Leaf dorsoventrality candidate gene CpARF4 has conserved expression pattern but divergent tasiR-ARF regulation in the water fern Ceratopteris pteridoides.

PREMISE: Leaves are traditionally classified into microphylls and megaphylls, and recently have been regarded as independently originating in lycophytes, ferns, and seed plants. The developmental genetics of leaf dorsoventrality, a synapomorphy in vascular plants, has been extensively studied in flowering plants. AUXIN RESPONSE FACTOR4 (ARF4) genes are key to leaf abaxial identity in flowering plants, but whether they exist in ferns is still an open question. METHODS: ARF4 genes from Ceratopteris pteridoides, Cyrtomium guizhouense, and Parathelypteris nipponica were mined from transcriptomes and investigated in terms of evolutionary phylogeny and sequence motifs, with a focus on the tasiR-ARF binding site. In situ hybridization was used to localize expression of CpARF4 in Ceratopteris pteridoides. 5'RNA ligase-mediated-RACE was employed to verify whether CpARF4 transcripts were sliced by tasiR-ARF. RESULTS: ARF4 genes exist in ferns, and this lineage originates from a gene duplication in the common ancestor of ferns and seed plants. ARF4 genes are of a single copy in the ferns studied here, and they contain divergent and, at most, one tasiR-ARF binding site. CpARF4 is expressed in the abaxial but not the adaxial domain of leaf primordia at various developmental stages. Transcript slicing guided by tasiR-ARF is active in C. pteridoides, but CpARF4 probably has not been affected by it. CONCLUSIONS: Fern ARF4 genes differ in copy number and tasiR-ARF regulation relative to flowering plants, though they can be similarly expressed in the abaxial domain of leaves, revealing a key role for ARF4 genes in the evolution of leaf dorsoventrality of vascular plants.

Hymenasplenium volubile: documentation of its gametophytes and the first record of a hemiepiphyte in the Aspleniaceae.

BACKGROUND AND AIMS: Through careful field examination of the growth habit of the gametophytes and sporophytes of Hymenasplenium volubile across an ontogenetic series, we aim to understand better the evolution of epiphytism in this poorly understood group of ferns. METHODS: We made field observations of H. volubile sporophytes and gametophytes, and brought specimens back to the lab for microscopic analysis. In the field, sporophytes at each ontogenetic stage were photographed to document the species' growth habit. We used an existing phylogeny to optimize growth form of New World Hymenasplenium. KEY RESULTS: Young sporophytes were at first fully epiphytic and produced one or two long feeding roots that extend to the soil where they branch profusely. The feeding roots remain in contact with the soil throughout the life of the plant. Thus, H. volubile is a hemiepiphyte. While immature, gametophytes are appressed to the tree trunk, but, as their gametangia mature, their lower margin lifts upward, imparting a shelf-like appearance to the thallus. The thallus attaches to the substrate by branched rhizoids produced along the margin of the thallus in contact with the substrate. CONCLUSIONS: Hemiepiphytes are a key link in the evolution of epiphytic ferns and may act as a bridge between the forest floor and the canopy. Our finding is the first report of hemiepiphytism in Aspleniaceae, a large lineage with many epiphytic and terrestrial taxa. This work serves as an important model to understand the evolution of epiphytism in this group specifically and in ferns in general. The majority of our understanding of fern gametophyte biology is derived from laboratory studies. Our efforts represent a fundamental contribution to understanding fern gametophyte ecology in a field setting.

Integrated taxonomy of the Asplenium normale complex (Aspleniaceae) in China and adjacent areas.

The Asplenium normale D. Don complex comprises several taxa that are either diploid or tetraploid. The tetraploids are assumed to have originated from diploid ancestors by relatively recent autopolyploidization or allopolyploidization. Some of the diploids are readily recognized morphologically but most of the taxa have until now been placed into a single species. However, phylogenetic studies have challenged this treatment and emphasized the notion that the taxonomic treatment of this complex needs to be revised. An integrative taxonomic approach was employed to delimit species in the complex using cytological, morphological, and DNA sequence data. Initially, we employed a diploid first approach to establish a robust taxonomic framework. Special efforts were made to collect and identify the diploid progenitors of each polyploid lineage identified in the plastid DNA based phylogenetic hypothesis. A total of six distinct diploid species were identified. The distinctive nature of the six diploids is strongly supported by sequence differences in plastid DNA and nuclear loci, as well as by the results of morphometric analysis. Diagnostic morphological characters were identified to distinguish the six diploid species, resulting in their revised taxonomy, which includes two novel species, namely, Asplenium normaloides and A. guangdongense. Further studies to strengthen the taxonomic classification of all of the tetraploid taxa are warranted.

Allotetraploid cryptic species in Asplenium normale in the Japanese Archipelago, detected by chemotaxonomic and multi-locus genotype approaches.

PREMISE OF THE STUDY: Delimitation of cryptic species provides an understanding of biodiversity and opportunities to elucidate speciation processes. Extensive flavonoid variation has been reported in the tetraploid cytotype of the fern, Asplenium normale, although related species have no intraspecific variations in flavonoid composition. We hypothesized that Japanese A. normale still harbors multiple cryptic species with different flavonoid compositions, and tested this hypothesis using chemotaxonomic and multilocus genotyping approaches. METHODS: We determined the multilocus genotypes (MLGs) of 230 samples from 37 populations for one chloroplast DNA region and three nuclear genes. MLGs were used to delimit reproductively isolated lineages by population-genetic approaches. We also tested the correspondence between genetically recognized groups and flavonoid compositions. To identify the origins of putative cryptic species, we conducted phylogenetic analysis of the DNA markers used in genotyping. KEY RESULTS: The genetic clusters and flavonoid compositions showed clear correspondence. We recognized three putative cryptic species in tetraploid Asplenium normale in Japan. Phylogenetic analyses revealed that cryptic species I and III originated from allopolyploidization between a diploid A. normale and an unknown diploid of A. boreale, and cryptic species II originated from allopolyploidization between a diploid A. normale and A. oligophlebium. CONCLUSIONS: Our study demonstrated that intraspecific variation of secondary metabolites can be a good indicator of cryptic species in ferns. The presence of the two cryptic species having the same progenitor diploid pair suggests that speciation between allopolyploid lineages of independent origin may be more common than previously considered.

The complete chloroplast genome of the neo-allotetraploid fern, Asplenium pseudocapillipes S.H.Park et al. (Aspleniaceae).

This study analyzed the complete plastome sequence of the neo-allotetraploid Asplenium pseudocapillipes S.H.Park et al. Asplenium pseudocapillipes has a typical circular plastome that comprises 157,242 bp with a large single copy (84,105 bp), a small single copy (21,503 bp), and two inverted repeats (IRs; 25,817 bp). The complete sequence comprises 127 genes, including 87 protein-coding genes (CDSs), eight ribosomal RNAs (rRNAs), 31 transfer RNAs (tRNAs), and one pseudogene. Among these genes, five CDSs, four rRNAs, and five tRNAs are duplicated in IRs. The guanine-cytosine content of the genome was 41.5%. The enlarged noncoding regions by Mobile Open Reading Frames in Fern Organelles were found once in other Asplenium species and twice in A. pseudocapillipes. Phylogenetic analysis based on 83 coding gene sequences revealed that A. pseudocapillipes is embedded in the A. varians subclade along with its progenitors.

The complete chloroplast genome sequence and phylogenetic analysis of Asplenium antiquum Makino 1929, an Endangered species in Korea.

Asplenium antiquum Makino 1929 is one of the Endangered endemic species on the Korean Peninsula. The complete chloroplast of A. antiquum is 150,690 bp in length with typical quadripartite structure comprised of large single-copy region of (83,166 bp), a small single copy region (21,932 bp), and two inverted repeat regions, each 22,796 bp in length. 114 genes were detected in the chloroplast genome of A. antiquum, comprising 84 protein-encoding genes, 26 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed a monophyletic relationship, placing A. antiquum as a sister to voth A. Prolongatum and A. nidus, forming a subclade of Asplenium species within the Aspleniaceae family. The genomic data obtained from this study will serve as valuable information for the species' genetic classification of Asplenium.

Understanding mechanisms of rarity in pteridophytes: competition and climate change threaten the rare fern Asplenium scolopendrium var. americanum (Aspleniaceae).

PREMISE OF THE STUDY: Understanding the ecology of rare species can inform aspects of conservation strategies; however, the mechanisms of rarity remain elusive for most pteridophytes, which possess independent and ecologically distinct gametophyte and sporophyte generations. To elucidate factors contributing to recent declines of the rare fern Asplenium scolopendrium var. americanum, we studied the ecology and ecophysiology of its gametophyte generation, focusing on responses to competition, temperature, and water stress. METHODS: Gametophytes of A. scolopendrium var. americanum, its widespread European relative A. scolopendrium var. scolopendrium, and five co-occurring fern species were grown from spores. Gametophytes were grown at 20°C and 25°C, and germination rates, intra- and interspecific competition, desiccation tolerance, and sporophyte production were determined for all species. KEY RESULTS: Gametophytes of A. scolopendrium var. americanum had the lowest rates of germination and sporophyte production among all species studied and exhibited the greatest sensitivity to interspecific competition, temperature increases, and desiccation. Mature gametophytes of A. scolopendrium var. americanum grown at 25°C were 84.6% smaller than those grown at 20°C, and only 1.5% produced sporophytes after 200 d in culture. Similar responses were not observed in other species studied. CONCLUSIONS: The recent declines and current status of populations of A. scolopendrium var. americanum are linked to its gametophyte's limited capacity to tolerate competition and physiological stress linked to climate change. This is the first study to develop a mechanistic understanding of rarity and decline in a fern and demonstrates the importance of considering the ecology of the gametophyte in plants with independent sporophyte and gametophyte generations.

Taxonomic importance of spore morphology of selected taxa of Asplenium (Aspleniaceae) from Pakistan.

Taxonomic importance of spore morphology of seven taxa of genus Asplenium (Aspleniaceae) from Pakistan is illustrated with SEM. Spore morphology of the taxa were monolete with bilateral symmetry, distal and proximal view were ellipsoidal, spheroidal, equatorial view were hemicircular; perispore surface were alate, costate, costate-alate, with reticulate and tuberculate ornamentation. Taxonomic importance of spore morphology of seven taxa of Asplenium (Aspleniaceae, polypodiales) from Pakistan. Basionym, Synonyms with updated nomenclature. Spores are monolete, distal and proximal view ellipsoidal, spheroidal, equatorial view hemicircular, perispore with alate, costate, reticulate, and tuberculate surface. Habitat ecology with specimens examined from different areas of Pakistan and their worldwide general distribution.

2-O-ß-d-Glucopyranosyl l-Ascorbic Acid, a Stable Form of Vitamin C, Is Widespread in Crop Plants.

2-O-ß-d-Glucopyranosyl l-ascorbic acid (AA-2ßG) is a stable, bioavailable vitamin C (AA) derivative. We report the distribution and seasonal variation of AA-2ßG in apples and its occurrence in other domesticated crops and in wild harvested Ma̅ori foods. Liquid chromatography-mass spectrometry analyses showed high AA-2ßG concentrations in crab apples (Malus sylvestris) but low concentrations in domesticated apples. Leaves of crab and domesticated apple cultivars contained similar intermediate AA-2ßG concentrations. Fruits and leaves of other crops were analyzed: mainly Rosaceae but also Actinidiaceae and Ericaceae. AA-2ßG was detected in all leaves (0.5-6.1 mg/100 g fr. wt.) but was at lower concentrations in most fruits (0.0-0.5 mg/100 g fr. wt.) except for crab apples (79.4 mg/100 g fr. wt.). Ma̅ori foods from Solanaceae, Piperaceae, Asteraceae, and a fern of Aspleniaceae also contained AA-2ßG. This extensive occurrence suggests a general role in AA metabolism for AA-2ßG.

Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity.

The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae-Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.

Development and characterization of EST-SSR markers via transcriptome sequencing in Brainea insignis (Aspleniaceae s.l.).

PREMISE OF THE STUDY: Brainea insignis (Aspleniaceae) is an endangered tree fern in China whose wild populations have been seriously damaged due to overexploitation. Expressed sequence tag-simple sequence repeat (EST-SSR) primers were developed to investigate its genetic diversity and provide resources for future conservation studies. METHODS AND RESULTS: We obtained 72,897 unigenes of B. insignis using transcriptome sequencing and detected 15,006 SSRs in 12,058 unigenes. Based on these results, we designed 100 EST-SSR primer pairs and successfully amplified 52 of them in six individuals; 27 demonstrated polymorphisms after amplification against 72 individuals across three populations. Allele numbers ranged from three to 10, and the observed and expected heterozygosities ranged from 0.105 to 1.000 and from 0.523 to 0.865, respectively, in the tested populations. Most of these primers could be successfully amplified in two other fern species (Blechnumorientale and Chieniopteris harlandii). CONCLUSIONS: These selected EST-SSRs are valuable for genetic diversity and conservation studies in B. insignis and other related fern species.