The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing

Dicranum motuoense (Bryophyta): A New Taxon from China, with Special References to Its Complete Organelle Genomes

Dicranum is one of the most diverse and widespread genera within the family Dicranaceae, encompassing ca. 110 accepted species worldwide. However, the taxonomy of this genus remains notoriously complex, with the circumscription of several species still unresolved, thereby limiting our understanding of the Dicranum's diversity. During a recent survey of Dicranum in China, we found an intriguing species characterized by a unique combination of morphological traits including stiff and fragile leaves, sharply denticulate leaf apices, elongated, rectangular and porose laminal cells throughout, bistratose or partially bistratose laminal cells in the distal part, 1-2 stratose alar cells, and a transverse section of the costa in the lower portion of leaf with two stereid bands and undifferentiated epidermal layers. Morphological and molecular phylogenetic analyses, based on five chloroplast markers and one nuclear marker, support the recognition of this moss as a new species, which we described here as Dicranum motuoense sp. nov. Furthermore, we present the complete organellar genomes of this newly identified species. The chloroplast genome of D. motuoense is 123.94 kb in length, while the mitochondrial genome is 105.77 kb in length. A total of 127 genes and 66 genes were identified in the chloroplast and mitochondrial genomes, respectively. This study not only advances our understanding of species diversity with Dicranum but also contributes to the broader knowledge of its evolution. Additionally, a key for the identification of Dicranum species with fragile leaves is included.

From barcodes to genomes: a new era of molecular exploration in bryophyte research

Bryophytes represent a diverse and species-rich group of plants, characterized by a remarkable array of morphological variations. Due to their significant ecological and economic roles worldwide, accurate identification of bryophyte taxa is crucial. However, the variability in morphological traits often complicates their proper identification and subsequent commercial utilization. DNA barcoding has emerged as a valuable tool for the precise identification of bryophyte taxa, facilitating comparisons at both interspecific and intraspecific levels. Recent research involving plastomes, mitogenomes, and transcriptomes of various bryophyte species has provided insights into molecular changes and gene expression in response to environmental stressors. Advances in molecular phylogenetics have shed light on the origin and evolutionary history of bryophytes, thereby clarifying their phylogenetic relationships. Despite these advancements, a comprehensive understanding of the systematic relationships within bryophytes is still lacking. This review synthesizes current molecular studies that have been instrumental in unraveling the complexity of bryophyte taxonomy and systematics. By highlighting key findings from recent genetic and genomic research, we underscore the importance of integrating molecular data with traditional morphological approaches. Such integration is essential for refining the classification systems of bryophytes and for understanding their adaptive strategies in various ecological niches. Future research should focus on expanding the molecular datasets across underrepresented bryophyte lineages and exploring the functional significance of genetic variations under different environmental conditions. This will not only enhance our knowledge of bryophyte evolution, but also inform conservation strategies and potential applications in biotechnology.

Complete Organelle Genome of the Desiccation-Tolerant (DT) Moss Tortula atrovirens and Comparative Analysis of the Pottiaceae Family

Tortula atrovirens (Sm.) Lindb. is an important component of biological soil crusts and possesses an extraordinary tolerance against desiccation in dryland habitats. However, knowledge of the organelle genome of this desiccation-tolerant (DT) moss is still lacking. Here, we assembled the first reported Tortula organelle genome and conducted a comprehensive analysis within the Pottiaceae family. T. atrovirens exhibited the second largest chloroplast genome (129,646 bp) within the Pottiaceae, whereas its mitogenome (105,877 bp) and those of other mosses were smaller in size compared to other land plants. The chloroplast and mitochondrial genomes of T. atrovirens were characterized by the expansion of IR boundaries and the absence of homologous recombination-mediated by large repeats. A total of 57 RNA editing sites were detected through mapping RNA-seq data. Moreover, the gene content and order were highly conserved among the Pottiaceae organelle genomes. Phylogenetic analysis showed that bryophytes are paraphyletic, with their three lineages (hornworts, mosses, and liverworts) and vascular plants forming successive sister clades. Timmiella anomala is clearly separated from the monophyletic Pottiaceae, and T. atrovirens is closely related to Syntrichia filaris within the Pottioideae. In addition, we detected four hypervariable regions for candidate-molecular markers. Our findings provide valuable insights into the organelle genomes of T. atrovirens and the evolutionary relationships within the Pottiaceae family, facilitating future discovery of DT genetic resources from bryophytes.

Characterization of the complete chloroplast genome of Barbella flagellifera (Cardot) Nog. 1938 (Bryidae, Meteoriaceae)

Whether Barbella flagellifera (Cardot) Nog. belongs to Neodicladiella has not yet been determined, and a study of the complete chloroplast (cp) genome of B. flagellifera would aid in determining its evolutionary position. In this study, we aimed to sequence the complete cp genome of B. flagellifera, an epiphytic species found in tropical and subtropical forests. The complete cp genome is 125,025 base pairs (bp) long and appears as a typical quadrilateral structure with a large single-copy (86,854 bp), a small single-copy (18,473 bp), and a pair of inverted repeats (19,698 bp). The overall GC content of the sequence is 41.0% and the genome encodes 127 genes, including 82 protein-coding genes, 37 tRNAs, and eight rRNAs. Phylogenetic analysis reveals that B. flagellifera clustered into a clade with other Hypnales groups with high bootstrap support. The complete cp genome presented here will provide helpful information for species identification of Barbella genus and Neodicladiella genus in Meteoriaceae.

Plastome diversity and evolution in mosses: Insights from structural characterization, comparative genomics, and phylogenetic analysis

Mosses play a significant role in ecology, evolution, and the economy. They belong to the nonvascular plant kingdom and are considered the closest living relatives of the first terrestrial plants. The circular chloroplast DNA molecules (plastomes) of mosses contain all the genetic information essential for chloroplast functions and represent the source of the evolutionary history of these organisms. This study comprehensively analyzed the plastomes of 47 moss species belonging to 14 orders, focusing on their size, GC content, gene loss, gene content, synteny, and evolution. The findings revealed great differences among plastome sizes, with Takakia lepidozioides (Takakiopsida) and Funaria hygrometrica (Funariales) having the largest and smallest plastomes, respectively. Moss plastomes included 69 to 89 protein-coding genes, 8 rRNA genes, and 34 to 42 tRNA genes, resulting in the total number of genes in a plastome ranging between 115 and 138. Various genes have been lost from the plastomes of different moss species, with Atrichum angustatum lacking the highest number of genes. This study also examined plastome synteny and moss evolution using comparative genomics and repeat sequence analysis. The results demonstrated that synteny and similarity levels varied across the 47 moss examined species, with some exhibiting structure similarity and others displaying structural inversions. Maximum likelihood and Bayesian approaches were used to construct a phylogenetic tree using 36 concatenated protein-coding genes, and the results revealed that the genera Sphagnum and Takakia are sister groups to the other mosses. Additionally, it was found that Tetraphidales, Polytrichales, Buxbaumiales, and Diphysciales are closely related. This research describes the evolutionary diversity of mosses and offers guidelines for future studies in this field. The findings also highlight the need for more investigations into the factors regulating plastome size variation in these plants.

Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet

The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010-2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.

Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56

The mitochondrial C-to-U RNA editing factor PPR56 of the moss Physcomitrium patens is an RNA-binding pentatricopeptide repeat protein equipped with a terminal DYW-type cytidine deaminase domain. Transferred into Escherichia coli, PPR56 works faithfully on its two native RNA editing targets, nad3eU230SL and nad4eU272SL, and also converts cytidines into uridines at over 100 off-targets in the bacterial transcriptome. Accordingly, PPR56 is attractive for detailed mechanistic studies in the heterologous bacterial setup, allowing for scoring differential RNA editing activities of many target and protein variants in reasonable time. Here, we report (i) on the effects of numerous individual and combined PPR56 protein and target modifications, (ii) on the spectrum of off-target C-to-U editing in the bacterial background transcriptome for PPR56 and two variants engineered for target re-direction and (iii) on combinations of targets in tandem or separately at the 5'- and 3'-ends of large mRNAs. The latter experimentation finds enhancement of RNA editing at weak targets in many cases, including cox3eU290SF as a new candidate mitogenome target. We conclude that C-to-U RNA editing can be much enhanced by transcript features also outside the region ultimately targeted by PPRs of a plant editing factor, possibly facilitated by its enrichment or scanning along transcripts.