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ABSTRACT: Phylogenetics of the Scrub Mint Clade (Lamiaceae)

PROVIDER: PRJNA1024994 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26347200_1.fastq.gz	Fastqsanger.gz
	SRR26347200_2.fastq.gz	Fastqsanger.gz
	SRR26347201_1.fastq.gz	Fastqsanger.gz
	SRR26347201_2.fastq.gz	Fastqsanger.gz
	SRR26347202_1.fastq.gz	Fastqsanger.gz

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Project description:BACKGROUND: Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance.FINDINGS: We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs.CONCLUSIONS: Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.

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Orientsia tsutsugamushi stimulates an original gene expression program in monocytes: relationship with gene expression in patients with scrub typhus

Project description:Comparative analysis of Genome wide expression was performed to demonstrate diagnostic potential of expression profiling and to identify host response genes in scrub typhus. The results showed that there is a unique expression pattern in peripheral blood leukocytes of scrub typhus infected patients that could discriminate scrub typhus from the other infections and also provided insight into host transcriptional responses to this paticular infection. Genome-wide expression in peripheral blood mononuclear cells (PBMCs) from patients with scrub typhus were compared to those from healthy control and from patients with dengue fever, murine typhus or malaria.

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Project description:The Lamiaceae family contains numerous diterpenoids, offering a valuable model system for the study of diterpenoid chemical diversity. In this study we report that the ent-kaurene diterpenoids in I. rubescens have the largest diTPS gene family identified in Lamiaceae. Three genes are predicted to be involved in ent-kaurene diterpenoid synthesis while another two KSL genes are functional enzymes utilizing ent-CPP as a substrate. We also showed the presence of a normal-CPP mediated biosynthesis pathway in I. rubescens and that three KSL genes possessing different domain architectures are involved in this pathway. This study provides new information regarding the understanding of diterpenoid chemical diversity and this compounds’ evolution in the Lamiaceae family.

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