Alsophila Spinulosa Research Articles

Complete chloroplast genome sequence of the medical fern Drynaria roosii and its phylogenetic analysis

In this study, the complete chloroplast genome of the medical fern Drynaria roosii was completed and analyzed in order to understand the evolution of the genome of the fern lineages. In D. roosii, the circular double-stranded cpDNA sequence of 154,305 bp consists of two inverted repeat (IRA and IRB) regions of 23,416 bp each, a large single-copy (LSC) region of 86,040 bp and a small single-copy (SSC) region of 21,433 bp. The overall GC content is 40.92% and the GC contents of LSC, IRs, and SSC are 39.75%, 45.07%, and 36.60%, respectively. D. roosii with 108 annotated unique genes included 85 protein-coding genes, 19 tRNA genes, and 4 rRNA genes. Using the whole chloroplast genome sequences alignment of 18 species from ferns, the phylogenetic relationship was built. The phylogenetic position of D. roosii was closely clustered with Adiantum capillus-veneris, Cheilanthes lindheimeri, and Pteridium aquilium subsp. Aquilinum as sister species and then clustered with Alsophila spinulosa, Lygodium japonicum, Diplopterygium glaucum, and Osmundastrum cinnamomeum. D. roosii belongs to Polypodiales. The complete chloroplast genome of D. roosii provides utility information for ferns evolutionary and genomic studies.

Niche Characteristics of Dominant Plant Populations of Alsophila spinulosa Community of Danxia Landform in North Guizhou

Niche Characteristics of Dominant Plant Populations of Alsophila spinulosa Community of Danxia Landform in North Guizhou

A New Organic Acid Derived from the Stem of Alsophila spinulosa (Hook.) Tryo

A New Organic Acid Derived from the Stem of Alsophila spinulosa (Hook.) Tryo

Population Genetic Variation in the Tree Fern Alsophila spinulosa (Cyatheaceae): Effects of Reproductive Strategy

BackgroundEssentially all ferns can perform both sexual and asexual reproduction. Their populations represent suitable study objects to test the population genetic effects of different reproductive systems. Using the diploid homosporous fern Alsophila spinulosa as an example species, the main purpose of this study was to assess the relative impact of sexual and asexual reproduction on the level and structure of population genetic variation.Methodology/Principal FindingsInter-simple sequence repeats analysis was conducted on 140 individuals collected from seven populations (HSG, LCH, BPC, MPG, GX, LD, and ZHG) in China. Seventy-four polymorphic bands discriminated a total of 127 multilocus genotypes. Character compatibility analysis revealed that 50.0 to 70.0% of the genotypes had to be deleted in order to obtain a tree-like structure in the data set from populations HSG, LCH, MPG, BPC, GX, and LD; and there was a gradual decrease of conflict in the data set when genotypes with the highest incompatibility counts were successively deleted. In contrast, in population ZHG, only 33.3% of genotypes had to be removed to achieve complete compatibility in the data set, which showed a sharp decline in incompatibility upon the deletion of those genotypes. All populations examined possessed similar levels of genetic variation. Population ZHG was not found to be more differentiated than the other populations.Conclusions/SignificanceSexual recombination is the predominant source of genetic variation in most of the examined populations of A. spinulosa. However, somatic mutation contributes most to the genetic variation in population ZHG. This change of the primary mode of reproduction does not cause a significant difference in the population genetic composition. Character compatibility analysis represents an effective approach to separate the role of sexual and asexual components in shaping the genetic pattern of fern populations.

Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes

BackgroundFerns have generally been neglected in studies of chloroplast genomics. Before this study, only one polypod and two basal ferns had their complete chloroplast (cp) genome reported. Tree ferns represent an ancient fern lineage that first occurred in the Late Triassic. In recent phylogenetic analyses, tree ferns were shown to be the sister group of polypods, the most diverse group of living ferns. Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae).ResultsThe Alsophila cp genome is 156,661 base pairs (bp) in size, and has a typical quadripartite structure with the large (LSC, 86,308 bp) and small single copy (SSC, 21,623 bp) regions separated by two copies of an inverted repeat (IRs, 24,365 bp each). This genome contains 117 different genes encoding 85 proteins, 4 rRNAs and 28 tRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome. A unique trnR-UCG gene (derived from trnR-CCG) is found between rbcL and accD. The Alsophila cp genome shares some unusual characteristics with the previously sequenced cp genome of the polypod fern Adiantum capillus-veneris, including the absence of 5 tRNA genes that exist in most other cp genomes. The genome shows a high degree of synteny with that of Adiantum, but differs considerably from two basal ferns (Angiopteris evecta and Psilotum nudum). At one endpoint of an ancient inversion we detected a highly repeated 565-bp-region that is absent from the Adiantum cp genome. An additional minor inversion of the trnD-GUC, which is possibly shared by all ferns, was identified by comparison between the fern and other land plant cp genomes.ConclusionBy comparing four fern cp genome sequences it was confirmed that two major rearrangements distinguish higher leptosporangiate ferns from basal fern lineages. The Alsophila cp genome is very similar to that of the polypod fern Adiantum in terms of gene content, gene order and GC content. However, there exist some striking differences between them: the trnR-UCG gene represents a putative molecular apomorphy of tree ferns; and the repeats observed at one inversion endpoint may be a vestige of some unknown rearrangement(s). This work provided fresh insights into the fern cp genome evolution as well as useful data for future phylogenetic studies.

Isolation and Characterization of Microsatellite Loci in the Tree Fern Alsophila spinulosa

ABSTRACT Alsophila spinulosa is a famous relict tree fern. Three polymorphic microsatellite makers were developed and characterized using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol. The polymorphism was quantified for a single population from Guizhou province, China. The number of alleles per locus varied from 2 to 4. The ranges of observed and expected heterozygosity were 0.000–0.750 and 0.218–0.651, respectively. These were the first microsatellites reported for the Cyatheaceae and will be useful for the ongoing population and conservation genetic studies of other remaining extant populations.

Genetic differentiation of relictual populations of Alsophila spinulosa in southern China inferred from cpDNA trnL–F noncoding sequences

The genetic differentiation and phylogeographical pattern of 11 relictual populations of Alsophila spinulosa distributed across Hainan, Guangdong, and Guangxi in southern China were inferred from sequence variations of trnL–F noncoding regions of chloroplast DNA (cpDNA). The length of trnL–F noncoding sequences varied from 863 to 940 bp. The A + T content was 62.23–63.36%. Sequences were neutral in terms of evolution (Tajima’s criterion D = −0.62417, P > 0.10 and Fu and Li’s test D* = −1.45455, P > 0.10; F* = −1.32798, P > 0.10). Thirty-four haplotypes were identified based on nucleotide variation. Relatively high levels of haplotype diversity ( h = 0.929) and nucleotide diversity ( Dij = 0.022263) were detected in A. spinulosa, probably associated with its long evolutionary history which allowed the accumulation of genetic variation within lineages. Both the minimum spanning network and the strict consensus tree of the most parsimonious trees generated for haplotypes demonstrated that the investigated populations of A. spinulosa were subdivided into two geographical groups: Hainan and Guangdong–Guangxi. An analysis of molecular variance (AMOVA) indicated that most of the genetic variation (87.48%, P < 0.001) was partitioned among regions. Spatial structure measurements revealed that population genetic structure was not related to geographical distance. This research suggests that blocked gene flow by Qiongzhou strait and an inbreeding system might result in the geographical subdivision between Hainan and Guangdong–Guangxi ( F ST = 0.92, Nm = 0.09). Within each region, the “star like” pattern of phylogeography of haplotypes implied a population expansion process during evolutionary history. Gene genealogies together with coalescent theory were useful tools for uncovering the phylogeography of A. spinulosa.

Population genetic structure and phylogeographical pattern of a relict tree fern, Alsophila spinulosa (Cyatheaceae), inferred from cpDNA atpB- rbcL intergenic spacers.

Sequences of chloroplast DNA (cpDNA) atpB- rbcL intergenic spacers of individuals of a tree fern species, Alsophila spinulosa, collected from ten relict populations distributed in the Hainan and Guangdong provinces, and the Guangxi Zhuang region in southern China, were determined. Sequence length varied from 724 bp to 731 bp, showing length polymorphism, and base composition was with high A+T content between 63.17% and 63.95%. Sequences were neutral in terms of evolution (Tajima's criterion D=-1.01899, P>0.10 and Fu and Li's test D*=-1.39008, P>0.10; F*=-1.49775, P>0.10). A total of 19 haplotypes were identified based on nucleotide variation. High levels of haplotype diversity (h=0.744) and nucleotide diversity (Dij=0.01130) were detected in A. spinulosa, probably associated with its long evolutionary history, which has allowed the accumulation of genetic variation within lineages. Both the minimum spanning network and neighbor-joining trees generated for haplotypes demonstrated that current populations of A. spinulosa existing in Hainan, Guangdong, and Guangxi were subdivided into two geographical groups. An analysis of molecular variance indicated that most of the genetic variation (93.49%, P<0.001) was partitioned among regions. Wright's isolation by distance model was not supported across extant populations. Reduced gene flow by the Qiongzhou Strait and inbreeding may result in the geographical subdivision between the Hainan and Guangdong + Guangxi populations (FST=0.95, Nm=0.03). Within each region, the star-like pattern of phylogeography of haplotypes implied a population expansion process during evolutionary history. Gene genealogies together with coalescent theory provided significant information for uncovering phylogeography of A. spinulosa.

Genetic structure and variation in the relict populations of Alsophila spinulosa from southern China based on RAPD markers and cpDNA atpB-rbcL sequence data.

RAPD markers and sequences of chloroplast DNA (cpDNA) atpB-rbcL intergenic spacers were used to characterize the pattern of genetic variation and the phylogenetic relationships of the relict populations of Alsophila spinulosa located in Jian Feng Ling (JFL) and Diao Luo Shan (DLS), Hainan, and Tang Lang Shan (TLS), Ding Hu Shan (DHS), and Da Xi Shan (DXS), Guangdong, of southern China. 28 random primers generated 118 bands, out of which 26 (22.03%) were polymorphic loci, distinguishing 17 different RAPD phenotypes. Percentage of polymorphic loci, Shannon phenotypic diversity and Nei's gene diversity comprehensively indicated that JFL possessed the highest diversity, TLS and DHS in intermediate and DLS or DXS the least; the corresponding values of the population appeared correlated with the population size. Differentiation was detected among populations of A. spinulosa (1-Hpop/Hsp=0.7453, GST=0.7763, and phist=0.8145). AMOVA showed that 47.44% of the variance was partitioned among regions (Hainan and Guangdong), 34.01% attributed among populations within regions, whereas only 18.55% occurring within populations. Low level of intra-specific diversity was maintained in A. spinulosa with Shannon diversity and gene diversity merely 0.0560 and 0.0590, repectively. Sequence length of atpB-rbcL intergenic spacer varied from 724 bp to 730 bp. Base composition was with A+T content between 63.17% and 63.70%. 13 haplotypes of atpB-rbcL noncoding spacers were identified. UPGMA dendrogram of RAPD phenotypes, principal components analysis based on RAPD patterns, minimum spanning network and neighbour-joining (NJ) tree established on atpB-rbcL haplotypes consistently suggested the geographical subdivision of populations of A. spinulosa between Hainan and Guangdong. Breeding system and conservation strategy of A. spinulosa was discussed based on the information of population genetic structure and variation.

Xanthine oxidase inhibitors from the leaves of Alsophila spinulosa (Hook) Tryon.

Diploptene(1), beta-sitosterol(2), a mixture of 6'-O-(E-P-coumaroyl)-alpha-glucopyranose and 6'-O-(E-P-coumaroyl)-beta-glucopyranose(3), a mixture of 6'-O-(E-P-caffeoyl)-alpha-glucopyranose and 6'-O-(E-P-caffeoyl)-beta-glucopyranose(4), caffeic acid(5) and astragalin(6) were isolated from an ethanolic extract of the leaves of Alsophila spinulosa Hook Tryon (Cyatheaceae). The plant has been used in folk medicine for hepatitis, gout, rheumatism, and tumor and these compounds were tested for their inhibitory effect on xanthine oxidase. Caffeic acid was the most potent constituent (IC50 = 39.21 microM; Ki = 28.2 microM) and was an uncompetitive inhibitor of the enzyme with respect to the substrate xanthine.

Chemistry and chemotaxonomy of pterophyten. 59. Chemical research on the components of Alsophila spinulosa Tryon.

From the fronds of Alsophila spinulosa TRYON biflavonoids Hegoflavone A (I) and B (II) were isolated and their structures were elucidated by spectroscopic analysis and chemical degradation to be 2, 3-dihydro-3'''-hydroxy-6, 6'''-biapigenin (I) and 2, 3-dihydro-6, 6'''-biluteolin (II) respectively. These are the first reports of a C-6/C-6'''-linked biflavonoid in nature.