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.

"zebra" mutants have alternating green and chlorotic crossbands on leaf blades and are widely distributed in monocotyledonous crops. Most recently, we cloned the first responsible gene from rice, ZEBRA2, which also leads to the phenotype of rice preharvest sprouting. ZEBRA2, a single-copy gene in the rice genome, encodes a carotenoid isomerase (CRTISO), the key enzyme catalyzing the conversion of cis-lycopene to all-trans lycopene. ZEBRA2 shares high identity with known CRTISOs from other species. Expression analysis via both RT-PCR and ZEBRA2-promoter-β-glucuronidase (GUS) transgenic rice indicates that ZEBRA2 is predominantly expressed in mesophyll cells of mature leaves where active photosynthesis occurs. Consistent with the alteration in agronomic traits, the zebra2 mutant exhibits decreased photosynthetic rate and chlorophyll content. Mutation of the ZEBRA2 gene results in the accumulation of all-trans-lycopene precursor, prolycopene (7Z,9Z,7'Z,9'Z tetra cis-lycopene), in dark-grown zebra2 tissues. Light-grown zebra2 mutant exhibits the characteristic "zebra" phenotype and decreased level of lutein, the xanthophyll that is essential for efficient chl triplet quenching. More severe phenotype of the zebra2 mutant under high light intensity indicates that "zebra" phenotype might be caused by photooxidative damages. We conclude that ZEBRA2 is involved in photoprotection in rice.

Magnolia biondii Pamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Determining the genome sequence of M. biondii would help resolve the phylogenetic uncertainty of magnoliids and improve the understanding of individual trait evolution within the Magnolia genus. We assembled a chromosome-level reference genome of M. biondii using ~67, ~175, and ~154 Gb of raw DNA sequences generated via Pacific Biosciences single-molecule real-time sequencing, 10X Genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was ~2.22 Gb, with a contig N50 value of 269.11 kb and a BUSCO complete gene percentage of 91.90%. Approximately 89.17% of the genome was organized into 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 47,547 protein-coding genes, accounting for 23.47% of the genome length, whereas 66.48% of the genome length consisted of repetitive elements. We confirmed a WGD event that occurred very close to the time of the split between the Magnoliales and Laurales. Functional enrichment of the Magnolia-specific and expanded gene families highlighted genes involved in the biosynthesis of secondary metabolites, plant–pathogen interactions, and responses to stimuli, which may improve the ecological fitness and biological adaptability of the lineage. Phylogenomic analyses revealed a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence of M. biondii could lead to trait improvement, germplasm conservation, and evolutionary studies on the rapid radiation of early angiosperms.

Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species.

Background In polyglutamine (polyQ) disease, the investigation of the prediction of a patient's age at onset (AAO) facilitates the development of disease‐modifying intervention and underpins the delay of disease onset and progression. Few polyQ disease studies have evaluated AAO predicted by machine‐learning algorithms and linear regression methods. Objective The objective of this study was to develop a machine‐learning model for AAO prediction in the largest spinocerebellar ataxia type 3/Machado–Joseph disease (SCA3/MJD) population from mainland China. Methods In this observational study, we introduced an innovative approach by systematically comparing the performance of 7 machine‐learning algorithms with linear regression to explore AAO prediction in SCA3/MJD using CAG expansions of 10 polyQ‐related genes, sex, and parental origin. Results Similar prediction performance of testing set and training set in each models were identified and few overfitting of training data was observed. Overall, the machine‐learning‐based XGBoost model exhibited the most favorable performance in AAO prediction over the traditional linear regression method and other 6 machine‐learning algorithms for the training set and testing set. The optimal XGBoost model achieved mean absolute error, root mean square error, and median absolute error of 5.56, 7.13, 4.15 years, respectively, in testing set 1, with mean absolute error (4.78 years), root mean square error (6.31 years), and median absolute error (3.59 years) in testing set 2. Conclusion Machine‐learning algorithms can be used to predict AAO in patients with SCA3/MJD. The optimal XGBoost algorithm can provide a good reference for the establishment and optimization of prediction models for SCA3/MJD or other polyQ diseases. © 2020 International Parkinson and Movement Disorder Society

Polymorphism refers to the phenomenon that crystals of the same chemical composition can crystallize into several different forms with different physicochemical conditions. Studying the polymorphism of drugs has become an indispensable and important part of daily predesign work for drug production and formulation. Here, we use ab initio computational calculations in combination with rational crystal structure design and morphology prediction to study the polymorphism of the pharmaceutical compound olanzapine, an effective drug to treat schizophrenia, using density functional theory and second-order Møller–Plesset perturbation methods. Different crystal polymorphs are found at the calculated energy landscape, and the analysis of Gibbs free energy and Raman spectra confirms that the long-accepted form I of olanzapine is identified as the most thermodynamically stable structure. With the increase of temperature, form I of olanzapine exhibits greater stability than that of form II. Rather than the traditional lattice energy calculations, we use the Gibbs free energy to evaluate the stability of crystal structure, which includes the effects of entropy and temperature and is more accurate when predicting the crystal structures. We also provide an effective method to identify different forms of polycrystalline structures based on the vibrational spectra and offer an advanced tool to predict the crystal morphologies. The present paper offers a platform for rational design of pharmaceutical molecules, which not only reestablishes the crystal structures of existing drugs but also provides motivation for the possibility of the exploration of new drugs with special efficacy.

Magnoliaceae, an assemblage of early diverged angiosperms, comprises two subfamilies, speciose Magnolioideae with approximately 300 species in varying numbers of genera and monogeneric Liriodendroideae with two species in Liriodendron L. This family occupies a pivotal phylogenetic position with important insights into the diversification of early angiosperms, and shows intercontinentally disjunct distribution patterns between eastern Asia and the Americas. Widespread morphological homogeneity and slow substitution rates in Magnolia L. s.l. resulted in poorly supported phylogenetic relationships based on morphology or molecular evidence, which hampers our understanding of the genus' temporal and spacial evolution. Here, based on the newly generated genome skimming data for 48 Magnolia s.l. species, we produced robust Magnolia phylogenies using genome-wide markers from both plastid genomes and single nucleotide polymorphism data. Contrasting the plastid and nuclear phylogenies revealed extensive cytonuclear conflicts in both shallow and deep relationships. ABBA-BABA and PhyloNet analyses suggested hybridization occurred within sect. Yulania, and sect. Magnolia, which is in concordance with the ploidy level of the species in these two sections. Divergence time estimates and biogeographic reconstruction indicated that the timing of the three tropical Magnolia disjunctions coincided with the mid-Eocene cooling climate and/or late Eocene climate deterioration, and two temperate disjunctions occurred much later, possibly during the warm periods of the Miocene, hence supporting the boreotropical flora concept of Magnolia s.l.

Three new nortriterpenoids, schigrandilactones A-C (1-3), along with eight known compounds, were isolated from an organic solvent extract of Schisandra grandiflora. Compounds 1 and 2 feature a spirocyclic moiety in their structures, and compound 3 was characterized with a new oxygenated pattern. The relative configurations of 1 and 3 were determined through single-crystal X-ray experiments. In addition, compounds 1 and 2 displayed cytotoxic activity against two human cancer cell lines, and compound 3 showed anti-HIV-1 inhibition in infected C8166 cells.