VIGS技术在禾本科植物中的应用研究进展

病毒诱导基因沉默(Virus-induced gene silencing,VIGS)是一种转录后基因沉默现象.近年来在植物基因功能研究中,VIGS技术作为一种快速、高效、高通量的反向遗传学新技术发挥了重要作用.尤其在禾本科植物基因功能研究中VIGS技术得到了广泛的应用.本文阐述了VIGS技术的发现及作用机制,并重点介绍了在禾本科植物中应用的VIGS载体及功能基因组学研究的应用实例,最后探讨了VIGS技术在禾本科植物中影响沉默效率的因素、局限性及应用前景.     

生物信息学及其在农业科学中的应用

综述了生物信息学的形成与发展及其数据库和功能基因组学研究;同时也概括了生物信息学在模式植物研究、种质资源保存、病虫害防治、作物遗传育种等方面的应用。     

一株河鲈源致病性虫草菌Cordyceps confragosa CHL02菌株的全基因组测序及比较基因组分析

致病性虫草菌Cordyceps confragosa CHL02菌株是从患病河鲈(Perca fluviavilis)鱼体分离鉴定的一株昆虫致病菌,其无性阶段蜡蚧轮枝菌(Lecanicillium lecanii)广泛用于农业中昆虫防治。本研究基于Illumina PE150测序平台进行CHL02菌株的全基因组测序,对测序数据进行组装和组分分析,进行基因预测与功能注释,预测次级代谢产物合成基因簇,并进行病原宿主互作以及比较基因组分析。测序结果显示,CHL02基因组大小为36.17 Mb,GC含量为53.09%;预测包含8093个编码基因、1618个转座因子(TEs)、4572个串联重复序列及114个tRNA;共注释7724个基因,其中,1985个基因获得KOG注释,GO聚类分析中,2687个基因参与代谢过程,预测到22个次级代谢产物合成基因簇,1162个基因参与病原宿主互作机制中。基因聚类分析和系统发育树均显示,CHL02菌株与参考菌株昆虫源粗糙虫草菌(C. confragosa) RCEF 1005具有较高的同源性。本研究首次报道了河鲈源致病性虫草菌C. confragosa CHL02菌株的全基因组序列并分析其基本特征,与参考菌株进行比较基因组分析,为后续深入开展该病菌侵染河鲈的作用机制等相关研究奠定理论基础。     

First report on the characterization of pathogenic Rahnella aquatilis KCL-5 from crucian carp: Revealed by genomic and proteomic analyses

Rahnella aquatilis is an important pathogen of several aquatic organisms and is found widely distributed in the freshwater, soil, fish and human clinical samples. Our previously published study reported a novel pathogenic R. aquatilis strain KCL-5 to crucian carp (Carassius auratus). To further investigate the characteristics and pathogenesis caused by R. aquatilis, we here report on the pathological changes, bacterial genomic and proteomic analyses of strain KCL-5. Significantly pathological changes in liver, intestine, spleen and gills were observed in infected fish. The genome consists of one circular chromosome 5,062,299 bp with 52.02% GC content and two plasmids (506,827 bp, 52.16%; 173,433 bp, 50.00%) and predicted 5,653 genes, 77 tRNAs and 22 rRNAs. Some virulence factors were characterized, including outer membrane protein, haemolysin, RTX toxin, chemotaxis and T3SS secretion system. Antimicrobial resistance genes such as EmrAB-TolC, MexABC-OpmB and RosAB efflux pump were found in strain KCL-5. KEGG analysis showed that mainly functional modules were ABC transporters, biosynthesis of amino acids, two-component system, quorum sensing, flagellum assembly and chemotaxis, in which most of them were identified by using 2-DE/MS analyses. To our knowledge, this was first report on the molecular characteristics of R. aquatilis by multi-omics approaches, which will provide insights into the pathogenic mechanism of R. aquatilis infection in fish.     

鱼源致病菌皮特不动杆菌Ap-W20的全基因组序列及其毒力特征分析

皮特不动杆菌是一种新兴的鱼源致病菌,为了对该菌的致病机理进行研究并为该菌引起的鱼类疾病防治提供技术储备,实验选取皮特不动杆菌菌株Ap-W20进行了全基因组测序,并对其毒力特征进行了分析。结果发现,Ap-W20全基因组序列总长为4 399 705 bp,GC含量为38.78%,共预测到4 230个编码序列(CDS),存在4个质粒,GenBank数据库登录号为CP027658～CP027662。ANI分析结果证实,Ap-W20属于皮特不动杆菌,且ApW20与已知人源皮特不动杆菌AP_882(96.69%)和环境源皮特不动杆菌PHEA-2(96.55%)相似度较高。Ap-W20与AP_882、PHEA-2的比较基因组学分析发现,Ap-W20中的基因岛、前噬菌体和质粒数量最多,这很可能与它们各自的分离环境和致病力有关。通过与毒力因子数据库(VFDB)比对,在Ap-W20全基因组中预测到286个毒力基因,主要与黏附和抗吞噬等有关。Ap-W20中还存在Ⅰ、Ⅱ和Ⅵ型分泌系统、多套双组分调控系统以及细菌素合成基因簇等,表明鱼源皮特不动杆菌可能存在复杂的致病机制。本研究对鱼源皮特不动杆菌全基因组进行了毒力特征分析,为该菌引起的鱼类疾病防治奠定了基础。     

A review of sex determination and searches for sex‐specific markers in sturgeon

The availability of monosex populations of caviar‐producing female sturgeon would considerably enhance the economic viability of domestic caviar production systems. However, it is not possible to distinguish males from females by morphological characters at larval, juvenile and even adult stages. The mechanism of sex determination in sturgeons is poorly understood, and to date no sex‐specific markers in sturgeon have been reported. This review concentrates on the methodologies used to elucidate the mode of sex determination in sturgeon species and provides information on the molecular tools used to determine genetic sex markers.     

Multi-omics-driven development of alternative crops for natural rubber production

Natural rubber (NR) is an irreplaceable biopolymer of economic and strategic importance owing to its unique physical and chemical properties.  The Pará rubber tree (Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg.) is currently the exclusive commercial source of NR, and it is primarily grown in plantations restricted to the tropical and subtropical areas of Southeast Asia.  However, current Pará rubber production barely meets the sharply increasing global industrial demand for rubber.  Petroleum-based synthetic rubber (SR) has been used to supplement the shortage of NR but its industrial performance is not comparable to that of NR.  Thus, there is an urgent need to develop new productive rubber crops with broader environmental adaptability.  This review summarizes the current research progress on alternative rubber-producing plants, including horticultural plants (Taraxacum kok-saghyz Rodin and Lactuca L. species), woody plants (Parthenium argentatum A. Gray and Eucommia ulmoides Oliv.), and other plant species with potential for NR production.  With an emphasis on the molecular basis of NR biosynthesis revealed by a multi-omics approach, we highlight new integrative strategies and biotechnologies for exploring the mechanism of NR biosynthesis with a broader scope, which may accelerate the breeding and improvement of new rubber crops.      

斑点叉尾鮰源嗜麦芽寡养单胞菌的全基因组测序及比较基因组学

嗜麦芽寡养单胞菌是近年来引起斑点叉尾鮰暴发高致死性传染病的主要病原之一。为了对防治该病提供技术储备,本研究对嗜麦芽寡养单胞菌XH.SM.1菌株进行全基因组测序与比较基因组学分析,同时用扫描电镜观察其超微形态特征。电镜观察显示,XH.SM.1为两端钝圆的短杆状细菌,菌体平均长度(1.73±0.35)μm,平均直径(0.43±0.04)μm。全基因组测序得到XH.SM.1基因组大小为4.56 Mb,GC含量为66.60%,编码4087个基因。将基因组序列上传NCBI,得到登录号:PYBO01000001.1。通过与VFDB数据库比对,预测得到3个可信度较高的毒力基因。共线性分析结果显示XH.SM.1与10株完成图水平的嗜麦芽寡养单胞菌有较好的共线性。ARDB数据库预测和基因组岛分析,共同发现XH.SM.1基因组中含有许多耐药基因。泛基因组分析显示XH.SM.1呈现开放性(open)结果,这与嗜麦芽寡养单胞菌为环境常在的条件致病菌的表型相吻合,说明其适应环境和与外界进行遗传物质交流的能力较好。     

芽孢杆菌蛋白酶基因的比较基因组学分析

【目的】研究芽孢杆菌产蛋白酶能力与携带的蛋白酶基因的关系，探寻影响芽孢杆菌产蛋白酶能 力的重要基因。【方法】通过 筛选培养基筛选能够产生蛋白酶的菌株，采用福林酚法 检测菌株产生的蛋白酶的活 性，对 15 株芽孢杆菌分离株进行全基因组测序，获得菌株染色体上携带的蛋白酶基因情况并将其分类；采用实 时荧光定量 PCR 方法检测蛋白酶基因 mRNA 的转录水平；通过比较基因组学和细菌全基因组关联分析（BGWAS）， 探讨影响细菌产蛋白酶能力高低的原因。【结果】根据菌株染色体上携带的蛋白酶基因情况，可分为 7 种基因 型（G1~G7）。比较基因组学和 BGWAS 分析发现，细菌染色体上携带的蛋白酶基因种类的多寡与其产蛋白酶能 力的高低有直接关系，且缺少 aprX 和 aprE 基因菌株的产蛋白酶能力明显下降。进一步研究基因 mRNA 水平发现， 芽孢杆菌产蛋白酶能力的差异与 aprX 的表达水平有关。【结论】 菌株染色体上携带的蛋白酶基因情况与菌株产 蛋白酶能力之间存在关联。aprX 是影响芽孢杆菌属细菌产胞外蛋白酶能力的重要基因。