Genomes shed light on the evolution of Begonia, a mega-diverse genus.

Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana and B. peltatifolia), and whole genome shotgun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22 059-23 444 protein-coding genes. Synteny analysis revealed a lineage-specific whole-genome duplication (WGD) that occurred just before the diversification of Begonia. Functional enrichment of gene families retained after WGD highlights the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.

ACSF2-mediated ferroptosis is involved in ulcerative colitis.

AIMS: To investigate the role of ferroptosis-related genes in the induction into ulcerative colitis (UC) and provide new strategies for the prevention and treatment of UC. MATERIALS AND METHODS: We screened the UC dataset from the GEO database and obtained ferroptosis-related genes from FerrDB and GeneCards. The R package "CancerSubtypes" was performed to identify the UC subtypes, followed by Short Time-series Expression Miner (STEM) analysis. The key genes were further screened by machine learning algorithms (LASSO and SVM-RFE). WB and IHC verified the changes in the expression content of ACSF2 in vivo and in vitro models. The changes in intracellular ROS and Fe2 + levels were detected. KEY FINDINGS: Through bioinformatics analysis, we selected the ferroptosis-related gene ACSF2 (acyl CoA synthetase family member 2), which is significantly associated with immune-related pathways "Toll-like receptor signaling pathway", "NF-kappa B signaling pathway" and "NOD-like receptor signaling pathway". The expression of ACSF2 was significantly down-regulated in UC animals, Salmonella typhimurium colitis models and cell models, while the ferroptosis inhibitor Fer-1 reversed the expression of ACSF2 in LPS-induced cell models, indicating that the ferroptosis-related gene ACSF2 plays an important role in mediating ferroptosis and inflammation, and is expected to become a new target for further research. SIGNIFICANCE: Ferroptosis is closely associated with the development of UC, and the ferroptosis-related gene ACSF2 can be used as a potential biomarker for the diagnosis and treatment of UC.

The complete plastid genome of an Antarctic moss Chorisodontium aciphyllum (Hook. f. & Wilson) Broth (Dicranaceae, Dicranales).

Plastid genomes are useful markers in resolving plant phylogenetic relationships for various taxonomic groups. Here, we sequenced and de novo assembled the complete plastid genome sequence of an Antarctic moss Chorisodontium aciphyllum (Hook. f. & Wilson) Broth using genome skimming data. The newly generated plastid genome is conserved in structure and gene content compared with that of other Bryopsida. Plastid phylogenetic analysis of mosses recovered a robust phylogeny in which Chorisodontium aciphyllum clustered with Fissidens nobilis from the Dicranales. The plastid genome sequence of C. aciphyllum will aid future evolution and diversification studies of land plants.

STAT3-mediated ferroptosis is involved in ulcerative colitis.

Ferroptosis is a form of iron-dependent lipid peroxidation cell death that plays an important role in inflammation. However, the mechanism of ferroptosis in ulcerative colitis (UC) remains to be further investigated. In the present study, we merged the differentially expressed genes (DEGs) of UC in GEO database with the ferroptosis-related genes of FerrDb for bioinformatics analysis and successfully screened out the ferroptosis-related hub gene STAT3 (signal transducer and activator of transcription 3). Then we further validated the role of STAT3-mediated ferroptosis in vitro and in vivo models of colitis. The results showed that ferroptosis was increased in DSS-induced colitis, salmonella typhimurium (S. Tm) colitis and H2O2-induced IEC-6 cells. And the phosphorylation level of the hub gene STAT3 was down-regulated in IEC-6 cells treated with H2O2, while Fer-1, an ferroptosis inhibitor, reactivated the phosphorylation level of STAT3. In addition, co-treatment of cells with H2O2 and STAT3 inhibitor (stattic) showed an additive effect on the extent of ferroptosis. Taken together, these findings suggest that ferroptosis is closely associated with the development of colitis and ferroptosis-related gene STAT3 could serve as a potential biomarker for diagnosis and treatment of ulcerative colitis.

The complete chloroplast genome of the fern Asplenium tenerum (Aspleniaceae).

Plastid genomes are useful markers in resolving plant phylogenetic relationships for various taxonomic groups. Here, we sequenced and de novo assembled the complete plastid genome sequence of the fern Asplenium tenerum Forst. (Aspleniaceae, Polypodiales) using the genome skimming data. The newly generated plastid genome is conserved in structure and gene content compared with that of closely related species. Plastid phylogenetic analysis of Polypodiales ferns recovered a robust phylogeny, supporting the close relationship of A. tenerum with Asplenium prolongatum.

The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms.

The mitochondrial genomes of flowering plants are well known for their large size, variable coding-gene set and fluid genome structure. The available mitochondrial genomes of the early angiosperms show extreme genetic diversity in genome size, structure, and sequences, such as rampant HGTs in Amborella mt genome, numerous repeated sequences in Nymphaea mt genome, and conserved gene evolution in Liriodendron mt genome. However, currently available early angiosperm mt genomes are still limited, hampering us from obtaining an overall picture of the mitogenomic evolution in angiosperms. Here we sequenced and assembled the draft mitochondrial genome of Magnolia biondii Pamp. from Magnoliaceae (magnoliids) using Oxford Nanopore sequencing technology. We recovered a single linear mitochondrial contig of 967,100 bp with an average read coverage of 122 × and a GC content of 46.6%. This draft mitochondrial genome contains a rich 64-gene set, similar to those of Liriodendron and Nymphaea, including 41 protein-coding genes, 20 tRNAs, and 3 rRNAs. Twenty cis-spliced and five trans-spliced introns break ten protein-coding genes in the Magnolia mt genome. Repeated sequences account for 27% of the draft genome, with 17 out of the 1,145 repeats showing recombination evidence. Although partially assembled, the approximately 1-Mb mt genome of Magnolia is still among the largest in angiosperms, which is possibly due to the expansion of repeated sequences, retention of ancestral mtDNAs, and the incorporation of nuclear genome sequences. Mitochondrial phylogenomic analysis of the concatenated datasets of 38 conserved protein-coding genes from 91 representatives of angiosperm species supports the sister relationship of magnoliids with monocots and eudicots, which is congruent with plastid evidence.