Transcriptomic profiling reveals MEP pathway contributing to ginsenoside biosynthesis in Panax ginseng.

BACKGROUND: Panax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from terpene precursors, IPP and DMAPP, through the cytoplasmic mevalonate (MVA) pathway. Another plastic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was proved also contributing to ginsenoside generation in the roots of P. ginseng by using specific chemical inhibitors recently. But their gene expression characteristics are still under reveal in P. ginseng. With the development of the high-throughput next generation sequencing (NGS) technologies, we have opportunities to discover more about the complex ginsenoside biosynthesis pathways in P. ginseng. RESULTS: We carried out deep RNA sequencing and comprehensive analyses on the ginseng root samples of 1-5 years old and five different tissues of 5 years old ginseng plants. The de novo assembly totally generated 48,165 unigenes, including 380 genes related to ginsenoside biosynthesis and all the genes encoding the enzymes of the MEP pathway and the MVA pathway. We further illustrated the gene expression profiles related to ginsenoside biosynthesis among 1-5 year-old roots and different tissues of 5 year-old ginseng plants. Particularly for the first time, we revealed that the gene transcript abundances of the MEP pathway were similar to those of the MVA pathway in ginseng roots but higher in ginseng leaves. The IspD was predicated to be the rate-limiting enzyme in the MEP pathway through both co-expression network and gene expression profile analyses. CONCLUSIONS: At the transcriptional level, the MEP pathway has similar contribution to ginsenoside biosynthesis in ginseng roots, but much higher in ginseng leaves, compared with the MVA pathway. The IspD might be the key enzyme for ginsenoside generation through the MEP pathway. These results provide new information for further synthetic biology study on ginsenoside metabolic regulation.

Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.

Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics.

In 2002, the first crop genome was published using the rice cultivar 93-11, which is the progenitor of the first super-hybrid rice. The genome sequence has served as a reference genome for the indica cultivars, but the assembly has not been updated. In this study, we update the 93-11 genome assembly to a gap-less sequence using ultra-depth single molecule real-time (SMRT) reads, Hi-C sequencing, reference-guided, and gap-closing approach. The differences in the genome collinearity and gene content between the 93-11 and the Nipponbare reference genomes confirmed to map the indica cultivar sequencing data to the 93-11 genome, instead of the reference. Furthermore, time-course transcriptome data showed that the expression pattern was consistently correlated with the stages of seed development. Alternative splicing of starch synthesis-related genes and genomic variations of waxy make it a novel resource for targeted breeding. Collectively, the updated high quality 93-11 genome assembly can improve the understanding of the genome structures and functions of Oryza groups in molecular breeding programs.

The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize.

Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequenced maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZS-related lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity-by-descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we demonstrated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function-related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.