Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna

Kato Y., Nitta J.H., Perez C.A.G., et al. Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Scientific Reports 14, 9407 (2024); https://doi.org/10.1038/s41598-024-59774-1.The cladoceran crustacean Daphnia exhibits phenotypic plasticity, a phenomenon that leads to diverse phenotypes from one genome. Alternative usage of gene isoforms has been considered a key gene regulation mechanism for controlling different phenotypes. However, to understand the phenotypic plasticity of Daphnia, gene isoforms have not been comprehensively analyzed. Here we identified 25,654 transcripts derived from the 9710 genes expressed during environmental sex determination of Daphnia magna using the long-read RNA-Seq with PacBio Iso-Seq. We found that 14,924 transcripts were previously unidentified and 5713 genes produced two or more isoforms. By a combination of Illumina short-read RNA-Seq, we detected 824 genes that implemented switching of the highest expressed isoform between females and males. Among the 824 genes, we found isoform switching of an ortholog of CREB-regulated transcription coactivator, a major regulator of carbohydrate metabolism in animals, and a correlation of this switching event with the sexually dimorphic expression of carbohydrate metabolic genes. These results suggest that a comprehensive catalog of isoforms may lead to understanding the molecular basis for environmental sex determination of Daphnia. We also infer the applicability of the full-length isoform analyses to the elucidation of phenotypic plasticity in Daphnia

Molecular Species Identification with Rich Floristic Sampling: DNA Barcoding the Pteridophyte Flora of Japan

BACKGROUND: DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking. METHODOLOGY/PRINCIPAL FINDINGS: The Japanese pteridophyte flora (733 taxa including subspecies and varieties) was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA) with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0%) taxa for rbcL and 617 (84.2%) taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances) did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52%) was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only. CONCLUSIONS/SIGNIFICANCE: This study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially anticipated to be helpful for identification of non-hybridizing gametophytes

Distribution, Ecology, and Systematics of the Filmy Ferns (Hymenophyllaceae) of Moorea, French Polynesia

Ferns present an interesting case in island biogeography because of their unusually high dispersal ability. A general survey of the filmy ferns (Hymenophyllaceae) of Moorea, French Polynesia was undertaken by observing distribution in the field, conducting tests of desiccation tolerance, and inferring a phylogeny based on morphological characters. A total of 12 filmy fern species (including three species previously unreported in the literature for Moorea) were found to occur in moist, wellcovered habitats throughout the island, with distinct sets of high elevation and low elevation species. Five species were included in an experiment to determine relative degree of desiccation tolerance; results indicate that terrestrial species have lower desiccation tolerance than epiphytic or epipetric species. In order to place the Moorea filmy ferns in the larger archipelago context, eight additional Society Island species were included in the phylogeny for a total of 20 taxa based on 21 morphological characters; interspecies relationships reflect the taxonomy of Hymenophyllaceae sensu lato. Filmy fern species are widely dispersed throughout the Society Islands, and there is no indication of an adaptive radiation on Moorea

Ecology and Evolution of the Ferns of Moorea and Tahiti, French Polynesia

Ferns are the only major lineage of land plants with haploid (gametophyte) and diploid (sporophyte) stages that can grow separately from each other for extended periods. Gametophytes, as the sexual stage, are critical to fern evolution. However, the ecology of fern gametophytes is poorly known due to their small size and cryptic morphology. In this dissertation, I use the ferns of Moorea and Tahiti, French Polynesia to investigate the relative roles of sporophytes and gametophytes in community assembly and evolution. In Chapter 1, I use DNA sequences to identify field-collected gametophytes to species and compare community diversity between fern sporophytes and gametophytes on Moorea and Tahiti. I find that phylogenetic community diversity decreases with elevation in sporophytes, but not gametophytes. I observe several species with gametophytes that are distributed beyond the range of conspecific sporophytes, and at least one species that may lack sporophytes on the islands completely. My results suggest that the transition from gametophyte to sporophyte functions as a filter restricting phylogenetic diversity of fern communities. In Chapter 2, I use the filmy ferns (Hymenophyllaceae) of Moorea to investigate how changes in physiology between fern gametophytes and sporophytes are correlated with ecological niche. I find that the gametophytes of filmy ferns are not more stress-tolerant than sporophytes. Rather, they are adapted for microhabitats that are buffered relative to those of sporophytes. I suggest that the gametophytes of filmy ferns rely on asexual reproduction via gemmae to achieve dense population sizes over a wide range. In Chapter 3, I conduct a phylogenetic investigation of epiphytic traits in the ferns of Moorea. I find that epiphytes tend to have shorter stipes, smaller rhizomes, and gametophytes with non-cordate morphotypes relative to terrestrial species. I demonstrate that epiphytic communities are clustered phylogenetically and functionally relative to terrestrial communities, supporting a scenario of extreme environmental conditions in the forest canopy acting as a filter on epiphytic ferns. In Chapter 4, I describe a new hybrid fern species, Microsorum × tohieaense, from Moorea based on morphological and molecular phylogenetic analysis, and discuss the significance of my findings to the taxonomy of microsoroid ferns.Biology, Organismic and Evolutionar

Data from: Microsorum × tohieaense (Polypodiaceae), a new hybrid fern from French Polynesia, with implications for the taxonomy of Microsorum

A new hybrid microsoroid fern, Microsorum × tohieaense (Microsorum commutatum × Microsorum membranifolium) from Moorea, French Polynesia is described based on morphology and molecular phylogenetic analysis. Microsorum × tohieaense can be distinguished from other French Polynesian Microsorum by the combination of sori that are distributed more or less in a single line between the costae and margins, apical pinna wider than lateral pinnae, and round rhizome scales with entire margins. Genetic evidence is also presented for the first time supporting the hybrid origin of Microsorum × maximum (Microsorum grossum × Microsorum punctatum), and possibly indicating a hybrid origin for the Hawaiian endemic Microsorum spectrum. The implications of hybridization for the taxonomy of microsoroid ferns are discussed, and a key to the microsoroid ferns of the Society Islands is provided

A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica.

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras

Pteridophytes of Mo\u27orea, French Polynesia: Additional New Records

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data_and_scripts

This zip file includes the data and scripts used to perform the analyses in our paper, including assembling a DNA alignment of all ferns on GenBank for three gene regions, phylogenetic analysis, identification of unknown fern gametophytes using a DNA barcode, and community phylogenetic analyses