RNA-seq analysis of Paris polyphylla var.yunnanensis roots identified candidate genes for saponin synthesis

Paris polyphylla Smith var.yunnanensis(Franch.) Hand.-Mazz.is a rhizomatous,herbaceous,perennial plant that has been used for more than a thousand years in traditional Chinese medicine.It is facing extinction due to overharvesting.Steroids are the major therapeutic components in Paris roots,the commercial value of which increases with age.To date,no genomic data on the species have been available.In this study,transcriptome analysis of an 8-year-old root and a 4-year-old root provided insight into the metabolic pathways that generate the steroids.Using Illumina sequencing technology,we generated a high-quality sequence and demonstrated de novo assembly and annotation of genes in the absence of prior genome information.Approximately 87,577 unique sequences,with an average length of 614 bases,were obtained from the root cells.Using bioinformatics methods,we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database.The unique transcripts were functionally classified using the Gene Ontology hierarchy and the Kyoto Encyclopedia of Genes and Genomes database.Of 3082 genes that were identified as significantly differentially expressed between roots of different ages,1518(49.25%) were upregulated and 1564(50.75%) were downregulated in the older root.Metabolic pathway analysis predicted that 25 unigenes were responsible for the biosynthesis of the saponins steroids.These data represent a valuable resource for future genomic studies on this endangered species and will be valuable for efforts to genetically engineer P.polyphylla and facilitate saponin-rich plant development.

Levels of rhizome endophytic fungi fluctuate in Paris polyphylla var.yunnanensis as plants age

Paris polyphylla var. yunnanensis is an important medicinal plant with abundant saponins that are widely used in the pharmaceuticals industry. It is unclear why the levels of active ingredients increase as these plants age. We speculated that the concentrations of those components in the rhizomes are mediated by fungal endophytes. To test this hypothesis, we took both culture-dependent and-independent(metagenomics) approaches to analyze the communities of endophytic fungi that inhabit those rhizomes in plants of different age classes(four, six, and eight years old). In all, 147 isolates representing 18 fungal taxa were obtained from 270 segments(90 per age class). Based on morphological and genetic characteristics, Fusarium oxysporum(46.55% frequency of occurrence) was the predominant endophyte,followed by Leptodontidium sp.(8.66%) and Trichoderma viride(6.81%). Colonization of endophytic fungi was maximized in the eight-year-old rhizomes(33.33%) when compared with four-year-old(21.21%) and six-year-old(15.15%) rhizomes. Certain fungal species were present only at particular ages. For example,Alternaria sp., Cylindrocarpon sp., Chaetomium sp., Paraphaeosphaeria sporulosa, Pyrenochaeta sp., Penicillium swiecickii, T. viride, and Truncatella angustata were found only in the oldest plants. Analysis of(metagenomics) community DNA extracted from different-aged samples revealed that, at the class level,the majority of fungi had the highest sequence similarity to members of Sordariomycetes, followed by Eurotiomycetes and Saccharomycetes. These results were mostly in accord with those we obtained using culture methods. Fungal diversity and richness also changed over time. Our investigation is the first to show that the diversity of fungi in rhizomes of P. polyphylla var. yunnanensis is altered as plants age, and our findings provide a foundation for future examinations of useful compounds.

Genome of Plant Maca （Lepidium meyenil） Illuminates Genomic Basis for High-Altitude Adaptation in the Central Andes

Maca (Lepidium meyenii Walp， 2n = 8x = 64 ) ，属于 Brassicaceae 家庭，经济植物在秘鲁(4000-4500 m ) 在中央安第斯山脉岭被栽培。认为快速中央安第斯山脉高举发生 5-10 百万年以前(妈) ，一个进化问题关于象 maca 那样的植物怎么在一个短地质的时期以内获得高高度的改编产生。这里，我们报导 maca 的高质量的染色体集会，在里面它二仔细 spaced maca 特定的整个染色体的复制(WGD；6.7 妈) 被识别。在 maca 和密切相关的 Brassicaceae 种类之间的比较 genomic 分析揭示了经由 WGD 涉及不能生活的压力反应，荷尔蒙发信号小径，和第二等的代谢物生合成的 maca 基因和基因家庭的扩大。保留和许多复制基因的随后的功能的分叉可以说明词法、生理的变化(即，小叶形状和自我富饶) 在在高高度的环境的 maca。另外，一些复制 maca 基因在词法改编与功能被识别(即，叶卷应答) 并且不能生活的压力反应(即， GLYCINE 富有的 RNA 有约束力的蛋白质和 DNA-DAMAGE-REPAIR/TOLERATION 2 ) 在积极选择下面。一起， maca 染色体提供有用信息在安第斯山脉在植物的高高度的改编理解 WGD 的重要角色。

Submergence induced changes of molecular species in membrane lipids in Arabidopsis thaliana

The composition of membrane lipids is sensitive to environmental stresses.Submergence is a type of stress often encountered by plants.However,how the molecular species of membrane lipids respond to submergence has not yet been characterised.In this study,we used a lipidomic approach to profile the molecular species of membrane lipids in whole plants of Arabidopsis thaliana that were completely submerged for three days.The plants survived one day of submergence,after which,we found that the total membrane lipids were only subtly decreased,showing significant decreases of monogalactosyldiacylglycerol(MGDG)and phosphatidylcholine(PC)and an increase of phosphatidic acid(PA);however,the basic lipid composition was retained.In contrast,three days of submergence caused plants to die,and the membranes deteriorated via the rapid loss of 96% of lipid content together with a 229% increase in PA.The turnover of molecular species from PG and MGDG to PA indicated that submergenceinduced lipid changes occurred through PA-mediated degradation.In addition,molecular species of extraplastidic PG degraded sooner than plastidic ones,lyso-phospholipids exhibited various patterns of change,and the double-bond index(DBI)remained unchanged until membrane deterioration.Our results revealed the unique changes of membrane lipids upon submergence and suggested that the major cause of the massive lipid degradation could be anoxia.