Identification of positive selection in disease response genes within members of the Poaceae

Millions of years of coevolution between plants and pathogens can leave footprints on their genomes and genes involved on this interaction are expected to show patterns of positive selection in which novel, beneficial alleles are rapidly fixed within the population. Using information about upregulated genes in maize during Colletotrichum graminicola infection and resources available in the Phytozome database, we looked for evidence of positive selection in the Poaceae lineage, acting on protein coding sequences related with plant defense. We found six genes with evidence of positive selection and another eight with sites showing episodic selection. Some of them have already been described as evolving under positive selection, but others are reported here for the first time including genes encoding isocitrate lyase, dehydrogenases, a multidrug transporter, a protein containing a putative leucine-rich repeat and other proteins with unknown functions. Mapping positively selected residues onto the predicted 3-D structure of proteins showed that most of them are located on the surface, where proteins are in contact with other molecules. We present here a set of Poaceae genes that are likely to be involved in plant defense mechanisms and have evidence of positive selection. These genes are excellent candidates for future functional validation.     

细菌必需基因、最小基因组和合成细胞

单细胞原核生物是原始的细胞生命形式,确定细菌必需基因和最小基因组对理解生命的本质、细胞生命的起源和进化有非常重要的意义。文中简要介绍近年来有关细菌的必需基因、最小基因组和合成细胞的研究方法、理论和进展。还特别介绍人工建立最小细菌基因组的策略以及应用前景。     

抗虫基因研究及在芸薹属作物上的应用

芸薹属作物属十字花科,包括多种重要的蔬菜和油料作物。该类作物易受病虫害侵袭,造成品质和产量严重受损。化学方法防治害虫不仅破坏环境而且费用昂贵,所以培育抗虫品种成为既经济又环保的措施之一。但由于目前抗虫资源匮乏,难以通过常规育种培育出抗虫的品种,植物基因工程技术的应用,能加快育种进程,提高育种效率。简要介绍近年来抗虫基因的发掘及其在芸薹属中的应用进展。     

转cry1Ac＋cry2Ab基因棉与转cry1Ac＋剧咯邢基因棉荒地的生存竞争能力

【背景】此研究为“十二五”转基因生物新品种培育国家项目中创建新的转基因棉花品种环境安全评价技术而设。【方法】以转双价双成抗虫基因（cry1Ac＋cry2Ab）棉和转双价抗虫、抗除草剂基因（cry1Ac＋肼强阳）棉为观察品种,非转基因棉赣棉11号为对照品种,在荒地用撒播和3cm深度播种2种方式,于2011年5月一2012年3月对棉花出苗率、株高、生育进程、棉吐絮瓣数、絮瓣脱落率、自生苗等生存竞争能力进行比较,检测、评价其杂草化的风险,并探讨、验证检测技术的可行性。【结果】在荒地条件下,以2种方式播种的转cry1Ac＋cry2Ab基因棉和转cry1Ac＋EP5P5基因棉与非转基因棉相比,上述各项指标的竞争能力总体上未表现显著优势。【结论与意义】转cry1Ac＋cry2Ab基因棉和转cry1Ac＋EPSPS基因棉在荒地条件下生长无杂草化风险。同时,研究证明,在荒地自然生态条件下,可以采用撒播和3cm深度播种方法检测新的转基因棉花品种在生存竞争能力上的杂草化风险,在测评上有互为参照效应,为定性评价新的转基因棉花品种的杂草化风险提供了保障。     

玉米与其他六种植物NBS类抗病基因的进化比较分析

具有核苷酸结合位点(nucleotide binding site,NBS)的抗病基因在植物抵抗各种病原菌侵染中起关键作用。对玉米全基因组中具有NBS结构的基因进行鉴定和分析,并结合水稻、高粱、拟南芥、百脉根、苜蓿和杨树的NBS类基因比较其在数量、复制、染色体定位和亲缘关系上的进化差异。发现玉米NBS类基因数量、复制数和成簇基因数均明显少于其他植物。低复制频率可能导致玉米NBS类基因较少,并推测可能导致其功能具有多样性。在基因染色体定位上,除高梁外,玉米与其他五种植物相似,呈不均衡分布。此外,进化树分析表明玉米NBS类基因与高粱的亲缘关系最近,与拟南芥的最远,在物种间表现出较高的保守性。结果对掲示玉米NBS基因的进化特点与发掘有益的NBS类抗病基因提供了重要的理论依据。     

番茄COBRA基因克隆、表达模式及生物信息学分析

COBRA作为一种重要的胞外糖基磷脂酰肌醇(GP-I)锚定蛋白,影响植物细胞壁中纤维素含量及细胞的定向伸长。目前已有多个拟南芥、玉米及水稻的COBRA基因的突变体被研究。而有关番茄COBRA基因克隆的研究尚未见报道。本研究利用RT-PCR技术克隆了一个假定编码番茄COBRA蛋白的SlCOBRA基因,并在GenBank注册(JN398667)。序列测定和分析表明,该序列由6个外显子组成,编码444个氨基酸残基;氨基酸序列中存在COBRA蛋白的CCVS保守基序,N端的跨膜信号肽及C-末端的疏水性尾部和GPI锚定ω-位点。系统进化分析表明番茄SlCOBRA与拟南芥AtCOB具有80%氨基酸序列同源性,聚在一个分支上。Real-time PCR分析番茄各个组织中COBRA基因的表达结果表明番茄COBRA为组成型表达,在营养器官(根、茎、叶)中的表达量高于花和果实,尤其在成熟的果实中(从转色期到红熟期)表达量明显减少。     

粪肠球菌生物被膜形成早期相关基因的表达研究

目的:以粪肠球菌为研究对象,探讨粪肠球菌基因srtA(转肽酶A编码基因)、esp(肠球菌表面蛋白)与粪肠球菌生物被膜形成早期的相关性。方法:用逆转录PCR与实时荧光定量PCR方法对生物被膜和浮游菌组细菌srtA、esp两种与生物被膜形成早期相关的基因其表达进行检测,并进行统计学分析。结果:srtA、esp基因与粪肠球生物被膜菌早期形成密切相关。生物被膜菌组srtA、esp表达量分别是浮游菌组的7.9与13.5倍。结论:srtA、esp基因与粪肠球生物被膜菌形成早期密切相关,可能是生物被膜早期形成的上调因子。     

Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria

Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2 m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this cluster was only detected on aggregates up to a few meters above the sediment surface, but never in the fraction of free-living bacteria. A quantitative real-time PCR approach revealed that the MMC constituted up to 13% of total bacterial 16S rRNA genes in surface sediments of the North Sea. In a global survey, including sediments from the Mediterranean Sea, the Atlantic, Pacific and Indian Ocean and various climatic regions, the MMC was detected in most samples and to a water depth of 4300 m. Two fosmids of a library from sediment of the southern North Sea containing 16S rRNA genes affiliated with the MMC were sequenced. Both fosmids have a single unlinked 16S rRNA gene and no complete rRNA operon as found in most bacteria. No synteny to other myxobacterial genomes was found. The highest numbers of orthologues for both fosmids were assigned to Sorangium cellulosum and Haliangium ochraceum. Our results show that the MMC is an important and widely distributed but largely unknown component of marine sediment-associated bacterial communities.