Genome Mining as an Alternative Way for Screening the Marine Organisms for Their Potential to Produce UV-Absorbing Mycosporine-like Amino Acid

Mycosporine-like amino acids (MAAs) are small molecules with robust ultraviolet (UV)-absorbing capacities and a huge potential to be used as an environmentally friendly natural sunscreen. MAAs, temperature, and light-stable compounds demonstrate powerful photoprotective capacities and the ability to capture light in the UV-A and UV-B ranges without the production of damaging free radicals. The biotechnological uses of these secondary metabolites have been often limited by the small quantities restored from natural resources, variation in MAA expression profiles, and limited success in heterologous expression systems. Overcoming these obstacles requires a better understanding of MAA biosynthesis and its regulatory processes. MAAs are produced to a certain extent via a four-enzyme pathway, including genes encoding enzymes dehydroquinate synthase, enzyme O-methyltransferase, adenosine triphosphate grasp, and a nonribosomal peptide synthetase. However, there are substantial genetic discrepancies in the MAA genetic pathway in different species, suggesting further complexity of this pathway that is yet to be fully explored. In recent years, the application of genome-mining approaches allowed the identification of biosynthetic gene clusters (BGCs) that resulted in the discovery of many new compounds from unconventional sources. This review explores the use of novel genomics tools for linking BGCs and secondary metabolites based on the available omics data, including MAAs, and evaluates the potential of using novel genome-mining tools to reveal a cryptic potential for new bioproduct screening approaches and unrevealing new MAA producers.     

结合基因关联和转录组分析鉴定小麦成株期抗条锈病位点YrZ501-2BL的候选基因

【目的】小麦条锈病是小麦的主要病害之一,每年都会对小麦产量安全造成严重危害,挖掘小麦抗条锈病基因,为小麦抗条锈病种质创新和揭示小麦抗条锈病遗传机制奠定基础。【方法】利用多组学手段结合全基因关联分析（GWAS）开展对小麦成株期抗条锈病性状的解析。首先对411份来自CIMMYT和ICARDA的春小麦进行全基因组关联分析,在小麦2BL染色体上定位到一个主效的成株期抗条锈病位点,并利用含有该位点的抗病材料Z501及感病亲本晋麦79的双亲群体进行连锁作图,成功验证了该位点抗性的稳定性,暂命名为YrZ501-2BL。在此基础上,通过基因注释、比较基因组分析、转录组分析和候选基因的关联分析对目标区间筛选候选基因。【结果】综合GWAS和连锁作图结果,将YrZ501-2BL锁定在小麦2B染色体0.26 Mb(575.706—576.587 Mb)范围内,根据中国春参考基因组注释信息分析,该区间含有12个基因,其中,高可信基因6个;利用在线网站,将目标区间所在的中国春参考基因组与其他已公布的不同倍性小麦基因组进行比较,发现该区间的6个高可信小麦基因基本都能在其他小麦材料中找到同源基因,且基因排列顺序相同,...     

Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows

Bacterial natural products possess potent bioactivities and high structural diversity and are typically encoded in biosynthetic gene clusters. Traditional natural product discovery approaches rely on UV- and bioassay-guided fractionation and are limited in terms of dereplication. Recent advances in mass spectrometry, sequencing and bioinformatics have led to large-scale accumulation of genomic and mass spectral data that is increasingly used for signature-based or correlation-based mass spectrometry genome mining approaches that enable rapid linking of metabolomic and genomic information to accelerate and rationalize natural product discovery. In this mini-review, these approaches are presented, and discovery examples provided. Finally, future opportunities and challenges for paired omics-based natural products discovery workflows are discussed.     

Development of the “Applied Proteomics” Concept for Biotechnology Applications in Microalgae: Example of the Proteome Data in Nannochloropsis gaditana

Most of the marine ecosystems on our planet are still unknown. Among these ecosystems, microalgae act as a baseline due to their role as primary producers. The estimated millions of species of these microorganisms represent an almost infinite source of potentially active biocomponents offering unlimited biotechnology applications. This review considers current research in microalgae using the “omics” approach, which today is probably the most important biotechnology tool. These techniques enable us to obtain a large volume of data from a single experiment. The specific focus of this review is proteomics as a technique capable of generating a large volume of interesting information in a single proteomics assay, and particularly the concept of applied proteomics. As an example, this concept has been applied to the study of Nannochloropsis gaditana, in which proteomics data generated are transformed into information of high commercial value by identifying proteins with direct applications in the biomedical and agri-food fields, such as the protein designated UCA01 which presents antitumor activity, obtained from N. gaditana.     

马铃薯与致病疫霉互作研究进展与展望

马铃薯是重要的粮食作物, 由致病疫霉侵染引发的晚疫病长期严重制约马铃薯产业的健康发展, 因此, 国内外均将马铃薯晚疫病列为重大病害。目前, 抗病品种选育栽培、晚疫病预测预报和化学防治等相结合的晚疫病综合防治手段已得到普遍推广, 但晚疫病局部大流行在全世界范围内仍时有发生, 给粮食安全和生态安全带来巨大挑战。本文回顾了我国晚疫病的部分研究历史, 集中关注致病疫霉与寄主的互作机制领域, 梳理了近年来关于致病疫霉侵入机理、效应蛋白毒力功能、病原菌变异规律、马铃薯抗病机理等方面的重要研究结果并展望未来主要的研究方向, 以期为晚疫病基础研究和防治技术革新提供参考。     

Bivalve Omics: State of the Art and Potential Applications for the Biomonitoring of Harmful Marine Compounds

The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse animal groups, relatively unexplored and without representation within the narrow collection of well established model organisms. Within this Phylum, bivalve molluscs play a fundamental role in the functioning of the marine ecosystem, constitute very valuable commercial resources in aquaculture, and have been widely used as sentinel organisms in the biomonitoring of marine pollution. Yet, it has only been very recently that this complex group of organisms became a preferential subject for omic studies, posing new challenges for their integrative characterization. The present contribution aims to give a detailed insight into the state of the art of the omic studies and functional information analysis of bivalve molluscs, providing a timely perspective on the available data resources and on the current and prospective applications for the biomonitoring of harmful marine compounds.     

Advances in “omics” approaches to tackle drought stress in grain legumes

Grain legumes being affordable sources of proteins, vitamins and essential micronutrients are key to human nutrition worldwide. However, frequent drought episodes present serious threat to grain legume production worldwide. Advances in legume omics in concert with evolving phenotyping and breeding techniques hold great promise to improve drought response of these crops. These resources could underpin prebreeding efforts to expedite discovery and deployment of novel drought tolerance traits into elite backgrounds. Fast-track transfer of traits that confer drought tolerance using marker technologies has been demonstrated in grain legumes like chickpea. However, complex genetic architecture of drought tolerance demands embracing more efficient tools like genomic selection (GS) for accelerated trait improvement. Recent studies on GS for addressing complex traits like drought tolerance have yielded encouraging results in these crops. Recently, speed breeding (SB) protocols have also been optimized for the improvement of long-day/day-neutral grain legumes. Efficacy of SB protocols with regard to complex traits awaits further evidences though. There remains immense scope for integrating SB with GS and gene editing to deliver drought-tolerant cultivars.     

Rigidoporus microporus and the white root rot disease of rubber

Rigidoporus microporus is an economically important plant pathogenic fungus causing particularly severe losses to the rubber industry worldwide. The pathogen is responsible for white root rot (WRR) disease, infecting the host roots via white fibrous mycelia, causing vascular disfunction, and visible symptoms including leaf discolouration and dieback in severely infected trees. The final stage of the disease is characterized by the appearance of basidiocarps at the tree collar. The development of WRR in rubber plantations is dependent on fungal diversity in the soil, pH, temperature, and cation levels. Several ‘-omics’ approaches have been undertaken to understand how R. microporus functions with the objective, ultimately, to control WRR. Unfortunately, no resistant rubber clone has been identified to date. The disease is managed through physical and chemical methods that are laborious and negatively impact the environment, respectively. Recent developments in research on R. microporus shed light on potential sustainable routes to WRR disease control using beneficial microorganisms and natural compounds. This review discusses the characteristics of R. microporus isolates from different geographical origins, the pathogenicity and virulence mechanisms of the necrotrophic fungal pathogen, factors that influence the development of WRR, recent findings from the multi-omics studies, and control methods that are available to combat this economically important pathogen.