MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data.

Advances in next-generation sequencing (NGS) technologies have led to an exponential increase in the number of whole genome sequences (WGS) in databases. This wealth of WGS data has greatly facilitated the recovery of full mitochondrial genomes (mitogenomes), which are vital for phylogenetic, evolutionary and ecological studies. Unfortunately, most existing software cannot easily assemble mitogenome reference sequences conveniently or efficiently. Therefore, we developed a seed-free de novo assembly tool, MEANGS, which applies the trie-search method to extend contigs from self-discovery seeds and assemble a mitogenome from animal WGS data. We then used data from 16 species with different qualities to compare the performance of MEANGS with three other available programs. MEANGS exhibited the best overall performance since it was the only one that completed all tests, and it assembled full or partial mitogenomes for all of the tested samples while the others failed. Furthermore, MEANGS selects superior assembly sequences and annotates protein-coding genes. Thus, MEANGS can be one of the most efficient software for generating high-quality mitogenomes so far, the further use of it will benefit the study on mitogenome based on whole genome NGS data. MEANGS is available at https://github.com/YanCCscu/meangs.

Timing of meristem initiation and maintenance determines the morphology of fern gametophytes.

The alternation of generations in land plants occurs between the sporophyte phase and the gametophyte phase. The sporophytes of seed plants develop self-maintained, multicellular meristems, and these meristems determine plant architecture. The gametophytes of seed plants lack meristems and are heterotrophic. In contrast, the gametophytes of seed-free vascular plants, including ferns, are autotrophic and free-living, developing meristems to sustain their independent growth and proliferation. Compared with meristems in the sporophytes of seed plants, the cellular mechanisms underlying meristem development in fern gametophytes remain largely unknown. Here, using confocal time-lapse live imaging and computational segmentation and quantification, we determined different patterns of cell divisions associated with the initiation and proliferation of two distinct types of meristems in gametophytes of two closely related Pteridaceae ferns, Pteris vittata and Ceratopteris richardii. Our results reveal how the simple timing of a switch between two meristems has considerable consequences for the divergent gametophyte morphologies of the two ferns. They further provide evolutionary insight into the function and regulation of gametophyte meristems in seed-free vascular plants.

Influence of Temperature on the Formation of Silver Nanoparticles by using a Seed-Free Photochemical Method under Sodium-Lamp Irradiation.

Silver nanoparticles can be prepared by using a seed-free photo-assisted citrate reduction method under the irradiation of a sodium lamp. Under the same irradiation intensity, bath temperatures are crucial in influencing the reaction rate, morphologies of final products, and shape evolution of the silver nanostructures. For example, when the bath temperature is 80 °C, the product yields of silver nanoplates, nanorods, and nanodecahedra are 38±6 %, 35±10 %, and 12±8 %, respectively. However, when the bath temperature is 30 °C, the product yields of silver nanoplates, nanorods, and nanodecahedra are 6±3 %, 0 %, and 83±16 %, respectively. Time-dependent UV/Vis spectra and TEM images show that silver nanoplates were formed at the earlier reaction stage and greatly decreased in amount at the later stage when the bath temperatures are less than or equal to 40 °C. This indicates that the silver nanoplates, which can be regarded as intermediates, are kinetically favored products. They are not thermodynamically favored products at these relatively low bath temperatures. The SERS spectra of crystal violet (CV) show that all the silver colloids synthesized at various temperatures exhibit good enhancement factors and that the colloids prepared at lower bath temperatures have a higher enhancement factor.

Organellar-genome analyses from the lycophyte genus Isoetes L. show one of the highest frequencies of RNA editing in land plants.

RNA editing is a post-transcriptional process that challenges the central dogma of molecular biology by modifying RNA sequences, introducing nucleotide changes at specific sites, and generating functional diversity beyond the genomic code, especially when it concerns organellar transcripts. In plants, this phenomenon is widespread, but its extent varies significantly among species and organellar genomes. Among land plants, the heterosporous lycophytes (i.e., Isoetes and Selaginella) stand out for their exceptionally high numbers of RNA-editing sites, despite their morphological stasis and ancient lineage. In this study, we explore the complete set of organellar protein-coding genes in the aquatic plant group Isoetes, providing a detailed analysis of RNA editing in both the mitochondrial and plastid genomes. Our findings reveal a remarkable abundance of RNA editing, particularly in the mitochondrial genome, with thousands of editing sites identified. Interestingly, the majority of these edits result in non-silent substitutions, suggesting a role in fine-tuning protein structure and function. Furthermore, we observe a consistent trend of increased hydrophobicity in membrane-bound proteins, supporting the notion that RNA editing may confer a selective advantage by preserving gene functionality in Isoetes. The conservation of highly edited RNA sequences over millions of years underscores the evolutionary significance of RNA editing. Additionally, the study sheds light on the dynamic nature of RNA editing, with shared editing sites reflecting common ancestry whereas exclusive edits matching more recent radiation events within the genus. This work advances our understanding of the intricate interplay between RNA editing, adaptation, and evolution in land plants and highlights the unique genomic features of Isoetes, providing a foundation for further investigations into the functional consequences of RNA editing in this enigmatic plant lineage.

A conserved GRAS-domain transcriptional regulator links meristem indeterminacy to sex determination in Ceratopteris gametophytes.

Most land plants alternate between generations of sexual gametophytes and asexual sporophytes. Unlike seed plants, fern gametophytes are free living and grow independently of their sporophytes. In homosporous ferns such as Ceratopteris, gametophytes derived from genetically identical spores exhibit sexual dimorphism, developing as either males or hermaphrodites. Males lack meristems and promote cell differentiation into sperm-producing antheridia. In contrast, hermaphrodites initiate multicellular meristems that stay undifferentiated, sustain cell division and prothallus expansion, and drive the formation of egg-producing archegonia. Once initiating the meristem, hermaphrodites secrete the pheromone antheridiogen, which triggers neighboring slower-growing gametophytes to develop as males, while the hermaphrodites themselves remain insensitive to antheridiogen. This strategy promotes outcrossing and prevents all individuals in the colony from becoming males. This study reveals that an evolutionarily conserved GRAS-domain transcriptional regulator (CrHAM), directly repressed by Ceratopteris microRNA171 (CrmiR171), promotes meristem development in Ceratopteris gametophytes and determines the male-to-hermaphrodite ratio in the colony. CrHAM preferentially accumulates within the meristems of hermaphrodites but is excluded from differentiated antheridia. CrHAM sustains meristem proliferation and cell division through conserved hormone pathways. In the meantime, CrHAM inhibits the antheridiogen-induced conversion of hermaphrodites to males by suppressing the male program expression and preventing meristem cells from differentiating into sperm-producing antheridia. This finding establishes a connection between meristem indeterminacy and sex determination in ferns, suggesting both conserved and diversified roles of meristem regulators in land plants.

Seed-free synthesis of 1D silver nanowires ink using clove oil (Syzygium Aromaticum) at room temperature.

HYPOTHESIS: Silver nanowires (AgNWs) have been demonstrated to be a promising next generation conducting material and an alternative to the traditional electrode (ITO) because of its high conductivity, transparency and stability. Generally, AgNWs are synthesized by chemical method (mainly polyol reduction method) at high temperature in the presence of exotic seeds. The present work aims at the green approach for preparation and characterization of 1D AgNWs ink using clove oil (Syzygium Aromaticum) at room temperature. EXPERIMENTS: AgNWs was prepared by green synthesis using clove oil as reducing as well as capping agent at room temperature. The obtained ink was purified, filtered and redissolved in methanol. FINDINGS: The prepared AgNWs showed an absorption peaks at 350 and 387nm in the UV-vis spectrum due to transverse SPR mode of silver. From the HR-TEM analysis, it was observed that the AgNWs possess an average diameter and length of ∼39±0.01nm and ∼3µm, respectively. The obtained AgNWs are crystalline in nature and are arranged in a perfect crystal lattice orientation, which was confirmed from the selected area electron diffraction studies. Moreover, the X-ray diffraction analysis confirms the face centered cubic structure. The AgNWs coated glass substrate shows an electrical conductivity of ∼0.48×10(6)S/m.