基因序列分析

为了解2007 ― 2008 年北京地区流行的肠道病毒71 型( EV71) 是否存在基因序列变异及其与病毒毒力的关系, 我们选择2007 年分离的3 株EV71( 其中1 株分离自重症手足口病患儿的咽拭子标本, 其余2 株分离自普通手足口病患儿咽拭子标本) 和2008 年分离的5 株EV71( 其中3 株分离自重症手足口病患儿的咽拭子或鼻拭子标本, 2 株分离自普通手足口病患儿的疱疹液标本) , 提取基因组RNA, 经反转录-聚合酶链反应( RT-PCR) 扩增得到VP4 基因片段, 并进行核苷酸序列测定, 使用生物信息软件与GenBank 中的EV71 VP4 基因进行序列及病毒型别分析。结果表明, 所测得的8 株EV71 VP4 基因全长均为207 bp, 编码69 个氨基酸, 理论相对分子质量( Mr) 为7 ×10³。8 株EV71 病毒VP4 基因的核苷酸同源性在94% ～100% , 与GenBank 中其他EV71 病毒株VP4 的核苷酸同源性为82% ～100% , 与阜阳、深圳和台湾等地区流行的EV71 VP4 的核苷酸同源性比其他地区高。除了与印度报道的VP4 编码的氨基酸在第7 和54 位不同外( 印度株: 7 位蛋氨酸, 54位苏氨酸; 其余株7 位苏氨酸,54 位丙氨酸) , 这8 株EV71 VP4 编码的氨基酸序列之间以及与其他EV71 VP4编码的氨基酸同源性均为100%。8 株EV71 病毒VP4 与文献报道的3 株重症感染病毒株VP4 ( BrCr、MS 和NCKU9822) 核苷酸有较大差别, 而8 株病毒株中从重症感染( BJ97、BJ110B、BJ110Y 和BJ4243) 与轻症感染( BJ25、BJ47、BJ65 和BJ67) 分离到的毒株之间VP4 基因序列未见明显改变, 只有几个核苷酸存在差别。VP4 核苷酸序列的进化树分析表明, 这8 株EV71 均属于C4 亚型, 显示2007 ― 2008 年北京地区流行的EV71的VP4 基因相当保守, 分离自伴有神经系统感染的重症手足口病和普通手足口病患儿的EV71 的VP4 基因之间在核苷酸水平未出现同样的变异。结果提示, 近2 年来北京地区所流行的EV71 属C4 亚型。     

基因序列拼接新技术

<正>新一代大规模平行测序技术能以相当低的单位成本下提高测序通量,但是大量DNA小片段的拼接组装极具挑战性,如果序列拼接这个关键步骤没有提高,整个基因组图谱绘制工作的速度就会被降低。华大基因研究院的汪建、王俊教授领衔的研究小组在基因组拼接技术方面取得新的突破,在最新一期的《Genome     

莴苣叶绿体psbA基因序列

1　Ｓｏｕｒｃｅ　ＴｈｅｓｅｑｕｅｎｃｅｗａｓｄｅｔｅｒｍｉｎｅｄｆｒｏｍａＰＣＲｐｒｏｄｕｃｔｏｆｃｈｌｏｒｏｐｌａｓｔｇｅｎｏｍｉｃＤＮＡｏｆＬａｃｔｕｃａｓａｔｉｖａ (ｌｅｔｔｕｃｅ) .2　Ｎａｍｅａｎｄｄｅｓｃｒｉｐｔｉｏｎ　Ｔｈｅｃｏｄｏｎｓｅｑｕ     

快速基因序列仪问世

目前,美国威斯康星大学的化学教授Lloyd Smith成功地制造了一台能快速分析基因序列的仪器,这台仪器序列分析速度为目前同类仪器的25倍。这台新的序列仪样机由Smith教授领导一个研究小组设计制造,五年前正是他创造了第一台自动基因序列仪。现在,数百台由他先前设计的这种机器(或技术上大同小异的同类序列仪)正在世界各地的实验室发挥作用。Smith设计的这种新装置将在三年内成为商品,它与过去同类仪器的主要不同是采用了毛细管灌胶,取代了目前所用的平板胶。现在较先进的序列分析仪采用的是激光测定法,这种方法采用双脱氧末端终止法的基本     

芸薹属蔬菜Chs基因序列多态性

为探讨我国芸薹属蔬菜的起源及遗传多样性,克隆、测序芸薹属不同种的Chs基因序列。A基因组二倍体、A基因组多倍体、B基因组多倍体和C基因组二倍体的Chs基因突变位点数分别为120、172、194和25个,Chs基因多态性表现为:B基因组多倍体A基因组二倍体A基因组多倍体C基因组多倍体。Tajima'D、Fu and Li'D和Fu and Li'F检验表明A基因组二倍体、C基因组二倍体Chs基因是中性进化基因。HKA平衡检验及误配分析表明A基因组多倍体和B基因组多倍体Chs基因进化中存在选择作用。A基因组和B基因组间存在较低的共有差异和较高的共有多态性,C基因组与A、B基因组存在较高的共有差异和较低的共有多态性。系统发育树将芸薹属Chs基因序列分成4个亚支、10个支系。网状分析表明,白菜可能是四倍体A基因组的供体,黑芥可能是四倍体B基因组的供体,甘蓝可能是四倍体C基因组的供体。中国芸薹属蔬菜在Chs基因位点有较高的遗传多态性,不同基因组间分化程度不一样,B基因组分化较大,A和C基因组分化较小。A和B基因组的亲缘关系较A和C基因组以及B和C基因组更为接近。建议根据基因组的不同将中国芸薹蔬菜分成白菜组、芥菜组和甘蓝组,研究结果支持芸薹属进化的禹式三角模型。     

乙型肝炎病毒全基因序列的测定

测定７ 例慢性 Ｈ Ｂ Ｖ 携带者 Ｈ Ｂ Ｖ 基因组全序列,经同源性比较,确定基因型。２ 例基因型为 Ｂ 型,余均为 Ｃ 型;血清型ａｄｒ ４ 例,ａｄｗ ３ 例。各序列间 Ｘ 基因差异最大。未见 Ａ１８９６ 、 Ｔ１７６２ Ａ１７６４等重要位点的变异。结合已有的２ 株 Ｈ Ｂ Ｖ 中国流行株全基因序列,初步建立以中国流行株序列为基础的 Ｈ Ｂ Ｖ 标准序列,该标准序列与国外标准序列仅有２２ 个位点的差异     

乙型肝炎病毒全基因序列的测定

Seven cases of chronic hepatitis B virus carriers were included for sequencing of whole gene sequences of hepatitis B virus (HBV). The serotype of 4 strains of HBV were adr, and 3 strains were adw. Two strains were classified to genotype B, and the other 5 strains to genotype C. No significant mutations, such as A¹⁸⁹⁶, T¹⁷⁶²A¹⁷⁶⁴ were present. With other reported 2 complete sequences of HBV strains prevailing in mainland China, 7 strains of HBV whole sequences of genotype C from mainland China were analyzed to produce the consensus sequence of HBV of China. Comparing of the consensus sequence with that from Genbank, there were only 22 sites with different nucleotides.     

如何在GenBank中注册基因序列

很多杂志要求论文提供所涉及的新基因序列具有GenBank 编号, 以下是如何向GenBank 递交新基因序列的一些建议。.......     

大绿蛙Sox基因和Dmrt基因的序列分析

Sox基因家族与Dmrt基因家族在胚胎发育及性别分化中起着重要作用。采用PCR方法,扩增了大绿蛙Sox基因和Dmrt基因的保守区,分别获得长约220 bp和140 bp的片段。序列分析表明,大绿蛙雌雄个体之间Sox基因、Dmrt基因序列没有差异,与人和其它动物的Sox基因、Dmrt基因有非常高的相似性,显示了Sox基因及Dmrt基因在系统进化上的高度保守性。本研究为探讨大绿蛙的性别决定机制及Sox基因与Dmrt基因的进化提供了分子资料。     

Utility of Low-Copy Nuclear Gene Sequences in Plant Phylogenetics

Low-copy nuclear genes in plants are a rich source of phylogenetic information. They hold a great potential to improve the robustness of phylogenetic reconstruction at all taxonomic levels, especially where universal markers such as cpDNA and nrDNA are unable to generate strong phylogenetic hypotheses. Low-copy nuclear genes, however, remain underused in plant phylogenetic studies due to practical and theoretical complications in unraveling the evolutionary dynamics of nuclear gene families. The lack of the universal markers or universal PCR primers of low-copy nuclear genes has also hampered their phylogenetic utility. It has recently become clear that low-copy nuclear genes are particularly helpful in resolving close interspecific relationships and in reconstructing allopolyploidization in plants. Gene markers that are widely, if not universally, useful have begun to emerge. Although utilizing low-copy nuclear genes usually requires extra lab work such as designing PCR primers, PCR-cloning, and/or Southern blotting, rapid accumulation of gene sequences in the databases and advances in cloning techniques have continued to make such studies more feasible. With the growing number of theoretical studies devoted to the gene tree and species tree problem, a solid foundation for reconstructing complex plant phylogenies based on multiple gene trees began to build. It is also realized increasingly that fast evolving introns of the low-copy nuclear genes will provide much needed phylogenetic information around the species boundary and allow us to address fundamental questions concerning processes of plant speciation. Phylogenetic and molecular evolutionary analyses of developmentally important genes will add a new dimension to systematic and evolutionary studies of plant diversity.     

Molecular Phylogeny of Rhizophoraceae Based on rbcL Gene Sequences

rbcL sequences to clarify the inter- and intrarelationships of Rhizophoraceae which have been variously discussed. The analyses included 12 of the 15 genera of Rhizophoraceae (4/7 of Macarisieae, 4/4 of Gynotrocheae, and 4/4 of Rhizophoreae) and a few putatively related taxa, including two of the four genera of Anisophylleaceae. The most parsimonious trees supported the monophyly of Rhizophoraceae as well as each of the three traditionally recognized tribes Macarisieae, Gynotrocheae, and Rhizophoreae. The family Rhizophoraceae is a sister taxon to Erythroxylum (Erythroxylaceae) and is further closely related to Byrsonima (Malpighiaceae), Passiflora (Passifloraceae), Turnera (Turneraceae), Ochna (Ochnaceae), Drypetes (Euphorbiaceae), and Humiria (Humiriaceae). Anisophylleaceae, which have often been included in Rhizophoraceae as a tribe or subfamily, are placed in a common clade with Begonia (Begoniaceae), Cucurbita (Cucurbitaceae), Coriaria (Coriariaceae), Corynocarpus (Corynocarpaceae), Datisca (Datiscaceae), Tetrameles (Datiscaceae), and Octomeles (Datiscaceae). Within Rhizophoraceae the mangrove tribe Rhizophoreae is sister to the inland tribe Gynotrocheae, with inland tribe Macarisieae positioned as a sister taxon to these two tribes. This pattern of relationships within the family basically agrees with those suggested by cladistic analyses based on morphological characters, except that Gynotrocheae are monophyletic with Crossostylis as a derived taxon within the tribe in the present study. Based on this cladogram for Rhizophoraceae, we discuss evolutionary trends of a few ecological and morphological characters, including the formation of aerial roots and the ovary position. Received 12 August 1999/ Accepted in revised form 11 October 1999