A molecular phylogeny of the bladed Bangiales (Rhodophyta) in China provides insights into biodiversity and biogeography of the genus Pyropia

Life cycle and reproduction dynamics of Bangiales in response to environmental stresses

Red algae of the order Bangiales are notable for exhibiting flexible promotion of sexual and asexual reproductive processes by environmental stresses. This flexibility indicates that a trade-off between vegetative growth and reproduction occurs in response to environmental stresses that influence the timing of phase transition within the life cycle. Despite their high phylogenetic divergence, both filamentous and foliose red alga in the order Bangiales exhibit a haploid-diploid life cycle, with a haploid leafy or filamentous gametophyte (thallus) and a diploid filamentous sporophyte (conchocelis). Unlike haploid-diploid life cycles in other orders, the gametophyte in Bangiales is generated independently of meiosis; the regulation of this generation transition is not fully understood. Based on transcriptome and gene expression analyses, the originally proposed biphasic model for alternation of generations in Bangiales was recently updated to include a third stage. Along with the haploid gametophyte and diploid sporophyte, the triphasic framework recognizes a diploid conchosporophyte-a conchosporangium generated on the conchocelis-phase and previously considered to be part of the sporophyte. In addition to this sexual life cycle, some Bangiales species have an asexual life cycle in which vegetative cells of the thallus develop into haploid asexual spores, which are then released from the thallus to produce clonal thalli. Here, we summarize the current knowledge of the triphasic life cycle and life cycle trade-off in Neopyropia yezoensis and 'Bangia' sp. as model organisms for the Bangiales.

The Identification of Filamentous Cyanobacteria Isolated from Neopyropia Germplasm Bank Illustrates the Pattern of Contamination

The germplasm bank of economic algae provides biological insurance against environmental changes and pressures for the cultivation industry. However, the red algal free-living conchocelis germplasm of Neopyropia was easily contaminated with filamentous cyanobacteria, which severely affected the growth of Neopyropia germplasm. To date, what and how the filamentous cyanobacteria contaminated Neopyropia germplasm remained unknown. Here, we combined cytological observations with light and electron microscopes and molecular analysis of the 16S rRNA gene to elucidate the pattern of cyanobacteria contamination. Nine filamentous cyanobacteria samples isolated from the Neopyropia germplasm bank were selected. Integrating microscopy observations and phylogenetic analyses of 16S rRNA gene sequences, nine cyanobacteria samples were divided into three groups, including two Leptolyngbya with red pigments (YCR1 and YCR2) and one Nodosilinea with green pigments (YCG3). They had the same asexual reproduction mode, releasing hormogonia to grow new filaments. Due to the high reproductive ability, Leptolyngbya and Nodosilinea were easy to spread in the Neopyropia germplasm. Based on 16S rRNA gene high-throughput sequencing analyses, we found the thallus of Neopyropia (NP1, NP2, and NP3) and surrounding seawater (SW1, SW2, and SW3) were enriched with cyanobacteria, especially with Leptolyngbya and Nodosilinea, indicating the filamentous cyanobacteria contaminated Neopyropia germplasm came from the thallus of Neopyropia or seawater. The results provided a better understanding of the prevention and control of cyanobacteria contamination in the Neopyropia germplasm bank.

Migration patterns of Gentiana crassicaulis , an alpine gentian endemic to the Himalaya–Hengduan Mountains

The Himalaya–Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai–Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological niche models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.

Biogeographic Population Structure of Chimeric Blades of Porphyra in the Northeast Atlantic Reveals Southern Rich Gene Pools, Introgression and Cryptic Plasticity

The genus Porphyra sensu lato (Bangiaceae, Rhodophyta), an important seaweed grown in aquaculture, is the most genetically diverse group of the Class Bangiophyceae, but has poorly understood genetic variability linked to complex evolutionary processes. Genetic studies in the last decades have largely focused on resolving gene phylogenies; however, there is little information on historical population biogeography, structure and gene flow in the Bangiaceae, probably due to their cryptic nature, chimerism and polyploidy, which render analyses challenging. This study aims to understand biogeographic population structure in the two abundant Porphyra species in the Northeast Atlantic: Porphyra dioica (a dioecious annual) and Porphyra linearis (protandrous hermaphroditic winter annual), occupying distinct niches (seasonality and position on the shore). Here, we present a large-scale biogeographic genetic analysis across their distribution in the Northeast Atlantic, using 10 microsatellites and cpDNA as genetic markers and integrating chimerism and polyploidy, including simulations considering alleles derived from different ploidy levels and/or from different genotypes within the chimeric blade. For P. linearis, both markers revealed strong genetic differentiation of north-central eastern Atlantic populations (from Iceland to the Basque region of Northeast Iberia) vs. southern populations (Galicia in Northwest Iberia, and Portugal), with higher genetic diversity in the south vs. a northern homogenous low diversity. For. P. dioica, microsatellite analyses also revealed two genetic regions, but with weaker differentiation, and cpDNA revealed little structure with all the haplotypes mixed across its distribution. The southern cluster in P. linearis also included introgressed individuals with cpDNA from P. dioica and a winter form of P. dioica occurred spatially intermixed with P. linearis. This third entity had a similar morphology and seasonality as P. linearis but genomes (either nuclear or chloroplast) from P. dioica. We hypothesize a northward colonization from southern Europe (where the ancestral populations reside and host most of the gene pool of these species). In P. linearis recently established populations colonized the north resulting in homogeneous low diversity, whereas for P. dioica the signature of this colonization is not as obvious due to hypothetical higher gene flow among populations, possibly linked to its reproductive biology and annual life history.

Floridean Starch and Floridoside Metabolic Pathways of Neoporphyra haitanensis and Their Regulatory Mechanism under Continuous Darkness

Floridean starch and floridoside are the main storage carbohydrates of red algae. However, their complete metabolic pathways and the origin, function, and regulatory mechanism of their pathway genes have not been fully elucidated. In this study, we identified their metabolic pathway genes and analyzed the changes in related gene expression and metabolite content in Neoporphyra haitanensis under continuous dark conditions. Our results showed that genes from different sources, including eukaryotic hosts, cyanobacteria, and bacteria, were combined to construct floridean starch and floridoside metabolic pathways in N. haitanensis. Moreover, compared with those in the control, under continuous dark conditions, floridean starch biosynthesis genes and some degradation genes were significantly upregulated with no significant change in floridean starch content, whereas floridoside degradation genes were significantly upregulated with a significant decrease in floridoside content. This implies that floridean starch content is maintained but floridoside is consumed in N. haitanensis under dark conditions. This study elucidates the "floridean starch-floridoside" metabolic network and its gene origins in N. haitanensis for the first time.

Genomic diversity of 39 samples of Pyropia species grown in Japan

Some Pyropia species, such as nori (P. yezoensis), are important marine crops. We conducted a phylogenetic analysis of 39 samples of Pyropia species grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and Chinese P. yezoensis. Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and Chinese P. yezoensis. Analysis of organellar genomes showed that the genetic diversity of Japanese P. yezoensis used in this study is lower than that of Chinese wild P. yezoensis. To analyze the genetic relationships between samples of Japanese Pyropia, we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding between P. yezoensis and P. tenera, nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of Japanese P. yezoensis is low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain of P. yezoensis showed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation of Pyropia species.

The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.

Redefining Pyropia (Bangiales, Rhodophyta): Four New Genera, Resurrection of Porphyrella and Description of Calidia pseudolobata sp. nov. From China

The cosmopolitan red algal genus Pyropia sensu lato is the most speciose of the bladed Bangiales genera. In a major revision of the Bangiales, Pyropia was resurrected from Porphyra, although there was evidence at the time that species of Pyropia could be separated into several genera. Subsequent global phylogenetic analyses continued to resolve species assigned to Pyropia into several major clades with strong support, and the latest biogeographic analyses indicated that species distribution was also a pointer to the underlying phylogeny of Pyropia sensu lato. Therefore, in the present study, we have redefined the genus Pyropia, resurrected Porphyrella, and proposed four new genera: Calidia, Neoporphyra, Neopyropia, and Uedaea. Based on a molecular phylogenetic study of the bladed Bangiales of China, a species which did not match any known taxa was resolved in the new genus Calidia. The species, Calidia pseudolobata sp. nov., is described based on both morphological and molecular data. Molecular sequence data for rbcL, 18S, and COI-5P were amplified for 15 samples in the present study. All the obtained rbcL sequences were identical to each other except for one (LYCN117) with one base pair difference. Two haplotypes of 18S (V9 region) were observed with one base pair difference (C/T₃₀ ). All the obtained COI-5P sequences were identical. Morphological comparisons were conducted not only with species in Calidia, but also with generically uncertain species currently assigned to Porphyra.

Extensive cryptic diversity in the widely distributed Polysiphonia scopulorum (Rhodomelaceae, Rhodophyta): Molecular species delimitation and morphometric analyses

Our knowledge of seaweed diversity and biogeography still largely relies on information derived from morphological identifications, but the use of molecular tools is revealing that cryptic diversity is common among algae. Polysiphonia scopulorum is a turf-forming red alga widely reported in tropical and temperate coasts worldwide. The only study based on material collected from its Australian type locality and the Iberian Peninsula indicates that it is a species complex, but the extent of cryptic diversity across its geographical range is not known. To investigate the species diversity in P. scopulorum, the geographical distribution of species-level lineages and their morphological characterization, we collected 135 specimens from Australia, South Africa and southern Europe. Two gene datasets (cox1 and rbcL) were used to delimit species using three methods (GMYC, PTP, ABGD), leading to a consensus result that our collections of the P. scopulorum complex comprise 12 species. Five of these species were resolved in a highly supported clade, while the other seven species were related to other taxonomically accepted species or in unresolved parts of the tree. Morphometric and statistical analysis of a set of ten quantitative characters showed that there are no clear morphological correlates of species boundaries, demonstrating true cryptic diversity in the P. scopulorum complex. Distribution patterns of the 12 species were variable, ranging from species only known from a single site to species with a wide distribution spanning three continents. Our study indicates that a significant level of undiscovered cryptic diversity is likely to be found in algal turfs, a type of seaweed community formed by small entangled species.

Genetic and morphological differentiation of Porphyra and Pyropia species (Bangiales, Rhodophyta) coexisting in a rocky intertidal in Central Chile

A recent molecular taxonomic study along the Chilean coast (18° S-53° S) described 18 candidate species of bladed Bangiales of which only two were formally described. Few studies focused on local genetic and morphological diversity of bladed Bangiales and attempted to determine their intertidal distribution in contrasting habitats, and none were performed in Chile. To delimit intertidal distributions of genetic species, 66 samples of bladed Bangiales were collected at Maitencillo (32° S) in four zones: a rocky platform, a rocky wall, and two boulders zones surrounded by sandy and rocky bottoms, respectively. These samples were identified based on sequences of the mitochondrial COI and chloroplast rbcL markers. We also collected 87 specimens for morphological characterization of the most common species, rapidly assessing their putative species identity using newly developed species-diagnostic (PCR-RFLP) markers. Eight microscopic and two macroscopic morphological traits were measured. We described and named three of four species that predominate in Maitencillo (including Pyropia orbicularis): Pyropia variabilis Zapata, Meynard, Ramírez, Contreras-Porcia, sp. nov., Porphyra luchea Meynard, Ramírez, Contreras-Porcia sp. nov., and Porphyra longissima Meynard, Ramírez, Contreras-Porcia, sp. nov. With the exception of Po. longissima restricted to boulders surrounded by sandy bottom, and a morphotype of Py. variabilis restricted to rocky walls, the other species/morphotypes have overlapping intertidal distributions. Except for Po. longissima, which is clearly differentiated morphologically (longest and thinnest blades), we conclude that morphology is not sufficient to differentiate bladed Bangiales. Our findings underscore the importance of refining our knowledge of intrinsic and environmental determinants on the distribution of bladed Bangiales.