大豆基因组保守序列及综合保守序列扩增多态性分子标记(ICSAP)的设计

采用VBA程序查找了大豆基因组保守序列——在基因组中出现次数较多的碱基序列片段,分析了这类保守序列的基本特性,在此基础上,设计了一种新型分子标记——综合保守序列扩增多态性分子标记.碱基数目越多,保守序列种类数和出现次数越少,从10个碱基到27个碱基,保守序列的GC含量先是逐渐增加,达到一个平台后又逐渐降低.碱基离保守序列3＇端越近,出现A或T的可能性越大,碱基在保守序列中的分布具有非随机性.不同长度的保守序列具有明显的进化关系.筛选出10个碱基的保守序列和长度为8个碱基的填充序列用来设计引物,共得到566对引物组合.该新型分子标记有望在条带多态性、引物一致性等方面超越现有分子标记,同时具有成本低廉等优点.该研究旨在为基因组保守序列查找和分子标记设计方面提供新的思路,分析这些保守序列特性有助于进一步探索分子进化机理.该新型分子标记有可能在大豆种质资源鉴定和基因图位克隆等方面得到应用,同时该分析方法也适用对其他物种.     

玉米全基因组批量化SSR多态性标记开发及PCR扩增验证

简单序列重复在真核生物的基因组中含量非常丰富,且常常随机、均匀分布于整个基因组中。SSR标记广泛应用于动、植物基因定位、群体遗传多样性分析、遗传连锁图谱构建、指纹图谱构建、种质鉴定、分子标记辅助选择等方向。随着大量全基因组序列的公布,NCBI等数据库中可利用的序列信息量激增。但在常规分子生物学研究中,仍然延续传统的小规模SSR标记开发模式,开发标记数量非常有限、效率较低。结合MISA脚本指令、Primer3引物设计软件、e-PCR特异性扩增分析软件,对玉米全基因组水平SSR位点进行搜索、引物设计、特异性扩增分析以及扩增长度差异分析,开发高密度的SSR标记。通过引物合成、PCR扩增和琼脂糖凝胶电泳,从常规分子生物学水平验证所开发标记的可靠性。     

大麦黑粉菌研究进展

大麦黑粉菌呈世界范围分布,是大麦生产中的主要病害之一,可造成严重经济损失,但在中医上又具有药用和食用价值。本文主要介绍大麦黑粉菌的分类及生理特性,大麦黑粉菌与寄主大麦的互作及其侵染机理,大麦黑粉菌的药用和食用价值,大麦黑粉菌转基因技术体系建立和大麦黑粉菌基因组研究的进展。     

DNA元素百科全书浅析

2012年9月,美国国家人类基因组研究中心资助的DNA元素百科全书(ENCODE)项目随着一系列研究成果,分成30多篇论文在Nature,Genome Research和Genome Biology 3种期刊上相继发表,标志着ENCODE项目的完成。2001年,人类基因组测序完成,解析了人类基因组是由ATGC 4个字母以怎样的排列顺序组成的。但对编码蛋白质的基因及这些基因是怎样调节控制的,基因组中的其他区域哪些参与调控等问题都未能了解。因此,科学界在2003年启动了ENCODE项目,结果表明80%的人类基因组都具有生物学活性。文中在ENCODE项目的相关信息进行论述,旨在引导人们正确认识、了解和应用ENCODE项目的研究成果为人类健康服务。     

Identification of a class of CFEM proteins containing a new conserved motif in Fusarium oxysporum

Fusarium oxysporum (Fo) is an important soil-borne fungus that cause huge economic losses worldwide. Fungal-specific Common in Fungal Extracellular Membrane (CFEM) proteins are known to be involved in some important physiological processes associated with pathogenicity. To date, few Fo CFEM proteins have been characterized. The recent publication of several genomes of Fo has allowed us to conduct a genome-wide comparison analysis of CFEM proteins in Fo. In this study, we identified CFEM proteins for 12 different Fo formae speciales(f. sp) and obtained an average of 16 CFEM proteins for each Fo. The Fo CFEM proteins were classified into three groups (groups 1–3) according to structural features. Importantly, we identified a new conserved motif containing about 50 amino acids (DR motif) in group 1 members. CFEM proteins containing DR motif (CFEM_DR proteins) are remarkably conserved among Fo, and their number is greater in Fo compared with other fungi. We found the expansion of CFEM_DR proteins in Fo can be attributed to the segmental duplications in the genomes. Expression analysis revealed that CFEM_DR genes had a higher expression level in mycelium than conidia, and their expressions increased dramatically in the host roots at 3 days post inoculation, indicating that Fo CFEM_DR genes have roles while colonizing and infecting their hosts.     

Bacteriophage OP1, lytic for Xanthomonas oryzae pv. oryzae, changes its host range by duplication and deletion of the small domain in the deduced tail fiber gene

The entire genome of bacteriophage OP₁, lytic for Xanthomonas oryzae pv. oryzae causing bacterial leaf blight of rice, and the partial genomes of related phages were sequenced and analyzed. The OP₁ genome comprises double-stranded, 4785-bp long DNA with 51.1% G + C content. Fifty-nine open reading frames (ORFs) were detected. ORF25 had similarity with the tail fiber gene of phages, whose product is related to host specificity. The ORF25 regions were amplified from four host-range mutants (OP_1h, OP_1hC, OP_1h2, and OP_1h2C) by polymerase chain reaction, and their deduced amino acid sequences were compared. Three mutants (OP_1hC, OP_1h2, OP_1h2C) had duplications of a small domain in the N-terminal portion, although there were slight differences in the position of the duplicated sequences. One mutant OP_1h had substituted amino acids in the duplication region. New mutants isolated in the laboratory (OP_1hC and OP_1h2C from OP₁ and OP_1h2) acquired the ability to lyse strain N5874 belonging to phagovar (lysotype) C. However, they rapidly lost this lytic ability when incubated with other phagovars. This loss was always accompanied by a loss of the characteristic repeats, suggesting that the host range of OP₁-related phages changed mainly through duplication and deletion of a small domain in ORF25. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AP008979, AB214312 to AB214316     

阿勒泰白头牛基因组结构变异分析

阿勒泰白头牛是新疆阿勒泰地区的乳肉役兼用地方品种,具有白头、抗病力强和性情温顺特点。结构变异(structure variations, SVs)是影响牛表型性状的重要遗传变异形式。本研究旨在获得阿勒泰白头牛基因组SVs的特征和种质特征的候选基因。以20头阿勒泰白头牛测序深度为17.32X的基因组序列为基础,通过Delly、Lumpy和Manta三个软件进行SVs的检测,并通过SURVIVOR软件取交集进行整合,总共鉴定到37847个SVs。从类型看,缺失、易位、倒位、复制和插入的比例分别为55.5%、26.7%、8.7%、8.9%和不足0.1%。从长度看,缺失、倒位和复制的分布呈现右偏态。以频率大于0.9为标准,获得636个高频SVs,涉及865个蛋白编码基因。基因注释和富集分析发现,阿勒泰白头牛的高频SVs与免疫抗病和神经功能相关,契合了抗病力强和性情温顺特征,可作为相关特征的候选基因(免疫抗病：BolA-DQB、TNIP3、IL1RAP和IL1R1,神经性情：EPHA6、GRM7和HTR2A)。值得注意的是,我们发现ASIP基因5′非编码区存在一个缺失,该基因可减少真黑素的合成,...     

苹果基因组分子生物学研究进展

借助分子标记手段苹果基因组研究取得了巨大成就,涉及苹果的抗性、生长发育、果实品质等各方面基因,综合有关文献,将其研究的主要成果,包括已发现的主要苹果遗传标记、已构建的苹果遗传连锁图谱及苹果的转基因研究进行综述,并对目前苹果基因组研究存在的问题和对策进行了分析,以期为苹果遗传育种提供参考。     

几种中国野生菊的染色体组分析及亲缘关系初步研究

通过对不同倍性的几种中国野生菊之间杂种F1减数分裂期染色体的配对分析,对它们的亲缘关系和演化过程进行了研究。观察到甘菊(Dendranthema lavandulifolium)和菊花脑(D.nankingense)是两个亲缘关系较近、但已发生了某种程度分化的二倍体;南京野菊(D.indicum)和尖叶野菊(D.indicum var.acutum)是含有相同染色体组的异源四倍体,毛华菊(D.sestitum)为异源六倍体,它们在减数分裂中期Ⅰ,染色体均能较好地配成二价体构型。尖叶野菊(4x)与菊花脑(2x)、南京野菊(4x)与毛华菊(6x)的F1,染色体配对构型分别接近于9Ⅰ 9Ⅱ和9Ⅰ 18Ⅱ,表明菊花脑或其近缘种是尖叶野菊染色体组之一的供体,南京野菊或其近缘种是毛华菊两个染色体组的供体。本文还对这几种菊属植物的演化过程进行了讨论。