to assess their discriminatory power as barcodes. We found that ITS alone or combined with plastid regions showed the best discrimination across different infrageneric ranks and at species level. We suggest rbcL + matK + ITS as the first choice at present to barcode Primula plants. Although the present barcoding combination performed poorly in many closely related species of Primula, it still provided many new insights into current Primula taxonomy, such as the underlying presence of cryptic species, and several potential improper taxonomic treatments. DNA barcoding is one useful technique in the integrative taxonomy of the genus Primula, but it still requires further efforts to improve its effectiveness in some taxonomically challenging groups. [ABSTRACT FROM AUTHOR]

Aim Rapid and accurate species identification is the foundation for biodiversity assessment. DNA barcoding has been shown to be an effective tool to overcome the taxonomic impediment to facilitate biodiversity conservation in temperate forests. However, this tool has rarely been considered for use in tropical forests. This study aims to investigate the utility and species resolution of DNA barcoding in a subtropical region. Location The Dinghushan National Nature Reserve ( DNNR) in China. Methods A DNA barcoding database was constructed for 531 trees present in the DNNR. We used a phylogenetic method (neighbour-joining trees) and sequence similarity (all-to-all BLASTn searches) to evaluate the utility and species resolution of five DNA barcode regions ( rbcL, matK, ITS, ITS2 and trnH-psbA), both singly and in combinations of two or three region. Results The combination of rbcL + matK + ITS had the highest species resolution (94.19%). However, when considering the difficulty of sequence recoverability, rbcL + ITS2 performed best (64.64%). Species resolution for large genera containing more than two species was substantially lower than that for small genera with one and two species per genus. Local small spatial scales (1-ha quadrats) resulted in moderately improved species resolution (70.82% for rbcL + ITS2) compared to larger spatial scales (20 and 1133 ha). We document incongruent signals between nuclear and cp DNA regions and the challenges associated with barcoding large genera inherent to subtropical floras. Main conclusions This study considerably expands the global DNA barcode database for subtropical trees. Based on cost-effectiveness and the trade-off between sequence recovery and species resolution, we suggest that the rbcL + ITS2 barcode combination is an effective tool for documenting plant diversity in the DNNR. This study also sheds some light on the limitations and challenges for the application of barcoding to conservation biogeography in subtropical forests. [ABSTRACT FROM AUTHOR]

Lithocarpus hancei (Benth.) Rehd is a widely distributed evergreen tree with broad-leaves that dominates the lower stories of the forest in China. Here, we sequenced and assembled the complete chloroplast genome of L. hancei. The genome is 161,304 bp with one large single copy (LSC: 90,585 bp), one small single copy (SSC: 18,959 bp), and two inverted repeat (IR) regions (IRa and IRb, each 25,880 bp). It contains 117 genes, including 80 protein-coding genes, 33 tRNA genes, and four rRNA genes. Phylogenetic analysis of 21 representative cp genomes of the Fagaceae suggests Lithocarpus is monophyletic with strong bootstrap support and also that L. hancei is closely related to L. polystachyus. The cp genome is important for constructing a robust phylogeny of Lithocarpus and Fagaceae for future study. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome (plastome) of Primula chrysochlora is a circular molecule of 151,944 bp and contains a pair of inverted repeats of 25,460 bp which is separated by a large single copy region of 83,953 bp and a small single copy region of 17,801 bp. The plastome encodes 131 genes, including 86 protein-coding genes (PCGs), 37 tRNA genes and eight ribosomal RNA genes. Of these, seven PCGs, seven tRNA genes and four rRNA genes are duplicated in inverted repeats region and 18 genes harbor one or two introns. Based on the SSR analysis, a total of 36 microsatellites with a length of at least 10 bp were detected in the P. chrysochlora genome. A phylogenetic analysis showed that section Proliferae is a monophyletic with high support, and P. chrysochlora is sister to P. poissonii. [ABSTRACT FROM AUTHOR]

Using an Illumina platform, we sequenced the complete chloroplast genome of Primula persimilis. The total length of the plastome is 152,756 bp, and the overall AT content is 62.8%. A pair of 25,753 bp inverted repeats (IRs) is separated by large and small single copy regions (LSC and SSC) of 83,537 bp and 17,713 bp, respectively, and the AT contents of the LSC, SSC and IR are 64.8%, 69.4% and 57.2%, respectively. The plastome encodes 130 genes, including 85 protein-coding genes (PCGs), 37 tRNA genes and eight ribosomal RNA genes. Of these, seven PCGs, seven tRNA genes and four rRNA genes are duplicated in inverted repeats, and 18 genes harbor one or two introns. The phylogenetic analysis suggested that the Primula species formed a monophyletic clade, and P. persimilis is closely related to P. kwangtungensis. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome (plastome) of Primula kwangtungensis was characterized through Illumina paired-end sequencing. The plastome is circular and 153,757 bp in length, comprising a pair of 25,855 bp inverted repeat regions (IRs) which are separated by a large single copy region (LSC) of 84,479 bp and a small single copy region (SSC) of 17,568 bp. The plastome contains 130 genes, including 85 protein-coding genes (PCGs), 37 tRNA genes and eight ribosomal RNA genes. Of these, seven PCGs, seven tRNA genes and four rRNA genes occur in double copies. The overall AT content of the P. kwangtungensis plastome is 62.9 %, while the corresponding values of the LSC, SSC and IR regions are 65, 69.6 and 57.3 %, respectively. The phylogenetic analysis suggested that the sampled Primula species formed a monophyletic clade, and P. kwangtungensis is closely related to P. sinensis. [ABSTRACT FROM AUTHOR]

The whole chloroplast genome (cp genome) of Primula stenodonta was sequenced using an Illumina platform. The cp genome is 150,785 bp in size, and exhibits a typical bicyclic and quadripartite structure, including a pair of inverted repeat regions (IRs) of 25,182 bp that are separated by large and small single copy regions of 82,682 and 17,739 bp, respectively. A total of 131 genes were identified, including 86 protein-coding genes (PCG), 37 tRNA genes, and eight ribosomal RNA (rRNA) genes. Among them, 18 genes occur in IRs, containing seven PCG, seven tRNA genes and four rRNA genes. The overall AT content of P. stenodonta cp genome is 62.9%, and the corresponding values of the LSC, SSC and IR regions are 65, 69.8 and 57%, respectively. The phylogenetic analysis suggested that the sampled Primula species formed a monophyletic clade, and P. stenodonta is closely related to Primula poissonii. [ABSTRACT FROM AUTHOR]

Ania Lindl. is a small genus of the tribe Collabieae subtribe Collabiinae (Orchidaceae). For the last 150 years, it has generally been treated as a synonym of Tainia Blume. In this study, we critically re-examined morphological characters that have been used to distinguish Ania from Tainia, and assessed the phylogeny of Tainia using morphological and palynological characters. Sequences of the nuclear ribosomal ITS, chloroplast trnL intron and combined DNA data sets were analysed to clarify the delimitation and the phylogeny of these groups. The morphological and palynological survey revealed a number of useful diagnostic characters which permit a clear definition of Ania, after the exclusion of a single taxonomically questionable species. Results confirmed that Ania is distinct from Tainia. Phylogenetic reconstructions based on molecular data provided the greatest resolution and produced a morphologically well differentiated clade of Ania. In addition to morphological and suggested palynological characters, the phylogenies were also supported by karyological evidence. Our results support the independent generic status of Ania. The genus name Ania is revived and re-established. [ABSTRACT FROM AUTHOR]

Aim Our goals were: (1) to assess the population genetic structure and demographic divergence history of a bird-dispersed tree, Neolitsea sericea, endemic to East Asian land-bridge islands; and (2) to interpret the results in the light of controversies over the dating and configurations of land bridges through the Japanese Ryukyu Island Arc. Location Japan-Ryukyu-Taiwan Island Arc and Chinese/Korean offshore islands. Methods We applied 10 nuclear microsatellites (nSSRs) and one chloroplast (cp) DNA sequence marker ( psbA- trnH intergenic spacer) to 31 populations (397 and 326 individuals, respectively) from throughout the species' range to infer current patterns of genetic diversity and structure, and pollen-to-seed migration ratios ( r). A coalescent-based isolation-with-migration (IM) model was applied to the combined nSSR/cpDNA data set to estimate lineage divergence times and population demographic parameters. Results The geographic structure of nSSRs and the distribution of most cpDNA haplotypes revealed two distinct lineages located in areas north and south of the 'Tokara Gap', a narrow ( c. 37 km wide) but deep (> 1000 m) sea-strait between the northern and central Ryukyus. Based on the IM analyses, we (1) dated the divergence of these northern and southern lineages to c. 0.07 Ma (90% highest posterior density interval: 0.02-0.38 Ma); (2) estimated a slightly smaller effective population size for the northern compared to the southern lineage; and (3) recovered only trivial signals of post-divergence gene flow between them. Main conclusions The estimated divergence time for northern and southern lineages is consistent with geological evidence for the existence of land connections in the Tokara region during cold stages of the latest Pleistocene; it is thus incompatible with an 'ancient sea-barrier hypothesis' for the Ryukyu Arc, where we would have expected much older divergences related to the initial formation of the Tokara and Kerama tectonic straits during the Pliocene. Multiple factors are likely to have had a role in the divergence of N. sericea, including not only land-bridge submergence, but also island configuration, and/or constraints on adaptation along a latitudinal temperature gradient. [ABSTRACT FROM AUTHOR]

The phylogeography of common and widespread species can help us to understand the history of local flora and vegetation. Here, we study the semi-evergreen shrub Rhododendron simsii Planch., which is found in most areas of current evergreen broad leaved forest in China. Two noncoding chloroplast DNA (cpDNA) regions ( rpl20-rps12 and trnL-F) and three amplified fragment length polymorphism (AFLP) primer sets (E-AAC/M-CTA, E-AGC/M-CTA and E-AGG/M-CAT) were used to examine the phylogeographic pattern in relation to past (last glacial maximum) and present distributions based on ecological niche modeling. The cpDNA data revealed four phylogeographic groups (East, South, West, and North groups) corresponding to geographic regions. Molecular dating suggests that lineage diversification within species likely occurred during the mid-to-late Pleistocene. In contrast, the four main cpDNA phylogeographic groups were not supported by the AFLP dataset. The highest likelihood of the AFLP data was obtained when samples were clustered into three groups ( K= 3). However, these groupings did not correspond to separate geographic regions supported by cpDNA data. Both mismatch distribution analysis and environmental niche modeling (ENM) indicated that multiple glacial refugia were maintained across the range of Rhododendron simsii during the last glacial maximum, contrary to the previous hypothesis that subtropical broad leaved evergreen forests were forced to retreat southward as far as 25° N. The discordance between the patterns revealed by cpDNA and AFLP data indicate that localized postglacial range expansions may facilitate extensive gene flow between the major glacial refugia. [ABSTRACT FROM AUTHOR]

To investigate the mechanisms responsible for the high diversity in central and adjacent southwestern China, we inferred the phylogeographic history of Primula ovalifolia from chloroplast DNA data. One hundred and thirty five individuals from 13 natural populations (including one Primula tardiflora population) were analyzed. A total of 23 haplotypes were identified. Most of them were exclusive to a single population. Strong phylogeography structure was detected, with NST (0.936) significantly higher than GST (0.784). Phylogenetic analysis showed that all haplotypes were clustered into three lineages (clades I, II, and III). High genetic diversity was revealed, possibly due to the interglacial contraction and glacial expansion. The three identified lineages may have undergone different historical processes after the mid-Pleistocene, due to their early divergent time. Multiple refugia were inferred for the three lineages. Pleistocene climatic oscillations, combined with the complex local topography, were responsible for the strong phylogeographic pattern of P. ovalifolia. Our analysis supports the hypothesis that the central and adjacent southwestern region of China was an important refugium for the survival, persistence, and further speciation of most East Asia flora, which has led to high species diversity in this region. [ABSTRACT FROM AUTHOR]

It has been suggested that rbcL and matK are the core barcodes in plants, but they are not powerful enough to distinguish between closely related plant groups. Additional barcodes need to be evaluated to improve the level of discrimination between plant species. Because of their well-studied taxonomy and extreme diversity, we used Chinese Lysimachia (Myrsinaceae) species to test the performance of core barcodes ( rbcL and matK) and two additional candidate barcodes ( trnH- psbA and the nuclear ribosomal ITS); 97 accessions from four subgenus representing 34 putative Lysimachia species were included in this study. And many closely related species pairs in subgen. Lysimachia were covered to detect their discriminatory power. The inefficiency of rbcL and matK alone or combined in closely related plant groups was validated in this study. TrnH- psbA combined with rbcL + matK did not yet perform well in Lysimachia groups. In contrast, ITS, alone or combined with rbcL and/or matK, revealed high resolving ability in Lysimachia. We support ITS as a supplementary barcode on the basis of core barcode rbcL and matK. Besides, this study also illustrates several mistakes or underlying evolutionary events in Lysimachia detected by DNA barcoding. [ABSTRACT FROM AUTHOR]

Magnolia omeiensis (W. C. Cheng) Dandy, belonging to Magnolia sect. Gynopodium Dandy (Magnoliaceae), is a critically endangered species. In this study, we assembled the complete plastid genome sequence of M. omeiensis. The plastid genome was 160,091 bp in length, consisting of a large single-copy (LSC) region of 88,160 bp, a small single-copy (SSC) region of 18,763 bp, and two inverted repeat (IR) regions of 26,584 bp. It contained 112 unique genes, including 80 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. Overall GC content was 39.3%. Phylogenetic analysis showed that M. omeiensis was closely related to Magnolia Yunnanensis, which was identified in the same section Gynopodium. [ABSTRACT FROM AUTHOR]

Rhizophora stylosa is a true mangrove distributed in the Indo-Pacific region. In this study, the whole chloroplast genome of R. stylosa was assembled and annotated. The chloroplast genome was 164,475 bp in length, consisting of a large single copy (LSC) region of 92,582 bp, a small single copy (SSC) region of 19,243 bp, and two inverted repeat (IR) regions of 26,325 bp. It contained 131 genes, including 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The overall GC content was 34.9%. Phylogenetic analysis showed that R. stylosa was sister to Erythroxylum novogranatense. [ABSTRACT FROM AUTHOR]

Sonneratia apetala is a true mangrove distributed in South Asia, Southeast Asia and China. Here the whole chloroplast genome of S. apetala was assembled. The chloroplast genome was 153,052 bp in length, consisting of a large single copy (LSC) region of 87,210 bp, a small single copy (SSC) region of 18,026 bp, and two inverted repeat (IR) regions of 23,908 bp. It contained 131 genes, including 86 protein-coding genes, 37 tRNA genes and eight rRNA genes. The overall GC content was 37.3%. Phylogenetic analysis showed that S. apetala was sister to Trapa maximowiczii in Lythraceae. [ABSTRACT FROM AUTHOR]

A new species of Lysimachia (Primulaceae), L. huchimingii G. Hao & H. F. Yan from China is described and illustrated. It is morphologically compared to its most closely related species in Lysimachia subgen. Lysimachia sect. Nummularia ser. Paridiformes. [ABSTRACT FROM AUTHOR]

Pogostemon Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of Pogostemon, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Pogostemon plectranthoides Desf., P. septentrionalis C. Y. Wu et Y. C. Huang, and two cultivars of P. cablin (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of P. yatabeanus (Makino) Press and P. stellatus (Lour.) Kuntze) suggested that Pogostemon cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (Pi) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and Pogostemon. For the overall mean substitution rates, the synonymous (dS) and nonsynonymous (dN) substitution rate values of protein-coding genes varied approximately threefold, while the dN values among different functional gene groups showed a wider variation range. Overall, the cp genomes of Pogostemon will be useful for phylogenetic reconstruction, species delimitation and identification in the future. [ABSTRACT FROM AUTHOR]