The Single Distinct Leader Protease Encoded by Alpinia oxyphylla Mosaic Virus (Genus Macluravirus) Suppresses RNA Silencing Through Interfering with Double-Stranded RNA Synthesis.

The genomic 5'-terminal regions of viruses in the family Potyviridae (potyvirids) encode two types of leader proteases: serine-protease (P1) and cysteine-protease (HCPro), which differ greatly in the arrangement and sequence composition among inter-genus viruses. Most potyvirids have the same tandemly arranged P1 and HCPro, whereas viruses in the genus Macluravirus encode a single distinct leader protease, a truncated version of HCPro with yet-unknown functions. We investigated the RNA silencing suppression (RSS) activity and its underpinning mechanism of the distinct HCPro from alpinia oxyphylla mosaic macluravirus (aHCPro). Sequence analysis revealed that macluraviral HCPros have obvious truncations in the N-terminal and middle regions when aligned to their counterparts in potyviruses (well-characterized viral suppressors of RNA silencing). Nearly all defined elements essential for the RSS activity of potyviral counterparts are not distinguished in macluraviral HCPros. Here, we demonstrated that aHCPro exhibits a similar anti-silencing activity with the potyviral counterpart. However, aHCPro fails to block both the local and systemic spreading of RNA silencing. In line, aHCPro interferes with the dsRNA synthesis, an upstream step in the RNA silencing pathway. Affinity-purification and NanoLC-MS/MS analysis revealed that aHCPro has no association with core components or their potential interactors involving in dsRNA synthesis from the protein layer. Instead, the ectopic expression of aHCPro significantly reduces the transcript abundance of RDR2, RDR6, SGS3, and SDE5. This study represents the first report on the anti-silencing function of Macluravirus-encoded HCPro and the underlying molecular mechanism.

Diverse function of the PISTILLATA, APETALA 3, and AGAMOUS-like MADS-box genes involved in the floral development in Alpinia hainanensis (Zingiberaceae).

Zingiberaceae is the vital clue and key node in the decreased process of fertile stamens in Zingiberales, helping to understand the evolution of the ginger families. This study focuses on Alpinia hainanensis to investigate the function of B- and C-class MADS-box genes in floral development. The introns size of two B-class genes AhPI and AhAP3, and one C-class gene AhAG are quite variable. By contrast, the positions of the corresponding introns are conserved, resulting in a similar exon size in homologs. The typical region 70 bp-CCAATCA element was not found in the second intron of AhAG compared to AG homologs. The subcellular localization showed that AhAP3 was in both intranuclear and extranuclear. The heterodimer was formed between APETALA3 and PISTILLATA but not between the B- and C-class proteins using Y2H and BiFC. The 35S::AhAG heterologous transformed Arabidopsis had curly and smaller rosette leaves with early flowering. Floral organs had no homeotic conversion, albeit sepals and petals reduced in size. Siliques development was affected and displayed wrinkled and shorter. By contrast, 35S::AhAP3 and 35S::AhPI did not show any modified phenotype in transgenic Arabidopsis thaliana. We first proposed the model for Alpinia flower development. MADS-box transcription factor binding at particular genomic locations and interaction with partners may be crucial for the development of the floral organ.

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences.

BACKGROUND: Alpinia species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal Alpinia species and correctly identify medicinal products derived from Alpinia species, we systematically analyzed the plastome sequences from five Alpinia species. Four of the Alpinia species: Alpinia galanga (L.) Willd., Alpinia hainanensis K.Schum., Alpinia officinarum Hance, and Alpinia oxyphylla Miq., are listed in the Chinese pharmacopeia. The other one, Alpinia nigra (Gaertn.) Burtt, is well known for its medicinal values. RESULTS: The four Alpinia species: A. galanga, A. nigra, A. officinarum, and A. oxyphylla, were sequenced using the Next-generation sequencing technology. The plastomes were assembled using Novoplasty and annotated using CPGAVAS2. The sizes of the four plastomes range from 160,590 bp for A. galanga to 164,294 bp for A. nigra, and display a conserved quadripartite structure. Each of the plastomes encodes a total of 111 unique genes, including 79 protein-coding, 28 tRNA, and four rRNA genes. In addition, 293-296 SSRs were detected in the four plastomes, of which the majority are mononucleotides Adenine/Thymine and are found in the noncoding regions. The long repeat analysis shows all types of repeats are contained in the plastomes, of which palindromic repeats occur most frequently. The comparative genomic analyses revealed that the pair of the inverted repeats were less divergent than the single-copy region. Analysis of sequence divergence on protein-coding genes showed that two genes (accD and ycf1) had undergone positive selection. Phylogenetic analysis based on coding sequence of 77 shared plastome genes resolves the molecular phylogeny of 20 species from Zingiberaceae. In particular, molecular phylogeny of four sequenced Alpinia species (A. galanga, A. nigra, A. officinarum, and A. oxyphylla) based on the plastome and nuclear sequences showed congruency. Furthermore, a comparison of the four newly sequenced Alpinia plastomes and one previously reported Alpinia plastomes (accession number: NC_048461) reveals 59 highly divergent intergenic spacer regions. We developed and validated two molecular markers Alpp and Alpr, based on two regions: petN-psbM and psaJ-rpl33, respectively. The discrimination success rate was 100 % in validation experiments. CONCLUSIONS: The results from this study will be invaluable for ensuring the effective and safe uses of Alpinia medicinal products and for the exploration of novel Alpinia species to improve human health.

A Draft Genome of the Ginger Species Alpinia nigra and New Insights into the Genetic Basis of Flexistyly.

Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a de novo assembly of the genome of Alpinia nigra using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high FST values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype.

Phylogeny of Alpinia coriandriodora D. Fang and Implications for Character Evolution and Conservation.

BACKGROUND AND OBJECTIVE: Alpinia, the largest genus of Zingiberaceae, includes ca. 250 species. The A. coriandriodora D. Fang was recognized for Vietnamese flora. However, the systematic position of this species within Alpinia genus was unclear. The study aimed to understand the phylogenetic placement of A. coriandriodora based on the molecular data and interpret evolution of the key morphological characters. MATERIALS AND METHODS: The phylogenetic analysis were conducted by using the combined dataset of two DNA regions by both Maximum Likelihood (ML) and Bayesian Inference (BI) methods. Seven morphological characters were selected for morphological character evolution and the analysis was performed in Mesquite. RESULTS: Alpinia coriandriodora was supported closely related to southern Chinese species of Alpinia. Morphological character optimizations suggest that the presence/absence of tomentum in leaf, inflorescence rachis and ovary is an important character for the taxonomy of Alpinia. The character evolution analyses indicated that panicle is ancestral character in Alpinia. The A. coriandriodora shares different evolutionary histories based on our character re-construction to most members of Southeast Asian Alpinia. The presence of filament is supposed to be an adaptation to the pollination by insects for species of Alpinia. CONCLUSION: The present study revealed the molecular phylogenetic relationship of A. coriandriodora within Alpinia. The presence of filament could be an adaptation to the pollination by insects for species of Alpinia. Some reasonable conservation strategies are proposed to protect the species including maintenance of the plant's natural habitats, seeds or seedlings collection for germplasm storage and artificial breeding using biotechnology.

The complete chloroplast genome sequence of Alpinia oxyphylla Miq. and comparison analysis within the Zingiberaceae family.

Alpinia oxyphylla Miq. (A. oxyphylla) is an important edible and traditional herbal medicine. In this study, the complete chloroplast genome of A. oxyphylla was sequenced, analysed, and compared to five species in the Zingiberaceae family. The size of the A. oxyphylla chloroplast genome was 161351 bp, which consisted of a large single-copy (LSC, 87248 bp) and small single-copy (SSC, 16175 bp) region separated by a pair of inverted repeats (IRa and IRb, 28964 bp each). The genome encoded 132 unique genes, including 87 protein-coding genes, 37 tRNAs and four rRNAs. The GC content of the genome was 36.17%. A total of 53 simple sequence repeats (SSRs) and 80 long repeats were identified in the A. oxyphylla chloroplast genome. The chloroplast genome of A. oxyphylla shared the highest sequence similarity of >90% with the chloroplast genome of A. zerumbet, and six chloroplast genomes in the Zingiberaceae family were compared by using CGView Comparison Tool (CCT). According to the phylogenetic tree, the Zingiberaceae family is divided into two categories, which coincide with the classification of the characteristics of sun-like and shade-like in plants. Our results reveal the phototrophic component of NADH-dehydrogenase (ndhB and ndhC), photosystem II (psbZ) and ATP synthase (atpE, atpF) exhibit adaptive evolution under different environments, and the strength of light is an important trigger for the adaptations at the chloroplast level.

Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis.

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

Agrobacterium-mediated transformation in Alpinia galanga (Linn.) Willd. for enhanced acetoxychavicol acetate production.

Agrobacterium-mediated transformations ensure elevated amounts of secondary metabolite accumulation with genetic and biosynthetic stability. In the present study, Alpinia galanga rich in bioactive compounds was genetically transformed using different strains of Agrobacterium rhizogenes viz. LBA 9402, A(4), 532, 2364 and PRTGus. Even though a higher growth rate was obtained with the LBA 9402 strain, maximum acetoxychavicol acetate accumulation (ACA) was seen in the PRTGus transformant. PRTGus root line has shown 10.1 fold higher ACA content in comparison to the control roots. The lowest ACA production was shown by the A(4) transformant (4.9 fold). The quantification of ACA in the transformed roots was carried out by using HPLC, which was found to be in the order of PRTGus > LBA 9402 > 2364 > 532 > A(4). The fast growth rate of hairy roots, genetic stability and their ability to synthesize more than one metabolite offer a promising system for the production of valuable secondary metabolites.

[Cloning and expression regulation of 1-deoxy-D-xylulose-5-phosphate reductoisomerase cDNA from Alpinia officinarum].

The rhizome of Alpinia officinarum is a widely used Chinese herbal medicine. The essential oil in A. officinarum rhizome is mainly composed of 1, 8-cineole and other monoterpenes, as the major bioactive ingredients. In plants, monoterpenes are synthesized through the methylerythritol phosphate (MEP) pathway in the plastids, and 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) is an enzyme catalyzing a committed step of the MEP pathway. In the present study, the full-length cDNA encoding DXR was cloned from the rhizome of A. officinarum, using homology-based RT-PCR and rapid amplification of cDNA ends (RACE) techniques. The new cDNA was designated as AoDXR and submitted to GenBank to be assigned with an accession number HQ874658. The full-length cDNA of AoDXR was 1 670 bp containing a 1 419 bp open reading frame encoding a polypeptide of 472 amino acids with a calculated molecular mass of 51.48 kDa and an isoelectric point of 6.15. Bioinformatic analyses revealed that AoDXR showed extensive homology with DXRs from other plant species and contained a conserved plastids transit peptide, a Pro-rich region and two highly conserved NADPH-binding motifs in its N-terminal region characterized by all plant DXRs. The phylogenetic analysis revealed that AoDXR belonged to angiosperm DXRs. The structural modeling of AoDXR showed that AoDXR had the typical V-shaped structure of DXR proteins. The tissue expression pattern analysis indicated that AoDXR expressed strongly in leaves, weak in rhizomes of A. officinarum. Exogenous methyl jasmonate (MeJA) could enhance the expression of AoDXR and the production of 1, 8-cineole in A. officinarum rhizomes. The cloning and characterization of AoDXR will be helpful to reveal the molecular regulation mechanism of monoterpene biosynthesis in A. officinarum and provides a candidate gene for metabolic engineering in improving the medicinal quality of A. officinarum rhizome.

[AFLP analysis of genetic diversity of Alpinia officinarum].

OBJECTIVE: To explore the genetic diversity and relationship of different Alpinia officinarum germplasm. METHOD: Amplified fragment length polymorphism (AFLP) markers were developed to analyze genetic polymorphism in A. officinarun from eight resources. The amplified fragments were used as primary matrix with NTSYSpc-2.11F software to analyze the similarity between the A. officinarum germplasm and to construct the genetic phylogenetic tree. RESULT: A total of 1,120 fragments were genotyped using AFLP with eight prime combinations. Analysis identified 1,044 polymorphic fragments, accounting for 92.57% of the total detected variation. Genetic phylogenetic tree analysis indicates that three categories can be divided among the eight resources of A. officinanrum. CONCLUSION: Significant polymorphism and genetic diversity can be observed among A. officinarum germplasm resources.

Why do stigmas move in a flexistylous plant?

Flexistyly is a recently documented stylar polymorphism involving both spatial and temporal segregation of sex roles within hermaphroditic flowers. Using the experimental manipulation of stigma movement in self-compatible Alpinia mutica, we tested the hypothesis that selection for reducing interference between male and female function drives the evolution and/or maintenance of stigma movement. In experimental arrays, anaflexistylous (protogynous) flowers served as pollen donors competing for mating opportunities on cataflexistylous (protandrous) flowers. The pollen donors were either manipulated so their stigmas could not move or were left intact, and their success was determined using allozymes to assess the paternity of recipient seeds. We found that manipulated flowers sired a significantly smaller proportion of seeds, showing that stigma movement in unmanipulated plants increased male fitness. This result was strongest under conditions in which pollen competition was expected to be highest, specifically when pollinators visited multiple donor plants before visiting recipient flowers.

Isolation and characterization of a SEP- like gene from Alpinia hainanensis (Zingiberaceae).

A cDNA clone, AhSEP3 was isolated from the young inflorescences of Alpinia hainanensis. AhSEP3 cDNA is 891 bp long with an open reading frame of 726 bp that encodes a 241-amino acid protein. Sequence comparisons showed that AhSEP3 is very similar to SEP3 homologues. Phylogenetic analyses indicated that AHSEP3 is a new member of AGL2 subfamily. In situ hybridization analyses showed the expression pattern of the AhSEP3 is very similar to those of SEP3 and SEP3 homologs in other plant species, i.e. the signals of AhSEP3 are present in the inner three whorl of the floral organ.

New Rev-export inhibitor from Alpinia galanga and structure-activity relationship.

Bioassay-guided separation by use of the fission yeast expressing NES of Rev, an HIV-1 viral regulatory protein, disclosed 1'-acetoxychavicol acetate (ACA, 1) as a new inhibitor for nuclear export of Rev from the roots of Alpinia galanga. Both analysis for mechanism of action with biotinylated probe (2) and several synthesized analogs established crucial portions in 1 for Rev-export inhibitory activity.

Identification and expression of floral organ homeotic genes from Alpinia oblongifolia (Zingiberaceae).

Current understanding of the classical ABC model of floral development has provided a new set of characters to evaluate floral evolution. However, what is still lacking is a clear assessment of this genetic program across monocots. Here, to investigate the evolution of members of class A and B genes in monocots, we report the sequence characteristic and transcript expression of three new MADS-box genes in Alpinia oblongifolia Hayata. Sequence and phylogenetic analysis reveals that these genes are FUL-like and AP3-like. Therefore, they were termed AoFL1, AoFL2 and AoAP3. AoFL1 contains the FUL motif, but AoFL2 lacks this motif. Their expression revealed by in situ hybridization may reflect the ancestral function of FUL-like genes in the specification of inflorescence and floral meristems. The AoAP3 gene contains two conserved motifs, the PI-derived and paleoAP3 motifs. The AoAP3 transcripts located to the corolla and stamen, and hybridization signals were detected in the central whorl. These expression patterns suggest that the functions of homologous organ identity genes are diversified in A. oblongifolia. The implications of these findings on the conservation of homologous gene function are discussed.

Adaptive significance of flexistyly in Alpinia blepharocalyx (Zingiberaceae): a hand-pollination experiment.

BACKGROUND AND AIMS: Flexistyly is a sexual dimorphism where there are two morphs that differ in the temporal expression of sexual function and also involve reciprocal movement of the stigmatic surface through a vertical axis during the flowering period. The adaptive significance of flexistyly has been interpreted as a floral mechanism for outcrossing, but it may also function to reduce sexual interference in which styles and stigmas impede the pollen export. Here these two explanations of flexistyly were tested in Alpinia blepharocalyx through a hand-pollination experiment. METHODS: Hand-pollinations were performed in two temporal morphs and consisted of two sequential pollination treatments, namely self-pollination in the morning and inter-morph pollination in the afternoon (treatment 1) or conversely inter-morph pollination in the morning and self-pollination in the afternoon (treatment 2), and two simultaneous self- and inter-morph cross-pollination treatments either in the morning (treatment 3) or in the afternoon (treatment 4). Seed paternity was then determined to assess relative success of self- versus cross-pollen using allozyme markers. KEY RESULTS: In the sequential pollination treatments, whether the stigmas of recipients are receptive in the morning is crucial to the success of the pollen deposited. When the cataflexistylous (protandrous) morph served as pollen recipient, early-arriving pollen in the morning can sire only a very small proportion (<15%) of seeds because the stigmas were then unreceptive. However, when the anaflexistylous (protogynous) morph served as pollen recipient, early pollen did gain a large competitive advantage over the late pollen, particularly when cross-pollen arrived first. Simultaneous self- and inter-morph cross-pollination indicated that outcross-pollen is more competitive than self-pollen on receptive stigmas. CONCLUSIONS: Differential maturing of male and female organs in Alpinia blepharocalyx is sufficient for selfing avoidance, obviating the need for style movements. Instead, the upward style curvature of the cataflexistylous morph in the morning and the anaflexistylous morph in the afternoon most likely represents a means of reducing interference with pollen export.