High-quality ice plant reference genome analysis provides insights into genome evolution and allows exploration of genes involved in the transition from C3 to CAM pathways

Ice plant (Mesembryanthemum crystallinum), a member of the Aizoaceae family, is a typical halophyte crop and a model plant for studying the mechanism of transition from C3 photosynthesis to crassulacean acid metabolism (CAM). Here, we report a high-quality chromosome-level ice plant genome sequence. This 98.05% genome sequence is anchored to nine chromosomes, with a total length of 377.97 Mb and an N50 scaffold of 40.45 Mb. Almost half of the genome (48.04%) is composed of repetitive sequences, and 24 234 genes have been annotated. Subsequent to the ancient whole-genome triplication (WGT) that occurred in eudicots, there has been no recent whole-genome duplication (WGD) or WGT in ice plants. However, we detected a novel WGT event that occurred in the same order in Simmondsia chinensis, which was previously overlooked. Our findings revealed that ice plants have undergone chromosome rearrangements and gene removal during evolution. Combined with transcriptome and comparative genomic data and expression verification, we identified several key genes involved in the CAM pathway and constructed a comprehensive network. As the first genome of the Aizoaceae family to be released, this report will provide a rich data resource for comparative and functional genomic studies of Aizoaceae, especially for studies on salt tolerance and C3-to-CAM transitions to improve crop yield and resistance

STING activation in TET2-mutated hematopoietic stem/progenitor cells contributes to the increased self-renewal and neoplastic transformation

Somatic loss-of-function mutations of the dioxygenase Ten-eleven translocation-2 (TET2) occur frequently in individuals with clonal hematopoiesis (CH) and acute myeloid leukemia (AML). These common hematopoietic disorders can be recapitulated in mouse models. However, the underlying mechanisms by which the deficiency in TET2 promotes these disorders remain unclear. Here we show that the cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS)-stimulator of interferon genes (STING) pathway is activated to mediate the effect of TET2 deficiency in dysregulated hematopoiesis in mouse models. DNA damage arising in Tet2-deficient hematopoietic stem/progenitor cells (HSPCs) leads to activation of the cGAS-STING pathway which in turn promotes the enhanced self-renewal and development of CH. Notably, both pharmacological inhibition and genetic deletion of STING suppresses Tet2 mutation-induced aberrant hematopoiesis. In patient-derived xenograft (PDX) models, STING inhibition specifically attenuates the proliferation of leukemia cells from TET2-mutated individuals. These observations suggest that the development of CH associated with TET2 mutations is powered through chronic inflammation dependent on the activated cGAS-STING pathway and that STING may represent a potential target for intervention of relevant hematopoietic diseases

Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery

Celery (Apium graveolens L.), a plant from Apiaceae, is one of the most important vegetables and is grown worldwide. Carotenoids can capture light energy and transfer it to chlorophyll, which plays a central role in photosynthesis. Here, by performing transcriptomics and genomics analysis, we identified and conducted a comprehensive analysis of chlorophyll and carotenoid-related genes in celery and six representative species. Significantly, different contents and gene expression patterns were found among three celery varieties. In total, 237 and 290 chlorophyll and carotenoid-related genes were identified in seven species. No notable gene expansion of chlorophyll biosynthesis was detected in examined species. However, the gene encoding ζ-carotene desaturase (ZDS) enzyme in carotenoid was expanded in celery. Comparative genomics and RNA-seq analyses revealed 16 and 5 key genes, respectively, regulating chlorophyll and carotenoid. An intriguing finding is that chlorophyll and carotenoid-related genes were coordinately regulated by transcriptional factors, which could be distinctively classified into positive- and negative-regulation groups. Six CONSTANS (CO)-like transcription factors co-regulated chlorophyll and carotenoid-related genes were identified in celery. In conclusion, this study provides new insights into the regulation of chlorophyll and carotenoid by transcription factors

The genome of Stephania japonica provides insights into the biosynthesis of cepharanthine

Summary: Stephania japonica is an early-diverging eudicotyledon plant with high levels of cepharanthine, proven to be effective in curing coronavirus infections. Here, we report a high-quality S. japonica genome. The genome size is 688.52 Mb, and 97.37% sequences anchor to 11 chromosomes. The genome comprises 67.46% repetitive sequences and 21,036 genes. It is closely related to two Ranunculaceae species, which diverged from their common ancestor 55.90–71.02 million years ago (Mya) with a whole-genome duplication 85.59–96.75 Mya. We further reconstruct ancestral karyotype of Ranunculales. Several cepharanthine biosynthesis genes are identified and verified by western blot. Two genes (Sja03G0243 and Sja03G0241) exhibit catalytic activity as shown by liquid chromatography-mass spectrometry. Then, cepharanthine biosynthesis genes, transcription factors, and CYP450 family genes are used to construct a comprehensive network. Finally, we construct an early-diverging eudicotyledonous genome resources (EEGR) database. As the first genome of the Menispermaceae family to be released, this study provides rich resources for genomic studies