Enantiomeric Cephalotaxus alkaloids from seeds of Cephalotaxus oliveri.
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ABSTRACT:
SUBMITTER: Yu GX
PROVIDER: S-EPMC9249953 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Cephalotaxus oliveri is a tertiary relict conifer endemic to China, regarded as a national second-level protected plant in China. This species has experienced severe changes in temperature and precipitation in the past millions of years, adapting well to harsh environments. In view of global climate change and its endangered conditions, it is crucial to study how it responds to changes in temperature and precipitation for its conservation work. In this study, single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing were combined to generate the complete transcriptome of C. oliveri. Using the RNA-seq data to correct the SMRT sequencing data, the four tissues obtained 63,831 (root), 58,108 (stem), 33,013 (leaf) and 62,436 (male cone) full-length unigenes, with a N50 length of 2523, 3480, 3181, and 3267 bp, respectively. Additionally, 35,887, 11,306, 36,422, and 25,439 SSRs were detected for the male cone, leaf, root, and stem, respectively. The number of long non-coding RNAs predicted from the root was the largest (11,113), and the other tissues were 3408 (stem), 3193 (leaf), and 3107 (male cone), respectively. Functional annotation and enrichment analysis of tissue-specific expressed genes revealed the special roles in response to environmental stress and adaptability in the different four tissues. We also characterized the gene families and pathways related to abiotic factors. This work provides a comprehensive transcriptome resource for C. oliveri, and this resource will facilitate further studies on the functional genomics and adaptive evolution of C. oliveri.
| S-EPMC7830723 | biostudies-literature
Project description:Evaluating the contributions of geographic distance and environmental heterogeneity to the genetic divergence can inform the demographic history and responses to environmental change of natural populations. The isolation-by-distance (IBD) reveals that genetic differentiation among populations increases with geographic distance, while the isolation-by-environment (IBE) assumes a linear relationship between genetic variation and environmental differences among populations. Here, we sampled and genotyped 330 individuals from 18 natural populations of Cephalotaxus oliveri throughout the species' distribution. Twenty-eight EST-SSR markers were applied to analyze population genetics, for the investigation of the driving factors that shaped spatial structure. In addition, we identified the outlier loci under positive selection and tested their association with environmental factors. The results showed a moderate genetic diversity in C. oliveri and high genetic differentiation among populations. Population structure analyses indicated that 18 populations were clustered into two major groups. We observed that the genetic diversity of central populations decreased and the genetic differentiation increased towards the marginal populations. Additionally, the signatures of IBD and IBE were detected in C. oliveri, and IBE provided a better contribution to genetic differentiation. Six outlier loci under positive selection were demonstrated to be closely correlated with environmental variables, among which bio8 was associated with the greatest number of loci. Genetic evidence suggests the consistency of the central-marginal hypothesis (CMH) for C. oliveri. Furthermore, our results suggest that temperature-related variables played an important role in shaping genetic differentiation.
| S-EPMC10008294 | biostudies-literature
Project description:Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3'UTR, and 5'UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.
| S-EPMC8635753 | biostudies-literature
Project description:Cephalotaxus oliveri is a scarce medicinal conifer endemic to the south central region of China and Vietnam. A small fragmented population presently exists due to anthropogenic disturbance. C. oliveri has been used for its alkaloids harringtonine and homoharringtonine, which are effective against leucocythemia and lymphadenosarcoma. Monoecious plants have been detected in nature, although they were understood to be dioecious. In order to study the mating system, population genetics and the genetic effects of habitat fragmentation on C. oliveri, 15 polymorphic and 12 monomorphic microsatellite loci were developed for C. oliveri by using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol. The polymorphisms were assessed in 96 individuals from three natural populations (32 individuals per population). The number of alleles per locus ranged from two to 33, the observed and expected heterozygosity per locus ranged from 0.000 to 1.000 and from 0.000 to 0.923, respectively. These loci would facilitate a comprehensive understanding of the genetic dynamics on C. oliveri, which will be useful for establishing effective conservation strategies for this species.
| S-EPMC3472736 | biostudies-literature
Project description:We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.
| S-EPMC3641632 | biostudies-literature
Project description:Five new alkaloids (1-5) were isolated from the leaves and twigs of Cephalotaxus lanceolata and C. fortunei var. alpina along with 24 known alkaloids. The new structures were elucidated based on spectroscopic data including 1D and 2D NMR, FTIR, UV and MS. These new alkaloids showed no cytotoxicity to HeLa, SGC-7901 gastric cancer, and A-549 lung cancer cell lines.
| S-EPMC5385657 | biostudies-literature
Project description:Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22 C. oliveri natural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition, C. oliveri possessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations of C. oliveri from south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies.
| S-EPMC4844950 | biostudies-literature
Project description:Dysregulated activation of the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway by self-DNA contributes to interferonopathy and promotes autoimmune diseases. To identify potential suppressors of STING-induced type I interferon (IFN) induction, ethanol extracts of medicinal plants were screened for inhibitory activity against IFN-ß promoter activation. Notably, 70% ethanol extract of Cephalotaxus koreana specifically down-regulated STING-induced, but not TBK1- or IRF3-induced, IFN-ß promoter activity. The compounds exerting inhibitory activity specifically against STING-mediated IFN-ß promoter activation were identified as ester alkaloids isolated from the genus, Cephalotaxus, homoharringtonine and harringtonine. Furthermore, these two compounds inhibited 2'3'-cGAMP-induced IFN-stimulated gene expression and interaction between STING and TBK1. These suppressive effects were not observed with cephalotaxine devoid of the ester side-chain. Our data support the potential utility of homoharringtonine and harringtonine to treat STING-associated interferonopathy and autoimmune diseases.
| S-EPMC5542643 | biostudies-other
Project description:Investigation of the alkaloids from Peganum harmala seeds yielded two pairs of unique racemic pyrroloindole alkaloids, (±)-peganines A-B (1-2); two rare thiazole derivatives, peganumals A-B (3-4); six new β-carboline alkaloids, pegaharmines F-K (5-10); and 12 known analogues. Their structures, including stereochemistry, were elucidated through spectroscopic analyses, quantum chemistry calculations, and single-crystal X-ray diffraction. Notably, the incorporation of pyrrole and indole moieties in peganines A-B, thiazole fragments in peganumals A-B, and a C-1 α,β-unsaturated ester motif in pegaharmine F (5) are all rare, and their presence in the genus Peganum were demonstrated for the first time. All isolates were tested for antiproliferative activities against the HL-60, PC-3, and SGC-7901 cancer cell lines, and compounds 9, 11, 12, and 13 exhibited moderate cytotoxicity against HL-60 cancer cell lines with IC50 values in the range of 4.36-9.25 μM.
| S-EPMC5518681 | biostudies-literature