Evaluation of reference genes and expression patterns of CONSTANS-LIKE genes in Tetrastigma hemsleyanum under different photoperiods.

CONSTANS-LIKE (COL ) genes are a key signalling molecule that regulates plant growth and development during the photoperiod. Our preliminary experiments showed that the photoperiod greatly influence the formation of Tetrastigma hemsleyanum root tubers. In this study, we examined the oscillation patterns and expression characteristics of COL genes in leaves of T. hemsleyanum under different photoperiod conditions. Six genes were selected as candidate reference genes for further analyses: (1) 18S ribosomal RNA (18S rRNA ); (2) α-tubulin (TUBA ); (3) 30S ribosomal RNA (30S rRNA ); (4) TATA binding protein (TBP ); (5) elongation factor 1α (EF-1α ); and (6) RNA polymerase II (RPII ). The geNorm, NormFinder, and BestKeeper software programs were used to evaluate expression stability. Two ThCOL genes were screened in the T. hemsleyanum transcriptome library, and their expression patterns under different photoperiod conditions were analysed using quantitative reverse transcription PCR. The genes EF-1α , TUBA , and 18S rRNA were used to analyse the expression profiles of CONSTANS genes (ThCOL4 and ThCOL5 ) under different photoperiods. The expression peaks of ThCOL4 and ThCOL5 appeared at different times, demonstrating that their oscillation patterns were influenced by the photoperiod. We speculate that these two ThCOL genes may be involved in different biological processes.

Revealing quality chemicals of Tetrastigma hemsleyanum roots in different geographical origins using untargeted metabolomics and random-forest based spectrum-effect analysis.

Tetrastigma hemsleyanum root is a popular functional food in China, and the price varies based on the origin of the product. The link between the origin, metabolic profile, and bioactivity of T. hemsleyanum must be investigated. This study compares the metabolic profiles of 254 samples collected from eight different areas with 49 potential key chemical markers using plant metabolomics. The metabolic pathways of the five critical flavonoid metabolites were annotated and enriched using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Moreover, a random forest model aiding the spectrum-effect relationship analysis was developed for the first time indicating catechin and darendoside B as potential quality markers of antioxidant activity. The findings of this study provide a comprehensive understanding of the chemical composition and bioactive compounds of T. hemsleyanum as well as valuable information on the evaluation of the quality of various samples and products in the market.

Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis.

A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies.

Chromosome-level reference genome of Tetrastigma hemsleyanum (Vitaceae) provides insights into genomic evolution and the biosynthesis of phenylpropanoids and flavonoids.

Here, we present a high-quality chromosome-scale genome assembly (2.19 Gb) and annotation of Tetrastigma hemsleyanum, a perennial herbaceous liana native to subtropical China with diverse medicinal applications. Approximately 73% of the genome was comprised of transposable elements (TEs), of which long terminal repeat retrotransposons (LTR-RTs) were a predominant group (69% of the genome). The genome size increase of T. hemsleyanum (relative to Vitis species) was mostly due to the proliferation of LTR-RTs. Of the different modes of gene duplication identified, transposed duplication (TRD) and dispersed duplication (DSD) were the predominant ones. Genes, particularly those involved in the phenylpropanoid-flavonoid (PF) pathway and those associated with therapeutic properties and environmental stress resistance, were significantly amplified through recent tandem duplications. We dated the divergence of two intraspecific lineages in Southwest (SW) versus Central-South-East (CSE) China to the late Miocene (approximately 5.2 million years ago). Of those, the former showed more upregulated genes and metabolites. Based on resequencing data of 38 individuals representing both lineages, we identified various candidate genes related to 'response to stimulus' and 'biosynthetic process', including ThFLS11, which is putatively involved in flavonoid accumulation. Overall, this study provides abundant genomic resources for future evolutionary, ecological, and functional genomics studies in T. hemsleyanum and related species.

Multi-omics analyses revealed key factors involved in fluorescent carbon-dots-regulated secondary metabolism in Tetrastigma hemsleyanum.

BACKGROUND: Luminescent nanomaterials (LNMs), especially newly-exploited fluorescent carbon-dots (CDs), have demonstrated promising candidates for sunlight harvesting and enhanced photosynthesis efficiency of crops. However, most of the studies focus on the design and synthesis of LNMs and primary metabolism in biomass acceleration, secondary metabolism that closely associated with the quality ingredients of plants is rarely mentioned. RESULTS: UV-absorptive and water-soluble NIR-CDs were harvested via a facile microwave-assisted carbonization method. The effect and regulatory mechanism of NIR-CDs on the secondary metabolism and bioactive ingredients accumulation in Tetrastigma hemsleyanum were explored. A total of 191 differential secondary metabolites and 6874 differentially expressed genes were identified when the NIR-CDs were adopted for enhancing growth of T. hemsleyanum. The phenolic acids were generally improved, but the flavonoids were more likely to decrease. The pivotal differentially expressed genes were involved in biosynthesis of secondary metabolites, flavonoid biosynthesis, porphyrin and chlorophyll metabolism, etc. The gene-metabolite association was constructed and 44 hub genes highly related to quality ingredients accumulation and growth were identified, among which and the top 5 genes of the PPI network might be the key regulators. CONCLUSION: This research provided key regulatory genes and differentially accumulating quality ingredients under NIR-CDs-treatment, which could provide a theoretical basis for expanding the applications of nanomaterial in industrial crop agriculture.

Historical biogeography of Tetrastigma (Vitaceae): Insights into floristic exchange patterns between Asia and Australia.

Biodiversity exchanges across the Malesian region, linking the distinct biotas of Asia and Australia, have long attracted the curiosity of biologists. Tetrastigma (Vitaceae) has a wide distribution in Asia through the Sunda archipelago to Australia and provides a good case to elucidate floristic exchange between Asia and Australia. Tetrastigma species have fleshy fruits that are consumed by birds, representing a lineage with a predictable dispersal across island chains. We herein estimate the divergence times and reconstruct the biogeographic history of Tetrastigma with intensive taxon sampling (96 of approximately 120 species; >80%) using 10 chloroplast loci. The biogeographic history of Tetrastigma was reconstructed with 4-area and 6-area divisions by delineating the Sunda region into one or three areas of endemism based on a phylogenetic bioregionalization analysis and the geological history of Malesia. The 4-area division shows that Tetrastigma originated in continental Asia and diverged from the recently segregated genus Pseudocayratia in the early Eocene (49.43 Ma). Dispersal from continental Asia might have started in the late Eocene but mainly occurred in the last 10 Myr. Continental Asia is indicated to be the most important source area while Sunda is the biggest sink, with 16 of the 27 dispersal events inferred from continental Asia to Sunda. Only seven dispersal events are inferred arriving in the Sahul plate and one reverse dispersal from Sahul back to Asia. The 6-area division suggests that the Philippines have been an active junction between Asia and Australia. The biogeographic history of Tetrastigma illustrates an asymmetric floristic exchange between Asia and Australia in this genus, which has been facilitated by the formation of terrestrial connections in the late Miocene and the expansion of wet tropical forests across Wallace's Line and beyond.

Molecular cloning and structural analysis of key enzymes in Tetrastigma hemsleyanum for resveratrol biosynthesis.

Resveratrol (RES), a plant antitoxin, has antioxidant, anti-inflammatory, anti-cancer and cardiovascular protection effects. It has been reported that RES can be stably detected in a Chinese herbal medicinal plant Tetrastigma hemsleyanum. At present, the research of T. hemsleyanum mainly focused on the discovery of new compounds and pharmacology. However, there were few studies on the molecular mechanism of the synthesis of secondary metabolites in T. hemsleyanum. In this experiment, four key enzymes (ThPAL/ThC4H/Th4CL/ThRS) involved in the RES biosynthesis pathway were cloned and obtained. They contained an open reading frame (ORF) of 2139 bp, 1518 bp, 1716 bp and 1035 bp, encoding 712, 505, 571 and 344 amino acids, separately. Various bioinformatics tools were used to analyze these deduced protein domains, secondary structures, three-dimensional (3D) structures and phylogenetic trees. Subsequently, quantitative primers were designed to conduct the tissue-specific expression. Quantitative results displayed that the four genes were expressed in all tested tissues, and their expression in root tubers was more stable. Moreover, the subcellular localization of the four genes was studied by constructed recombinant green fluorescent expression vectors. Herein, by digging out the key enzyme genes in the biosynthesis of RES in T. hemsleyanum, this experiment tried to reveal the expression patterns of these key enzyme genes. It also provided the basis for the research on the molecular level, which will help people further illuminate and clarify the biosynthesis and regulation mechanism of secondary metabolites in T. hemsleyanum.

Digital RNA-seq transcriptome plus tissue anatomy analyses reveal the developmental mechanism of the calabash-shaped root in Tetrastigma hemsleyanum.

Tetrastigma hemsleyanum Diels & Gilg ex Diels is a liana plant with promising medicinal and ornamental values. Its calabash-shaped roots (CRs) are served as a traditional Chinese herb. However, it takes a long growth period to form CRs. In this study, three types of architectural roots, including fibrous roots (FRs), bar-shaped roots (BRs) and CRs, were employed as materials, and the characteristics of histo-anatomy and digital RNA-seq transcriptome profiles were analyzed. Among the three types of roots, the vascular bundles in FRs were intact, while some of the vascular bundles degenerated in BRs, and only few traces of vascular bundles existed in CRs. Meanwhile, no obvious cell inclusions were found in the cytoplasm of FRs, while a few inclusions were found in BRs, and abundant inclusions were detected in CRs, which might be the main source of medicinal components in roots. The transcriptome profiles and qRT-PCR validation indicated that seven upregulated genes, encoding xyloglucan glycosyltransferase, ACC oxidase, CYP711A1, SHORT-ROOT transcript factor, galacturonosyltransferas, WAT1 and WRKY, and two downregulated genes, encoding LRR receptor-like serine/threonine-protein kinase and CYP83B1, were probably involved in the formation and development of CRs. In addition, Gene Ontology terms of intrinsic component of membrane, integral component of membrane, cell periphery, membrane part, plasma membrane, membrane, intrinsic component of plasma membrane, cellular chemical homeostasis and plasma membrane part were probably related to the formation of CRs. Kyoto Encyclopedia of Genes and Genomes pathways related to the development of CRs probably included MAPK signaling pathway-plant, plant hormone signal transduction and circadian rhythm-plant. Our finding suggested a probable mode for the formation of CRs.

The research progresses and future prospects of Tetrastigma hemsleyanum Diels et Gilg: A valuable Chinese herbal medicine.

ETHNOPHARMACOLOGICAL RELEVANCE: Tetrastigma hemsleyanum Diels et Gilg, known as Sanyeqing in China, was an extensively used folk Chinese herbal medicine. This plant had been validated to be highly effective for treating high fever, pneumonia, hepatitis, gastritis, cervicitis, lymphatic tuberculosis, septicemia, and viral meningitis. AIM OF THE REVIEW: As a review in T. hemsleyanum, this article aims to provide a critical and comprehensive evaluation for future research as well as the development of new drugs. The possible uses and future research directions of this plant were also discussed. MATERIALS AND METHODS: A literature search was conducted on different scientific search engines, including Google Scholar, Science Direct, PubMed, Web of Science, and CNKI. Additional information was obtained from classic books about Chinese herbal medicine and scientific databases. RESULTS: T. hemsleyanum was a perennial herb climbing vine, which was mainly based on field cultivation. About 150 chemical compounds have been isolated from T. hemsleyanum, including flavonoids, phenolic acids, polysaccharides, triterpenoids, steroids, and organic acids. Studies on the physiological aspects of T. hemsleyanum have been focused on the effects of light and fertilizer on their growth, and few other studies have been conducted. The plant had widespread pharmacological effects on the immune system, as well as anti-tumor, anti-inflammatory, analgesic, and antipyretic. CONCLUSIONS: T. hemsleyanum was a valuable traditional Chinese medical herb with pharmacological activities that mainly affected the immune system. This review summarized its botanical description, cultivation techniques, physiology, ethnopharmacology, chemical components, and pharmacological functions. This information suggested that we should focus on the development of new drugs related to T. hemsleyanum. Meanwhile, it was important to emphasize the traditional use of T. hemsleyanum, avoiding over-harvesting that exerted a great impact on resource scarcity. And developing its new clinical usage and comprehensive utilize would augment the therapeutic potentials of T. hemsleyanum.

Phylogenomic relationships and character evolution of the grape family (Vitaceae).

The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.

Integrated analysis of the transcriptome and metabolome of purple and green leaves of Tetrastigma hemsleyanum reveals gene expression patterns involved in anthocyanin biosynthesis.

To gain better insight into the regulatory networks of anthocyanin biosynthesis, an integrated analysis of the metabolome and transcriptome in purple and green leaves of Tetrastigma hemsleyanum was conducted. Transcript and metabolite profiles were archived by RNA-sequencing data analysis and LC-ESI-MS/MS, respectively. There were 209 metabolites and 4211 transcripts that were differentially expressed between purple and green leaves. Correlation tests of anthocyanin contents and transcriptional changes showed 141 significant correlations (Pearson correlation coefficient >0.8) between 16 compounds and 14 transcripts involved in the anthocyanin biosynthesis pathway. Some novel genes and metabolites were discovered as potential candidate targets for the improvement of anthocyanin content and superior cultivars.

Transcriptome profiling reveals candidate flavonol-related genes of Tetrastigma hemsleyanum under cold stress.

BACKGROUND: Tetrastigma hemsleyanum Diels et Gilg is a valuable medicinal herb, whose main bioactive constituents are flavonoids. Chilling sensitivity is the dominant environmental factor limiting growth and development of the plants. But the mechanisms of cold sensitivity in this plant are still unclear. Also, not enough information on genes involved in flavonoid biosynthesis in T. hemsleyanum is available to understand the mechanisms of its physiological and pharmaceutical effects. RESULTS: The electrolyte leakage, POD activity, soluble protein, and MDA content showed a linear sustained increase under cold stress. The critical period of cold damage in T. hemsleyanum was from 12 h to 48 h. Expression profiles revealed 18,104 differentially expressed genes (DEGs) among these critical time points. Most of the cold regulated DEGs were early-response genes. A total of 114 unigenes were assigned to the flavonoid biosynthetic pathway. Fourteen genes most likely to encode flavonoid biosynthetic enzymes were identified. Flavonols of T. hemsleyanum might play a crucial role in combating cold stress. Genes encoding PAL, 4CL, CHS, ANR, FLS, and LAR were significantly up-regulated by cold stress, which could result in a significant increase in crucial flavonols (catechin, epicatechin, rutin, and quercetin) in T. hemsleyanum. CONCLUSIONS: Overall, our results show that the expression of genes related to flavonol biosynthesis as well as flavonol content increased in T. hemsleyanum under cold stress. These findings provide valuable information regarding the transcriptome changes in response to cold stress and give a clue for identifying candidate genes as promising targets that could be used for improving cold tolerance via molecular breeding. The study also provides candidate genes involved in flavonoid biosynthesis and may be useful for clarifying the biosynthetic pathway of flavonoids in T. hemsleyanum.

Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum.

BACKGROUND: Tetrastigma hemsleyanum is of great medicinal importance and used as a model system to address the evolutionary history of warm-temperate evergreen (WTE) forest biomes in East Asia over Neogene time scales. However, further studies on the neutral and adaptive divergence processes of T. hemsleyanum are currently impeded by a lack of genomic resources. In this study, we de novo assembled and annotated a reference transcriptome for two cpDNA lineages (Central-South-East vs. Southwest) of T. hemsleyanum. We further used comparative genomic and multilocus coalescent approaches to investigate the tempo and mode of lineage diversification in T. hemsleyanum. RESULTS: A total of 52,838 and 65,197 unigenes with an N50 of 1,667 and 1,841 bp for Central-South-East (CSE) and Southwest (SW) lineages, respectively, were recovered, and 6,692 putative orthologs were identified between the two lineages. Estimation of Ka/Ks ratios for these orthologs revealed that ten genes had Ka/Ks values significantly greater than 0.5 (P < 0.05), whereas 2,099 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. Based on three bioinformatic strategies, we identified a total of 1,018 single-copy nuclear genes (SCNGs) from the orthologs. We successfully designed eight nuclear gene primer pairs with high intraspecific variation (e.g. hT = 0.923, πT = 1.68×10-3), when surveyed across a subset of T. hemsleyanum individuals. Concordant with the previous cpDNA data, the haplotype networks constructed for most nuclear gene loci clearly identified the two lineages. A multilocus coalescence analysis suggested that the separation between the two lineages appears to have occurred during the mid-Pliocene. Despite their ancient divergence, both lineages experienced expansion at rather localized scales and have continued to exchange genes at a low rate. CONCLUSIONS: This study demonstrated the utility of transcriptome sequencing as a basis for SCNG development in non-model species and the advantages of integrating multiple nuclear loci for phylogeographic and phylogenetic studies.

Left-right leaf asymmetry in decussate and distichous phyllotactic systems.

Leaves in plants with spiral phyllotaxy exhibit directional asymmetries, such that all the leaves originating from a meristem of a particular chirality are similarly asymmetric relative to each other. Models of auxin flux capable of recapitulating spiral phyllotaxis predict handed auxin asymmetries in initiating leaf primordia with empirically verifiable effects on superficially bilaterally symmetric leaves. Here, we extend a similar analysis of leaf asymmetry to decussate and distichous phyllotaxy. We found that our simulation models of these two patterns predicted mirrored asymmetries in auxin distribution in leaf primordia pairs. To empirically verify the morphological consequences of asymmetric auxin distribution, we analysed the morphology of a tomato sister-of-pin-formed1a (sopin1a) mutant, entire-2, in which spiral phyllotaxy consistently transitions to a decussate state. Shifts in the displacement of leaflets on the left and right sides of entire-2 leaf pairs mirror each other, corroborating predicted model results. We then analyse the shape of more than 800 common ivy (Hedera helix) and more than 3000 grapevine (Vitis and Ampelopsis spp.) leaf pairs and find statistical enrichment of predicted mirrored asymmetries. Our results demonstrate that left-right auxin asymmetries in models of decussate and distichous phyllotaxy successfully predict mirrored asymmetric leaf morphologies in superficially symmetric leaves.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

Molecular authentication of Tetrastigma hemsleyanum from its adulterant species using ISSR, CAPS, and ITS2 barcode.

Tetrastigma hemsleyanum is a rare and endangered herb, which is commercialized as the resource of anti-cancer drugs. Wild T. hemsleyanum plants are on the verge of extinction recently, there are increasing numbers of counterfeits on the market. In the present study, inter-simple sequence repeat (ISSR), Cleaved amplified polymorphic sequence (CAPS), and the internal transcribed spacer region II (ITS2) barcode were used for the first time for the authentication of T. hemsleyanum from its commonly counterfeits. ISSR analysis suggested that it was a useful method for distinguishing T. hemsleyanum from its adulterants of different genus. However, it was insufficient to distinguish T. hemsleyanum from those adulterants of the same genus. ITS2 of T. hemsleyanum and the commonly counterfeits were amplified and sequenced. The Neighbor-Joining tree constructed from the ITS2 sequences showed that T. hemsleyanum was clearly differentiated from all counterfeits samples. A mutation site in the ITS2 region of T. hemsleyanum had been found which could be recognized by the restriction endonuclease NcoI. T. hemsleyanum could be readily distinguished from counterfeits as the PCR products from T. hemsleyanum could be digested sufficiently by NcoI, while the PCR products from counterfeits could not be digested. The results indicated that CAPS and ITS2 barcode methods provided effective and accurate identification of T. hemsleyanum from all its adulterants, while ISSR could only distinguish T. hemsleyanum from its adulterants of different genus. The CAPS method developed in the present study will serve as a reliable tool for safe and effective use of T. hemsleyanum in the clinic application. It will also play an important role for the identification, management and conservation of this endangered species.

Phylogeny of the Ampelocissus-Vitis clade in Vitaceae supports the New World origin of the grape genus.

The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus-Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus-Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4Ma, 95% HPD: 32.6-48.6Ma), then migrated to Eurasia in the late Eocene (37.3Ma, 95% HPD: 30.9-45.1Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism.

The complete chloroplast genome sequence of Tetrastigma hemsleyanum Diels at Gilg.

The complete chloroplast genome sequence of Tetrastigma hemsleyanum Diels at Gilg, a critical Chinese medicine, is reported here. The complete chloroplast genome of Tetrastigma hemsleyanum Diels at Gilg is 159 914 bp in length with 37.55% overall GC content. A pair of IRs (inverted repeats) of 26 510 bp were separated by LSC (87 927 bp) and SSC (18 967 bp). The phylogenetic analysis of 40 taxa showed a strong sister relationship with all other rosids. However, the placement of Myrtales still needs further verification.

Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber, Tetrastigma hemsleyanum (Vitaceae): insights into Plio-Pleistocene range dynamics of evergreen forest in subtropical China.

Warm-temperate evergreen (WTE) forest represents the typical vegetation type of subtropical China, but how its component species responded to past environmental change remains largely unknown. Here, we reconstruct the evolutionary history of Tetrastigma hemsleyanum, an herbaceous climber restricted to the WTE forest. Twenty populations were genotyped using chloroplast DNA sequences and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and ecological niche modeling (ENM) of the species distributions during the Last Glacial Maximum (LGM) and at present. Lineages in Southwest vs Central-South-East China diverged through climate/tectonic-induced vicariance of an ancestral southern range during the early Pliocene. Long-term stability in the Southwest contrasts with latitudinal range shifts in the Central-South-East region during the early-to-mid-Pleistocene. Genetic and ENM data strongly suggest refugial persistence in situ at the LGM. Pre-Quaternary environmental changes appear to have had a persistent influence on the population genetic structure of this subtropical WTE forest species. Our findings suggest relative demographic stability of this biome in China over the last glacial-interglacial cycle, in contrast with palaeobiome reconstructions showing that this forest biome retreated to areas of today's tropical South China during the LGM.

Development and characterization of microsatellite markers for the Chinese endangered medicinal plant Tetrastigma hemsleyanum.

Tetrastigma hemsleyanum (Vitaceae) is an endangered medicinal plant endemic to China. Because of its widely known efficacy for treating many health problems, wild resources of this species are currently undergoing a rapid decline. Few studies have been conducted examining the population genetics or development of microsatellite loci for this plant. In this study, 14 microsatellite loci were isolated and characterized for T. hemsleyanum using a double-suppression PCR method. Polymorphisms were tested with a total of 50 individuals from 2 natural populations. The number of alleles per locus ranged from 3-9, with an average of 7 alleles per locus. The observed and expected heterozygosity per locus ranged from 0-1 and from 0.068-0.803, respectively. The polymorphism information content value varied from 0.215-0.760. These loci may facilitate further genetic studies of populations of T. hemsleyanum and provide guidance for their conservation.

Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.

Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies for both homology and orthology assignment. The procedure first uses similarity scores to infer putative homologs that are then aligned, constructed into phylogenies, and pruned of spurious branches caused by deep paralogs, misassembly, frameshifts, or recombination. These final homologs are then used to identify orthologs. We explore four alternative tree-based orthology inference approaches, of which two are new. These accommodate gene and genome duplications as well as gene tree discordance. We demonstrate these methods in three published data sets including the grape family, Hymenoptera, and millipedes with divergence times ranging from approximately 100 to over 400 Ma. The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs. We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs. To explicitly evaluate sources of conflicting phylogenetic signals, we applied serial jackknife analyses of gene regions keeping each locus intact. The methods described here can scale to over 100 taxa. They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines. All scripts are available from https://bitbucket.org/yangya/phylogenomic_dataset_construction.