PubMed | Nanjing Southeast University, BGI Shenzhen, CAS Institute of Botany, BGI Wuhan and 2 more.
Type: Journal Article | Journal: GigaScience | Year: 2016
Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution.The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways.The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.
Wang Y.,State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical science |
Hoi P.M.,State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical science |
Chan J.Y.-W.,State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical science |
Lee S.M.-Y.,State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical science
Anti-Cancer Agents in Medicinal Chemistry | Year: 2014
Indirubin is an active ingredient mainly used to treat leukemia in China and is reported to be a leading inhibitor of cyclindependent kinases (CDKs) and glycogen synthase kinase-3 (GSK-3) by competing with ATP binding sites. New findings have indicated that its comprehensive structure may contribute to its polypharmacological activities particularly in cancer and neurodegenerative disease therapy, as both of these diseases are usually accompanied by a common molecular link related to abnormal phosphorylation of CDKs and GSK-3. In the elderly, cancer and neurodegenerative disease are tightly associated common diseases and sometimes unavoidably coexist. In this review, the underlying mechanisms of the dual actions of indirubin and its structurally-related compounds in cancer and neurodegenerative disease therapy are presented. © 2014 Bentham Science Publishers.
PubMed | Chinese University of Hong Kong, State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical science and CAS Beijing Institute of Genomics
Type: | Journal: BMC genomics | Year: 2015
Panax notoginseng (Burk.) F.H. Chen is one of the most highly valued medicinal plants in the world. The major bioactive molecules are triterpene saponins, which are also known as ginsenosides. However, its large genome size has hindered the assembly of a draft genome by whole genome sequencing. Hence, genomic and transcriptomic details about P. notoginseng, especially its biosynthetic pathways and gene expression in different parts of the plant, have remained largely unknown until now.In this study, RNA sequencing of three different P. notoginseng tissues was performed using next generation DNA sequencing. After assembling the high quality sequencing reads into 107,340 unigenes, biochemical pathways were predicted and 9,908 unigenes were assigned to 135 KEGG pathways. Among them, 270 unigenes were identified to be involved in triterpene saponin biosynthesis. In addition, 350 and 342 unigenes were predicted to encode cytochrome P450s and glycosyltransferases, respectively, based on the annotation results, some of which encode enzymes responsible for the conversion of the triterpene saponin backbone into different ginsenosides. In particular, one unigene predominantly expressed in the root was annotated as CYP716A53v2, which probably participates in the formation of protopanaxatriol from protopanaxadiol in P. notoginseng. The differential expression of this gene was further confirmed by real-time PCR.We have established a global transcriptome dataset for P. notoginseng and provided additional genetic information for further genome-wide research and analyses. Candidate genes involved in ginsenoside biosynthesis, including putative cytochrome P450s and glycosyltransferases were obtained. The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P. notoginseng.