父系遗传背景对小鼠体细胞核移植效率的影响

为了评价父系遗传背景对小鼠体细胞核移植效率的影响,本试验用129/Sv小鼠、C3H小鼠和ICR的雄鼠分别与昆明雌鼠(KM)杂交的F1代为研究对象,以KM自交鼠F1代为对照,比较卵母细胞的可操作性以及重构胚的激活率、卵裂率和囊胚发育率。结果显示:129/Sv×KM、C3H×KM和KM×KM的去核效率显著高于ICR×KM(78.0%、82.9%、81.0%vs63.9%;P<0.05);129/Sv×KM的注核成功率显著高于C3H×KM、ICR×KM和KM×KM(83.0%vs59.6%、55.5%、71.4%;P<0.05);129/Sv×KM的重构胚激活率显著高于C3H×KM、ICR×KM和KM×KM(97.3%vs85.2%、81.7%、78.3%;P<0.05);C3H×KM的卵裂率和囊胚率显著高于ICR×KM和KM×KM(84.5%、28.2%vs63.2%、11.4%,64.5%、16.5%;P<0.05)。研究表明129/Sv、C3H和ICR3个品系父系遗传背景影响小鼠体细胞核移植效率,其中C3H父系遗传背景的卵母细胞可提高体细胞核移植效率。     

小鼠Nucleophosmin基因的克隆及基因组结构分析

Nucleophosmin(NPM)是主要的核仁磷酸化蛋白,在一些退行性大细胞淋巴瘤、骨髓增生异常综合征、急性髓性白血病等病人中可见累及NPM基因的染色体易位。建立NPM基因剔除的小鼠模型对于研究NPM基因的生物学功能及其在淋巴瘤及白血病发病中的确切作用有非常重要的意义。为获得包含NPM基因组全长序列的噬菌体克隆,以小鼠NPM cDNA为探针对129S1系小鼠λ噬菌体基因组文库进行筛选,经3轮筛选鉴定出一个包含小鼠NPM基因组全序列的噬菌体克隆。用鸟枪法对这个λ噬菌体克隆全长15．3kb进行了测序,序列经BLAST分析显示,该克隆所包含的129Sl系小鼠NPM基因组序列与GenBank中C57BL／6系小鼠序列约99．8％相同。根据测序获得的基因组序列,应用生物信息学方法对小鼠NPM的基因组结构及NPM基因5’启动子区可能的转录因子结合位点等进行了分析。     

两种激活处理促进小鼠孤雌胚胎原核形成

不同人工处理方法激活哺乳动物卵母细胞的机理相似,但其激活效率存在差异。本研究以昆明(KM)、129/Sv×KM F1和C3H×KM F1雌鼠来源的卵母细胞为对象,利用氯化锶(SrCl2,Sr2+)联合细胞松弛素B(cytochalasin B,CB)(Sr2++CB)和离子霉素(ionomycin,Ion)联合6-二甲胺基嘌呤(6-dimethylaminopurine,6-DMAP)(Ion+6-DMAP)两种激活方法处理下对比分析不同品系小鼠卵母细胞的激活效率,并以卵母细胞原核形成率、原核数量和孤雌胚胎体外发育来评价两种激活剂的激活效率。研究结果表明,Ion+6-DMAP激活卵的1原核比率显著高于2原核(p0.05),Sr2++CB激活卵的2原核比率显著高于1原核(p0.05);KM、129/Sv×KM F1和C3H×KM F1各组孤雌胚胎卵裂率和激活率没有显著差异(P0.05),但129/Sv×KM F1和C3H×KM F1囊胚发育率显著高于KM组(p0.05)。3种小鼠品系的卵母细胞用Sr2++CB处理的孤雌胚胎发育率显著高于Ion+6-DMAP。结果证明,Sr2++CB处理小鼠卵母细胞的激活效率明显优于Ion+6-DMAP;129/Sv×KM F1和C3H×KM F1的孤雌胚胎体外发育率显著高于KM小鼠,为研究小鼠遗传背景影响孤雌胚胎发育的机理提供参考。     

高桥仁蚧线粒体全基因组测序与分析

【目的】测定和分析半翅目(Hemiptera)仁蚧科(Aclerdidae)首个线粒体全基因组——高桥仁蚧Aclerda takahashii线粒体全基因组序列,并探讨与其他蚧虫类群的系统发育关系。【方法】基于Illumina测序技术进行高桥仁蚧线粒体全基因组测序,并进行生物信息学分析;基于已报道的15科31种半翅目昆虫的线粒体全基因组序列运用最大似然法(ML)和贝叶斯推断法(BI)构建半翅目系统发育树。【结果】高桥仁蚧线粒体基因组全长16 599 bp, AT含量高达84.51%。在该线粒体基因组中,缩减tRNA非常普遍, 10个tRNA缺失二氢尿嘧啶(DHU)臂或TΨC臂, tRNAser(S1)和tRNAser(S2)缺失DHU臂和TΨC臂。系统发育树显示, 与仁蚧科亲缘关系最近的是蚧科(Coccidae)。【结论】本研究报道了首个仁蚧科的线粒体基因组, 发现在高桥仁蚧线粒体基因组中存在普遍的tRNA缺臂现象, 为进一步系统地研究蚧虫线粒体基因组提供了数据支持。     

基于k-mer组分信息的系统发生树构建方法

随着越来越多基因组的测序完成,基于全基因组的非比对的系统发生分析已成为研究热点。不同的生物物种或个体基因组之间的核酸组分不完全相同。遗传语言-DNA序列的信息很大程度上反映在其k—mer频数中。基于基因组序列k-mer频数的系统发生树则从新的角度为我们提供物种之间的亲缘关系。本文定义基于k-mer,频数的信息参数,并用它表征基因组序列,计算不同基因组之间信息参数的距离,用邻接法对84个病毒构建了系统发生树,发现构建的系统发生树很大程度上与已有的系统发生树相吻合。     

特异区段替换小鼠性发育表型的研究

目的了解性发育相关数量性状基因座(quantitative trait locus,QTL)(DXMit68-rs29053133)在近交系小鼠A/J和C3H/HeJ(C3H)中是否存在影响表型的序列差异,以帮助对候选基因进行筛选。方法利用A/J和C3H构建了针对该区段的特异区段替换系小鼠,并对其雌鼠的性发育相关性状进行研究。结果 A/J和C3H在这一QTL中染色体的序列差异,没有引起相关性状的明显差异。结论研究结果显示,A/J和C3H小鼠中该QTL区段中存在序列差异的基因并不是引起性发育表型产生差异的候选基因。     

mtDNA基因树拓扑距离比较和基因分群

基因树间拓扑距离数据的比较进一步证明：与分割拓扑距离相比,能经拓扑距离是一种更为精确的测度,利用相对通经拓扑距离构建了8个基因的拓扑距离树。基因的拓扑距离树能直观地反映不同基因树的拓扑结构差异大小,可用来对基因进行分群。此外,发现不同DNA序列用于构建多基因树中其系统发生信息存在“累加”,“合取”,“含盖”,“相斥”等数学关系。这可解释在mtDNA基因组中一些基因比另一些基因更适合用来的构建树的结果。结果提示从GenBank中应选择具有累加基因的DNA序列或蛋白质氨基酸序列合并来构建物种。在讨论中还提出了一种获得真树的新建树策略。     

基于ITS序列的不同产地裂叶荆芥系统发育分析

采用PCR法扩增来自国内5个不同产地的裂叶荆芥ITS全序列,测序后以产自河北的裂叶荆芥代表中国裂叶荆芥与来自不同国家的裂叶荆芥ITS序列进行比较,构建分子系统发育树,探讨国内5个不同产地及不同国家的裂叶荆芥的亲缘关系和系统进化。结果表明:国内5个不同产地的裂叶荆芥ITS1和ITS2序列均有较高的G/C含量;5个产地的裂叶荆芥的扩增序列长度均为749bp,且序列完全相同;其中ITS1序列长231bp,5.8S序列长168bp,ITS2序列长236bp。中国裂叶荆芥与日本、韩国裂叶荆芥ITS序列一致性为100%,与美国裂叶荆芥ITS序列一致性为99.0%。与美国裂叶荆芥相比,中国裂叶荆芥ITS序列有7个碱基发生变异。来自不同国家的裂叶荆芥形成单系群和2个分支(中、日、韩3国为1个分支,美国单独形成1个分支)。ITS序列的一致性表明国内5个不同产地裂叶荆芥为同一个种。     

一株辛德毕斯病毒的基因组序列测定及分析

目的：对引进的一株辛德毕斯病毒的基因组序列进行测定,阐明其与已报道毒株序列的关系。方法：对辛德毕斯病毒基因组编码区进行分段RT-PCR扩增,对非编码区采用RACE法进行扩增,将扩增产物直接进行测序,应用DNAStar软件将测序结果拼接得到基因组序列,采用MEGA3.1软件对9株辛德毕斯病毒基因组序列进行系统进化发生树的构建。结果与结论：此株辛德毕斯病毒基因组共11663nt,编码3745个氨基酸残基,其中5＇端的2/3基因组编码4种非结构蛋白NSp1、NSp2、NSp3和NSp4,3＇端的1/3基因组编码5种结构蛋白E1、E2、E3、6K和C;结构基因和非结构基因之间有48nt的连接区为非翻译区;病毒基因组5＇末端和3＇末端分别有59、318nt的非编码区;序列同源性分析结果表明,此株病毒与S.A.AR86株的同源性最高,两者核苷酸序列的同源性为99.7%,氨基酸序列的同源性为99.6%,而与本室保存的另一辛德毕斯病毒MEI株的遗传进化关系稍远,系统进化发生树处于不同分支上。     

天津市致病毒性脑炎柯萨奇病毒B组5型全基因组序列分析

肠道病毒是我国病毒性脑炎(Viral encephalitis,VE)的主要病原体。本文研究对4株引起VE的天津柯萨奇病毒B组5型(Coxsackievirus B5,CV-B5)分离株进行Illumina MiniSeq高通量测序,并对其全基因组特征、进化及重组特点进行分析。结果提示,4株CV-B5天津分离株的全基因组核苷酸和氨基酸序列同源性分别为84.5%~100.0%和98.1%~100.0%,与国内流行株的全基因组核苷酸序列同源性为83.2%~96.5%,氨基酸序列同源性为96.4%~99.4%。基于全基因组的系统进化分析将CV-B5流行株分为A-D四个基因型,其中天津与国内流行株均属于C基因型。C基因型进一步分为3个进化分支,而天津分离株处在两个不同的分支上。基于基因组各区段序列的系统进化与SimPlot重组分析结果显示,天津分离株15-39N、15-41N与埃可病毒30型(Echovirus 30,E-30)原型株在P3区3B、3C、3D区域均检测到重组信号。本研究有助于了解CV-B5的全基因组特点和重组规律,为相关疾病的防控提供依据。     

Characterization of a cluster comprising ∼100 odorant receptor genes in mouse

With ∼1000 genes, the odorant receptor (OR) gene repertoire is the largest gene family in the mouse genome. Here we have established a 129/Sv BAC contig for mouse OR gene cluster 7 (Olfr7) on Chromosome (Chr) 9. The assembled ∼2-Mb contig consists of 75 BACs and may contain as many as 100 OR genes, or ∼10% of the mouse repertoire. Facilitated by the lack of introns in the coding region, we have determined the nucleotide sequence of 37 full-length, 2 partial, and 3 pseudo coding regions. These 42 OR genes and 3 additional OR genes previously mapped to the mouse Olfr7 cluster can be organized into 13 classes based on OR probe cross-hybridizations with 129/Sv mouse genomic DNA. OR genes belonging to the same class tend to be located next to each other within the cluster. Comparison of published full-length mouse and rat OR coding sequences with those identified here shows that the Olfr7 OR genes are highly related to each other, clustering on two major branches of an unrooted phylogenetic tree. Eight ORs contain an unusual NXC sequon at the amino-terminal extracellular domain that may represent a novel N-linked glycosylation site. The BAC contig presented here provides the substrate for sequencing of the cluster. Received: 27 June 2000 / Accepted: 17 August 2000     

Fine-Scale Phylogenetic Discordance across the House Mouse Genome

Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified. The house mouse subspecies group provides a model system for examining phylogenetic discordance. House mouse subspecies are recently derived, suggesting that even if there has been a simple tree-like population history, gene trees could disagree with the population history due to incomplete lineage sorting. Subspecies of house mice also hybridize in nature, raising the possibility that recent introgression might lead to additional phylogenetic discordance. Single-locus approaches have revealed support for conflicting topologies, resulting in a subspecies tree often summarized as a polytomy. To analyze phylogenetic histories on a genomic scale, we applied a recently developed method, Bayesian concordance analysis, to dense SNP data from three closely related subspecies of house mice: Mus musculus musculus, M. m. castaneus, and M. m. domesticus. We documented substantial variation in phylogenetic history across the genome. Although each of the three possible topologies was strongly supported by a large number of loci, there was statistical evidence for a primary phylogenetic history in which M. m. musculus and M. m. castaneus are sister subspecies. These results underscore the importance of measuring phylogenetic discordance in other recently diverged groups using methods such as Bayesian concordance analysis, which are designed for this purpose.     

Single nucleotide polymorphism-based species phylogeny of greater fritillary butterflies (Lepidoptera: Nymphalidae: Speyeria) demonstrates widespread mitonuclear discordance

The systematics of Speyeria butterflies has historically been complicated by intraspecific variability that has challenged efforts to delimit species and reconstruct phylogenies. Our study presents a phylogenetic comparison of genomic single nucleotide polymorphisms (SNPs) and mitochondrial COI gene sequences, with comprehensive taxon sampling that includes 15 species and 46 subspecies. Increased sampling of genetic markers and taxa improved the match between genetic clusters, obtained with both phylogenetic and cluster-based analyses, and species previously detected using morphology, as well as showing two species delimitations that may need revision. We also recovered extensive mitonuclear discordance between genomic SNPs and the COI gene, confirming that mitochondrial DNA does not reliably identify several species at broad geographic scales. Resolution of the relationships of Speyeria species demonstrates the importance of sampling variation across the whole genome, and provides an essential foundation for understanding the evolution of this charismatic clade of North American butterflies.     

A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction

The majority of gene-targeting experiments in mice are performed in 129Sv-derived embryonic stem (ES) cell lines, which are generally considered to be more reliable at colonizing the germ line than ES cells derived from other strains. Gene targeting is reliant on homologous recombination of a targeting vector with the host ES cell genome. The efficiency of recombination is affected by many factors, including the isogenicity (H. te Riele et al., 1992, Proc. Natl. Acad. Sci. USA 89, 5128-5132) and the length of homologous sequence of the targeting vector and the location of the target locus. Here we describe the double-end sequencing and mapping of 84,507 bacterial artificial chromosomes (BACs) generated from AB2.2 ES cell DNA (129S7/SvEvBrd-Hprtb-m2). We have aligned these BACs against the mouse genome and displayed them on the Ensembl genome browser, DAS: 129S7/AB2.2. This library has an average insert size of 110.68 kb and average depth of genome coverage of 3.63- and 1.24-fold across the autosomes and sex chromosomes, respectively. Over 97% of the mouse genome and 99.1% of Ensembl genes are covered by clones from this library. This publicly available BAC resource can be used for the rapid construction of targeting vectors via recombineering. Furthermore, we show that targeting vectors containing DNA recombineered from this BAC library can be used to target genes efficiently in several 129-derived ES cell lines.     

Behavioural profiles of inbred mouse strains used as transgenic backgrounds. II: cognitive tests

One of the characteristic manifestations of several neurodegenerative diseases is the progressive decline in cognitive ability. In order to determine the suitability of six mouse strains (129S2/Sv, BALB/c, C3H/He, C57BL/6j, CBA/Ca and DBA/2) as transgenic background strains, we investigated the performance on a variety of tasks designed to identify subtle changes in cognition. In addition, a test of exploratory behaviour was used to probe the level of underlying anxiety in these mouse strains, as anxiety can be a confounding factor on behavioural performance generally. The C3H/He mice exhibited the least anxiogenic behavioural profile spending most time on the open arms of the maze, in contrast to the 129S2/Sv mice which spent the least amount of time in this location and were the quickest to move into a closed arm. The C3H/He mouse strain failed to acquire a visual discrimination task and failed to demonstrate learning on a water maze spatial learning task, in contrast to the CBA/Ca, DBA/2 and C57BL/6j strains which demonstrated a degree of learning in both tasks. No significant strain differences were identified on the object recognition task. These data, taken together, suggest that care must be taken when choosing cognitive tasks to be used with particular mouse strains and that task sensitivity must be considered as a critical element to research protocols with regard to these mouse strains.     

Isolation and characterization of a mouse subtelomeric sequence

A mouse subtelomeric sequence, ST1, was generated from genomic DNA of the mouse HR9 (129/Sv origin) cell line by the polymerase chain reaction (PCR) using a single telomeric primer. ST1 was cloned and characterized: it is composed of 670 bp of novel DNA sequence flanked on each end by inverted telomeric hexanucleotide repeats (TTAGGG)_n. PCR amplification from BALB/c mouse DNA using this single primer gave the same major product. Southern analysis and PCR using internal ST1 primers confirmed that the ST1 sequence is present in mouse genomic DNA. In situ hybridization to metaphase chromosomes of SJL origin mapped ST1 to many, if not every, mouse telomere. PCR experiments using different combinations of the telomeric, minor satellite, and ST1 primers indicated that some ST1 copies are adjacent to minor satellite sequences, that telomeric and ST1 sequences are not generally interspersed with minor satellite sequences,and that ST1 and the minor satellite have a consistent and specific orientation relative to each other and to the telomere.by H.F. Willard     

Genome Analysis of a Natural Hybrid with 2n= 63 Chromosomes in the Genus Elytrigia Desv. (Poaceae) Using the GISH Technique

Abstract: Genomic in situ hybridization (GISH), using genomic DNA probes from Thinopyrum elongatum (E genome, 2 n = 14), Th. bessarabicum (J genome, 2 n = 14), Pseudoroegneria stipifolia (S genome, 2 n = 14), Agropyron cristatum (P genome, 2 n = 28) and Critesion californicum (H genome, 2 n = 14), was used to identify the genome constitution of a natural hybrid population morphologically close to Elytrigia pycnantha and with somatic chromosome number of 2 n = 63. The GISH results indicated the presence of a chromosomal set more or less closely related to the E, P, S and H genomes. In particular, two sets of 14 chromosomes each showed close affinity to the E genome of Th. elongatum and to the P genome of A. cristatum. However, they included 2 and 10 mosaic chromosomes, respectively, with S genome specific sequences at their centromeric regions. Two additional sets (28 chromosomes) appeared to be very closely related to the S genome of Ps. stipifolia. The last genome involved (7 chromosomes) is related to the H genome of C. californicum but includes one chromosome with S genome-specific sequences around the centromere and two other chromosomes with a short interstitial segment also containing S genome related sequences. On a basis of GISH analysis and literature data, it is hypothesized that the natural 9-ploid hybrid belongs to the genus Elytrigia and results from fertilization of an unreduced gamete (n = 42) of E. pycnantha and a reduced gamete (n = 21) of E. repens. The genomic formula SSSSP^SP^SE^SE^SH^S is proposed to describe its particular genomic and chromosomal composition.     

Genome-Wide Comparative Analysis of Microsatellites in Pineapple

Pineapple (Ananas comosus (L.) Merrill) is the second most important tropical fruit in term of international trade. The availability of whole genomic sequences and expressed sequence tags (ESTs) offers an opportunity to identify and characterize microsatellite or simple sequence repeat (SSR) markers in pineapple. A total of 278,245 SSRs and 41,962 SSRs with an overall density of 728.57 SSRs/Mb and 619.37 SSRs/Mb were mined from genomic and ESTs sequences, respectively. 5′-untranslated regions (5′-UTRs) had the greatest amount of SSRs, 3.6–5.2 fold higher SSR density than other regions. For repeat length, 12 bp was the predominant repeat length in both assembled genome and ESTs. Class I SSRs were underrepresented compared with class II SSRs. For motif length, dinucleotide repeats were the most abundant in genomic sequences, whereas trinucleotides were the most common motif in ESTs. Tri- and hexanucleotides of total SSRs were more prevalent in ESTs than in the whole genome. The SSR frequency decreased dramatically as repeat times increased. AT was the most frequent single motif across the entire genome while AG was the most abundant motif in ESTs. Across six examined plant species, the pineapple genome displayed the highest density, substantially more than the second-place cucumber. Annotation and expression analyses were also conducted for genes containing SSRs. This thorough analysis of SSR markers in pineapple provided valuable information on the frequency and distribution of SSRs in the pineapple genome. This genomic resource will expedite genomic research and pineapple improvement.