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。     

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.     

二代测序技术在水稻基因组学和转录组学研究中的应用

二代测序技术是测序技术的一次革命性突破,它具有高通量、高精度、低成本的优势,为水稻基因组学研究提供了新的研究方法和解决方案。概述了以使用合成法测序和连接法测序为原理的二代测序技术的特点和发展,并总结了其在水稻基因组学,包括结构基因组学和功能基因组学以及转录组学研究中的应用,并就当前测序技术的发展趋势作了展望。     

Development of Genome-Wide Scan for Selection Signature in Farm Animals

Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.     

转基因技术在大豆性状改良上的应用

随着我国大豆需求量的逐年增加,培育超高产、优质、高抗性品种的需求变得越来越迫切。基因工程方法的应用为作物遗传育种开辟了一条新的道路,通过转基因技术,将控制优良性状的基因整合到作物基因组中,培育转基因植株,可以准确的、有目的对作物的农艺性状进行定向改良。近年来,功能基因组学的发展为转基因技术提供了新的指导。本文着重讲述了大豆遗传转化方法的新方向,同时介绍了国内外转基因技术在大豆性状(抗除草剂、抗虫、抗病、抗逆、品质性状等)改良中的研究进展,并对未来大豆转基因方向进行了展望。     

Comparative genome sequencing to assess the genetic diversity and virulence attributes of 15 Vibrio anguillarum isolates

Vibrio anguillarum is the causative agent of vibriosis, a deadly haemorrhagic septicaemic disease affecting various marine and fresh/brackish water fish, bivalves and crustaceans. However, the diversity and virulence mechanisms of this pathogen are still insufficiently known. In this study, we aimed to increase our understanding of V. anguillarum diversity and virulence through comparative genome analysis of 15 V. anguillarum strains, obtained from different hosts or non‐host niches and geographical regions, among which 10 and 5 strains were found to be virulent and avirulent, respectively, against sea bass larvae. First, the 15 draft genomes were annotated and screened for putative virulence factors, including genes encoding iron uptake systems, transport systems and non‐ribosomal peptide synthetases. Second, comparative genome analysis was performed, focusing on single nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels). Five V. anguillarum strains showed a remarkably high nucleotide identity. However, these strains comprise both virulent and avirulent strains towards sea bass larvae, suggesting that differences in virulence may be caused by subtle nucleotide variations. Clearly, the draft genome sequence of these 15 strains represents a starting point for further genetic research of this economically important fish pathogen.     

作物基因组学与作物科学革命

作物科学的发展对于世界粮食的增产起着重要的作用。本文回顾了第一次绿色革命的历史。通过比较中国与国际上矮化育种时间、矮源的来源以及同期主要绿色革命国家产量的提高幅度,证明中国应该是第一次绿色革命的策源地与发起国之一。包括“中国绿色革命”、杂交水稻等成果在内的中国作物科学研究成果对中国及世界作物生产作出了突出的贡献。当前中国的作物生产面临着严峻的挑战。第一次绿色革命之后的数十年间,中国小麦等主要粮食作物遗传改良年增长仅为0.7%-0.9%,远低于1.7%的需求;肥水利用效率仅为发达国家的1/3;机械化程度虽有较大的提高,但与发达国家相比仍有较大差距;农产品品质不能满足人们的需求,食品安全存在较大问题。鉴于上述情况,目前迫切需要开展一场以“更高产、更高效、更优质、更环保”为主要目标的新的绿色革命。尽管传统的作物科学对作物生产作出了巨大的贡献,但事实证明,仅靠传统的作物科学难以完成新的绿色革命重任。作物基因组学是当前生物科学领域发展最为迅速的一门新兴学科。当前大多数作物基因组测序已经完成,标志着作物科学已经进入基因组时代,为基于基因组学的作物科学研究奠定了基础。基因组学的发展正在促进作物科学在以下4个方面取得重要进展：（1）促进作物种质资源核心种质构建、重要农艺性状基因的克隆与种质资源的开发与利用,推动种质资源变异组学科的形成;（2）促进作物育种理论与育种方法的重大突破,推动育种基因组学的形成与发展;（3）推动环境条件与栽培措施影响基因表达调控的影响机制研究,一批受环境因素调控的基因将被发现,促进栽培学研究向栽培基因组学的方向发展;（4）迅速提高特色作物的研究水平,缩小作物间研究差距。当前是作物科学发展史上前所未有的高速发展时期,种质资源变异组学、育种基因组学与栽培基因组学的发展将引起作物科学的革命,并将由此引发新的绿色革命。文中分析了中国当前在研究队伍的组织、研究题目与研究材料的选择与研究成果的转化等方面存在的问题,并提出了解决方法及发展方向。     

中国农业昆虫基因组学研究概况与展望

昆虫种类繁多,变异惊人,是地球上最大的动物类群,其中不少种类是农业上的重要害虫或益虫。自从2000年黑腹果蝇（Drosophila melanogaster）基因组发表以来,当代的昆虫学研究已经越来越多地依赖于从基因组和转录组所获得的信息。为了更好地理解昆虫生物学特性和增强应对那些严重影响人类健康、粮食供应和经济安全的各种卫生、农林害虫的能力,更好地利用那些在维持自然和农业生态系统不可或缺的昆虫以及那些为人类提供丝、蜂蜜和药品的昆虫,需要了解它们的基因组和转录组信息。目前世界上已经有50多种昆虫的基因组被报道,近10年来中国科学家也已经完成了家蚕（Bombyx mori）、小菜蛾（Plutella xyllostella）、东亚飞蝗（Locusta migratoria manilensis）、榕小蜂（Ceratosolen solmsi）和褐飞虱（Nilaparvata lugens）的基因组测定和分析,还有一批重要农业昆虫的基因组正在分析中,这其中包括烟粉虱（Bemisia tabaci）、斜纹夜蛾（Spodoptera litura）、二化螟（Chilo suppressalis）、白背飞虱（Sogatella furcifera）、灰飞虱（Laodelphax striatellu）和若干寄生蜂种类。自从2010年中国率先在国际上报道了2种昆虫（烟粉虱和褐飞虱）的转录组和表达谱以来,短短几年仅国内就已经有上百个昆虫转录组得到分析。同时,家蚕、东亚飞蝗和褐飞虱的功能基因组研究也取得了很大的进展, 例如,用40个品系重测序揭示了家蚕在驯化过程中相关的基因变化,通过信号通路分析解析了东亚飞蝗散居型和群居型转换的分子机制,以及发现了2个胰岛素受体是控制稻飞虱长、短翅型可塑性发育的“分子开关”。在基因组和转录组基础上,通过基因功能的研究和挖掘,结合应用新的基因组定点编辑技术和RNAi技术,将使害虫的防治和益虫的利用出现革命性的变化。     

Comparative genomics of Brassicaceae crops

The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed.