Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.

Mosses compose one of the three lineages of bryophytes. Today, about 13,000 species of mosses are recognized from across the globe, and at least a third of this diversity composes the Hypnales, a lineage characterized by an early rapid radiation. We sequenced and de novo assembled the genomes of two hypnalean mosses, namely Entodon seductrix and Hypnum curvifolium, based on the 10x genomics and Hi-C data. The genome assemblies of E. seductrix and H. curvifolium comprise 348.4 Mb and 262.0 Mb, respectively, estimated by k-mer analyses to represent 93.3% and 97.2% of their total genome size. Both genomes were assembled at the chromosome-level, with scaffold N50 of 30.0 Mb and 20.7 Mb, respectively. The annotated genome of E. seductrix comprises 25,801 protein-coding genes and that of H. curvifolium 29,077, estimated to represent 96.8% and 97.2%, respectively, of the total gene spaces based on BUSCO assessment. For both genomes, most contigs were anchored to the largest 11 pseudomolecules, corresponding to the 11 chromosomes of the two species, and each with a putative sex-related chromosome characterized by low gene density. The chromosomes of E. seductrix and H. curvifolium are highly syntenic, suggests limited architectural shifts occurred following the rapid radiation of the Hypnales. We compared their genomic features to the model moss Physcomitrium patens. The hypnalean moss genomes lack signatures of recent whole genome duplication (WGD). The presented high-quality moss genomes provide new resources for comparative genomics to potentially unveil the genomic evolution of derived moss lineages.

(Folia Morphol 2017; 76, 1: 87-93)

Background and Aims With some 7,300 extant species, liverworts (Marchantiophyta) represent one of the major land plant lineages. The backbone relationships, such as the phylogenetic position of Ptilidiales, and the occurrence and timing of whole genome duplications, are still contentious. Methods Based on analyses of the newly generated transcriptome data for 38 liverworts and complemented with those publicly available, we reconstructed the evolutionary history of liverworts and inferred gene duplication events along the 55-taxon liverwort species tree. Key Results Our phylogenomic study provided an ordinal-level liverwort nuclear phylogeny and identified extensive gene tree conflicts and cyto-nuclear incongruences. Gene duplication analyses based on integrated phylogenomics and Ks distributions indicated no evidence of whole genome duplication events along the backbone phylogeny of liverworts. Conclusions With a broadened sampling of liverwort transcriptomes, we re-evaluated the backbone phylogeny of liverworts, and provided evidence for ancient hybridizations followed by incomplete lineage sorting that shaped the deep evolutionary history of liverworts. The lack of whole genome duplication along the deep evolution of liverworts indicates that liverworts might represent one of the few major embryophyte lineages whose evolution was not driven by whole genome duplications.

We investigated the constituents of Leucaena leucocephala foliage collected from Guangdong province in China and isolated 17 diverse flavonoids (1-17), including flavones (5-9, 11, and 12), flavonols (1, 10, and 16), flavanone 4, flavanonol 15, and flavonol glycosides (2, 3, 13, 14, and 17). Flavonoids quercetin (1), quercetin-3- O-α-rhamnopyranoside (2), and myricetin-3- O-α-rhamnopyranoside (17) were the major flavonoids components in L. leucocephala leaves, at a total concentration of about 2.5% of dry matter. pHRE-Luc inductive activity to mimic the activation of erythropoietin (EPO) gene, anti-inflammatory, antidiabetic, and antioxidant activities of isolated flavonoids (1-17) were evaluated. Flavonoids 7, 10, and 13 could strongly induce the transcriptional activity of pHRE-Luc, which indicated their potential to induce the expression of EPO. Flavonoids 7, 10, 13, and 17 displayed strong anti-inflammatory activity, relatively equal to the positive control dexamethasone. Flavonoids 1, 2, 3, 11, 12, 16, and 17 showed stronger antioxidant activities of DPPH radical scavenging capacity than ascorbic acid. Flavonoids 1, 2, and 10 showed weak cellular antioxidant activities against tert-butyl hydroperoxide (tBHP) induced ROS formation. Flavonoid rhamnoside 2 and arabinoside 3 undergone deglycosylation to the aglycone quercetin under anaerobic incubation with cattle rumen microorganisms. Furthermore, the potential health benefits for ruminant of flavonoids, which was rich in L. leucocephala foliage, was also discussed.

Gibberellins (GAs) are an important group of phytohormones associated with diverse growth and developmental processes, including cell elongation, seed germination, and secondary growth. Recent genomic and genetic analyses have advanced our knowledge of GA signaling pathways and related genes in model plant species. However, functional genomics analyses of GA signaling pathways in Panax ginseng, a perennial herb, have rarely been carried out, despite its well-known economical and medicinal importance. Here, we conducted functional characterization of GA receptors and investigated their physiological roles in the secondary growth of P. ginseng storage roots. We found that the physiological and genetic functions of P. ginseng gibberellin-insensitive dwarf1s (PgGID1s) have been evolutionarily conserved. Additionally, the essential domains and residues in the primary protein structure for interaction with active GAs and DELLA proteins are well-conserved. Overexpression of PgGID1s in Arabidopsis completely restored the GA deficient phenotype of the Arabidopsis gid1a gid1c (atgid1a/c) double mutant. Exogenous GA treatment greatly enhanced the secondary growth of tap roots; however, paclobutrazol (PCZ), a GA biosynthetic inhibitor, reduced root growth in P. ginseng. Transcriptome profiling of P. ginseng roots revealed that GA-induced root secondary growth is closely associated with cell wall biogenesis, the cell cycle, the jasmonic acid (JA) response, and nitrate assimilation, suggesting that a transcriptional network regulate root secondary growth in P. ginseng. These results provide novel insights into the mechanism controlling secondary root growth in P. ginseng.

In adults, the oblique cord or chorda obliqua separates the origins of the flexor pollicis longus (FPL) and flexor digitorum profundus (FDP) (Folia Morphol 2016; 75, 4: 493-502)

Background Major depressive disorder (MDD) is a severe disease characterized by multiple pathological changes. However, there are no reliable diagnostic biomarkers for MDD. The aim of the current study was to investigate the gene network and biomarkers underlying the pathophysiology of MDD. Methods In this study, we conducted a comprehensive analysis of the mRNA expression profile of MDD using data from Gene Expression Omnibus (GEO). The MDD dataset (GSE98793) with 128 MDD and 64 control whole blood samples was divided randomly into two non-overlapping groups for cross-validated differential gene expression analysis. The gene ontology (GO) enrichment and gene set enrichment analysis (GSEA) were performed for annotation, visualization, and integrated discovery. Protein–protein interaction (PPI) network was constructed by STRING database and hub genes were identified by the CytoHubba plugin. The gene expression difference and the functional similarity of hub genes were investigated for further gene expression and function exploration. Moreover, the receiver operating characteristic curve was performed to verify the diagnostic value of the hub genes. Results We identified 761 differentially expressed genes closely related to MDD. The Venn diagram and GO analyses indicated that changes in MDD are mainly enriched in ribonucleoprotein complex biogenesis, antigen receptor-mediated signaling pathway, catalytic activity (acting on RNA), structural constituent of ribosome, mitochondrial matrix, and mitochondrial protein complex. The GSEA suggested that tumor necrosis factor signaling pathway, Toll-like receptor signaling pathway, apoptosis pathway, and NF-kappa B signaling pathway are all crucial in the development of MDD. A total of 20 hub genes were selected via the PPI network. Additionally, the identified hub genes were downregulated and show high functional similarity and diagnostic value in MDD. Conclusions Our findings may provide novel insight into the functional characteristics of MDD through integrative analysis of GEO data, and suggest potential biomarkers and therapeutic targets for MDD.