A designer synthetic chromosome fragment functions in moss.

Rapid advances in DNA synthesis techniques have enabled the assembly and engineering of viral and microbial genomes, presenting new opportunities for synthetic genomics in multicellular eukaryotic organisms. These organisms, characterized by larger genomes, abundant transposons and extensive epigenetic regulation, pose unique challenges. Here we report the in vivo assembly of chromosomal fragments in the moss Physcomitrium patens, producing phenotypically virtually wild-type lines in which one-third of the coding region of a chromosomal arm is replaced by redesigned, chemically synthesized fragments. By eliminating 55.8% of a 155 kb endogenous chromosomal region, we substantially simplified the genome without discernible phenotypic effects, implying that many transposable elements may minimally impact growth. We also introduced other sequence modifications, such as PCRTag incorporation, gene locus swapping and stop codon substitution. Despite these substantial changes, the complex epigenetic landscape was normally established, albeit with some three-dimensional conformation alterations. The synthesis of a partial multicellular eukaryotic chromosome arm lays the foundation for the synthetic moss genome project (SynMoss) and paves the way for genome synthesis in multicellular organisms.

Near telomere-to-telomere genome of the model plant Physcomitrium patens.

The model plant Physcomitrium patens has played a pivotal role in enhancing our comprehension of plant evolution and development. However, the current genome harbours numerous regions that remain unfinished and erroneous. To address these issues, we generated an assembly using Oxford Nanopore reads and Hi-C mapping. The assembly incorporates telomeric and centromeric regions, thereby establishing it as a near telomere-to-telomere genome except a region in chromosome 1 that is not fully assembled due to its highly repetitive nature. This near telomere-to-telomere genome resolves the chromosome number at 26 and provides a gap-free genome assembly as well as updated gene models to aid future studies using this model organism.

Transcriptomic and metabolomic analyses revealed regulation mechanism of mixotrophic Cylindrotheca sp. glycerol utilization and biomass promotion.

BACKGROUND: Diatoms have been viewed as ideal cell factories for production of some high-value bioactive metabolites, such as fucoxanthin, but their applications are restrained by limited biomass yield. Mixotrophy, by using both CO2 and organic carbon source, is believed effective to crack the bottleneck of biomass accumulation and achieve a sustainable bioproduct supply. RESULTS: Glycerol, among tested carbon sources, was proved as the sole that could significantly promote growth of Cylindrotheca sp. with illumination, a so-called growth pattern, mixotrophy. Biomass and fucoxanthin yields of Cylindrotheca sp., grown in medium with glycerol (2 g L-1), was increased by 52% and 29%, respectively, as compared to the autotrophic culture (control) without compromise in photosynthetic performance. As Cylindrotheca sp. was unable to use glycerol without light, a time-series transcriptomic analysis was carried out to elucidate the light regulation on glycerol utilization. Among the genes participating in glycerol utilization, GPDH1, TIM1 and GAPDH1, showed the highest dependence on light. Their expressions decreased dramatically when the alga was transferred from light into darkness. Despite the reduced glycerol uptake in the dark, expressions of genes associating with pyrimidine metabolism and DNA replication were upregulated when Cylindrotheca sp. was cultured mixotrophically. Comparative transcriptomic and metabolomic analyses revealed amino acids and aminoacyl-tRNA metabolisms were enhanced at different timepoints of diurnal cycles in mixotrophic Cylindrotheca sp., as compared to the control. CONCLUSIONS: Conclusively, this study not only provides an alternative for large-scale cultivation of Cylindrotheca, but also pinpoints the limiting enzymes subject to further metabolic manipulation. Most importantly, the novel insights in this study should aid to understand the mechanism of biomass promotion in mixotrophic Cylindrotheca sp.

Regulatory Mechanism of ABA and ABI3 on Vegetative Development in the Moss Physcomitrella patens.

The moss Physcomitrella patens is a model system for studying plant developmental processes. ABSCISIC ACID INSENSITIVE3 (ABI3), a transcription factor of the ABA signaling pathway, plays an important role in plant growth and development in vascular plant. To understand the regulatory mechanism of ABA and PpABI3 on vegetative development in Physcomitrella patens, we applied physiological, cellular, and RNA-seq analyses in wild type (WT) plants and ∆abi3 mutants. During ABA treatment, the growth of gametophytes was inhibited to a lesser extent ∆abi3 plants compared with WT plants. Microscopic observation indicated that the differentiation of caulonemata from chloronemata was accelerated in ∆abi3 plants when compared with WT plants, with or without 10 µM of ABA treatment. Under normal conditions, auxin concentration in ∆abi3 plants was markedly higher than that in WT plants. The auxin induced later differentiation of caulonemata from chloronemata, and the phenotype of ∆abi3 plants was similar to that of WT plants treated with exogenous indole-3-acetic acid (IAA). RNA-seq analysis showed that the PpABI3-regulated genes overlapped with genes regulated by the ABA treatment, and about 78% of auxin-related genes regulated by the ABA treatment overlapped with those regulated by PpABI3. These results suggested that ABA affected vegetative development partly through PpABI3 regulation in P. patens; PpABI3 is a negative regulator of vegetative development in P. patens, and the vegetative development regulation by ABA and PpABI3 might occur by regulating the expression of auxin-related genes. PpABI3 might be associated with cross-talk between ABA and auxin in P. patens.