Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.

Manglietia crassipes, a critically endangered species narrowly distributed on Mount Dayao in Guangxi, China, is also a species of ornamental interest whose variability has not been explored. Key factors leading to its endangerment have also not been studied. Here, two experiments were conducted to test the effects of different plant growth regulators and different storage conditions on germination characteristics of M. crassipes seeds. Fruit morphology was measured, and germination characteristics of fresh mature seeds were tested in order to assess natural seed vigor. Seeds were soaked in distilled water (control), or gibberellic acid (GA₃), 6-benzylaminopurine (6-BA) or indoleacetic acid (IAA) solutions of different concentrations, for 48 h to determine their effects on seed germination. In addition, the effects of different seed storage conditions (constant 4 °C, −7 °C, −20 °C, or 25 °C for 100 days, wet stratification at 4 °C for 100 days) on seed germination were investigated. Results showed that the abortive rate of the mature fruits was high (28.9%) and fresh natural seeds had a low germination rate (G) and germination index (GI). Seed germination was inhibited with 6-BA at all concentrations, but only at less than 100 m·L⁻¹ IAA; otherwise, IAA slightly promoted seed germination. GA₃ broke seed dormancy and significantly accelerated seed germination by improving G, GI and initial germination time (IGT), especially over 2500 mg·L⁻¹. The viability of seeds declined no matter how they were stored. However, 4 °C wet stratification storage was preferable for seed vigor and germination power. Our results suggest that the high abortive rate of fruits, low germination of the natural seed, seed dormancy and its intolerance to storage, contributed to the endangerment of M. crassipes. GA₃ can break M. crassipes seed dormancy, which can be a benefit for future ornamental breeding and further protection or conservation.

Background: Paspalum notatum ‘Flugge’ is a diploid with 20 chromosomes (2n = 20) multi-purpose subtropical herb native to South America and has a high ecological significance. It is currently widely planted in tropical and subtropical regions. Despite the gene pool of P. notatum ‘Flugge’ being unearthed to a large extent in the past decade, no details about the genomic information of relevant species in Paspalum have been reported. In this study, the complete genome information of P. notatum was established and annotated through sequencing and de novo assembly of its genome. Results: The latest PacBio third-generation HiFi assembly and sequencing revealed that the genome size of P. notatum ‘Flugge’ is 541 M. The assembly result is the higher index among the genomes of the gramineous family published so far, with a contig N50 = 52Mbp, scaffold N50 = 49Mbp, and BUSCOs = 98.1%, accounting for 98.5% of the estimated genome. Genome annotation revealed 36,511 high-confidence gene models, thus providing an important resource for future molecular breeding and evolutionary research. A comparison of the genome annotation results of P. notatum ‘Flugge’ with other closely related species revealed that it had a close relationship with Zea mays but not close compared to Brachypodium distachyon, Setaria viridis, Oryza sativa, Puccinellia tenuiflora, Echinochloa crusgalli. An analysis of the expansion and contraction of gene families suggested that P. notatum ‘Flugge’ contains gene families associated with environmental resistance, increased reproductive ability, and molecular evolution, which explained its excellent agronomic traits. Conclusion: This study is the first to report the high-quality chromosome-scale-based genome of P. notatum ‘Flugge’ assembled using the latest PacBio third-generation HiFi sequencing reads. The study provides an excellent genetic resource bank for gramineous crops and invaluable perspectives regarding the evolution of gramineous plants.

Chesneya acaulis is a perennial herb, which restricts in Xizang (Tibet) of China, Afghanistan, and Pakistan. The complete chloroplast genome was sequenced using the Illumina Hiseq X-Ten platform. The genome lacks an inverted repeat (IR) region, containing 75 protein-coding genes, 29 tRNAs genes, and 4 rRNAs. The overall GC content is 34.6%. A phylogenetic tree based on the whole chloroplast genomes of 15 species indicated that C. acaulis had a close relationship with the genus Hedysarum, and it nested in the inverted repeat-lacking clade (IRLC), of the subfamily Papilionoideae (Leguminosae).

Chromosome traits may differ between closely related ferns growing in different geological landscapes. Adiantum series Gravesiana (Pteridaceae) includes six species, of which, five species are exclusively distributed in Karst landforms, and one, Adiantum juxtapositum, grows on Danxia landform. Additionally, there are some populations or individuals whose morphology are between different species, which may be the results of polyploidization or hybridization. Here we studied chromosome numbers of species in series Gravesiana primarily using crosiers. Results are: A. longzhouensis and A. juxtapositum were diploids with 2n = 60 and 2n = 64, respectively; A. dentatum was deduced to be diploids with 2n = ca. 60; A. mariesii had two cytotypes, 2n = 60 (diploid) and 2n = ca. 120 (tetraploid), respectively; A. gravesii had four cytotypes including 2n = ca. 60 (diploid), ca. 120 (tetraploid), ca. 150 (pentaploid), and ca. 180 (hexaploid). All these different cytotypes suggest polyploidization and hybridization have occurred in A. gravesii and A. mariesii, so we treated these two species as two “complex group”. All chromosome numbers in this study are the first record.

The ferns of Adiantum Series Gravesiana (Pteridaceae) consist of species that occur exclusively on Danxia (A. juxtapositum) and Karst (A. mariesii, A. longzhouensis, A. dentatum, A. obovatum, and A. gravesii) landforms. We cultured representatives of these six species from 20 different populations on both agar and soil to investigate and compare their gametophyte development. All species had the Vittaria-type pattern of spore germination except A. obovatum, for which we missed the best time to observe this developmental phase. However, two different patterns of subsequent development were observed: the Adiantum-type (i.e., naked, cordate mature gametophyte thallus) in A. mariesii, A. longzhouensis, A. juxtapositum, and A. gravesii and the Kaulinia-type (i.e., naked, ribbon-shaped mature gametophyte thallus) in A. dentatum and A. obovatum. All populations from A. juxtapositum and A. gravesii possess the same Adiantum-type, suggesting that Karst and Danxia soils were not the main factor causing the differences in gametophyte development. The Kaulinia-type adult thallus has not been observed previously in Adiantum and may be an adaptive strategy for survival within the relatively harsh micro-habitats experienced by A. dentatum and A. obovatum compared to other members of this series.