Mapping Chromosome Landmarks in the Centromere I Region ofNeurospora crassa

Chromosome translocation breakpoints, RFLP heterozygosity in partial chromosome duplications, and RFLP-marked crossover events have been used as chromosomal landmarks to find the position and orientation of cloned regions flanking centromere I ofNeurospora crassa.Determination of physical:genetic ratios in genomic regions flanking the locimei-3, un-2,andhis-2supports previous evidence indicating that recombinational activity is lower in regions flanking centromere I than in the generalN. crassagenome. The homogeneous distribution of crossover events found in these regions suggests that there is not a gradient of crossover inhibition in the vicinity of centromere I. Thus, a largely extended centromeric effect and/or a general crossover inhibitory effect operating on linkage group I (LGI) could constitute the basis of these abnormal physical:genetic ratios. A DNA element containing about 76% A + T was isolated from the centromeric end of a cloned region on LGIR. The fragment includes a previously undescribed DNA sequence, highly repeated in theNeurosporagenome, which may correspond to centromeric DNA.     

Expressed Sequences from Conidial, Mycelial, and Sexual Stages ofNeurospora crassa

In theNeurosporaGenome Project at the University of New Mexico, expressed sequence tags (ESTs) corresponding to three stages of the life cycle of the filamentous fungusNeurospora crassaare being analyzed. The results of a pilot project to identify expressed genes and determine their patterns of expression are presented. 1,865 partial complementary DNA (cDNA) sequences for 1,409 clones were determined using single-pass sequencing. Contig analysis allowed the identification of 838 unique ESTs and 156 ESTs present in multiple cDNA clones. For about 34% of the sequences, highly or moderately significant matches to sequences (of known and unknown function) in the NCBI database were detected. Approximately 56% of the ESTs showed no similarity to previously identified genes. Among genes with assigned function, about 43.3% were involved in metabolism, 32.9% in protein synthesis and 8.4% in RNA synthesis. Fewer were involved in defense (6%), cell signalling (3.4%), cell structure (3.4%) and cell division (2.6%).     

线虫核糖核蛋白基因内含子与相应编码序列的相互作用

对线虫核糖核蛋白基因内含子序列与相应编码序列采用Smith-Waterman方法做局域比对分析,探讨两者之间的相互作用机制．发现内含子中部序列确实存在与相应编码序列的相互作用区域．第一内含子的最佳匹配分布在内含子15%～55%的区域内,第二内含子的最佳匹配分布在内含子30%～80%的区域内．对于长内含子,在与外显子序列比对时,最佳匹配分布在内含子5%～20% 区域内,在与整个编码序列比对时,出现了两个峰区,一个位于内含子15%～30%区域内,另一个位于内含子54%～78%区域内．推测第一个峰区与外显子内部序列有关,第二个峰区与外显子-外显子结合区域的序列有关．还发现编码序列上存在多个与内含子序列的相互作用域和一些禁配区域分布．推测这些禁配区域与蛋白质结合区域有关．结论印证了内含子序列与相应编码序列协同进化的观点．     

结核分枝杆菌基因组学与基因组进化

在后基因组时代,特别是在新的测序理论和设备大发展的背景下,一些重大传染性致病微生物基因组序列正在被逐一测定,并且随后的基因功能注释,蛋白质三维结构重建等工作也正在开展,以期对致病微生物的生物学特性、诊断策略和治疗方法等有突破性的认识.作为对人类健康一直存在严重威胁的结核分枝杆菌,其基因组在进化中所发生的各种遗传事件对其生物学性质、致病能力和抗药性等各方面有重要作用.本文旨在阐述结核分枝杆菌的起源及其基因组特征,论述其基因组进化的研究进展.     

Cloning of the am (glutamate dehydrogenase) gene of Neurospora crassa through the use of a synthetic DNA probe

In a previous study the alteration in the amino acid sequence of Neurospora crassa NADP-specific glutamate dehydrogenase (GDH) resulting from two mutually compensating frameshift mutations was used to deduce the first 17 nucleotides of the coding sequence of the am gene. In the work reported here, a synthetic 17-mer corresponding to the deduced sequence was shown to hybridize strongly to a 9-kb HindIII fragment from N. crassa wild-type DNA but not to any corresponding fragment from the DNA of a mutant strain known to be deleted for most or all of the gene. Wild-type HindIII fragments were fractionated for size and a fraction centering around 9 kb was cloned in vector λL47. Two clones carrying the strongly hybridizing fragment were identified. The hybridization to the 17-mer was localized within a 2.7-kb BamHI fragment and, within this, to a 700-bp BamHI-BglII subfragment. 5' end-labelled polyadenylated RNA isolated from wild-type mycelium hybridized to the 2.7-kb BamHI fragment and not appreciably to flanking fragments. The partial sequence analysis of the BamHI-BglII fragment has confirmed that the 17-mer probe matches the coding sequence at the 5' end of the gene and has also revealed an intervening sequence 67 bp in length, interrupting codon 15. Both the 9-kb HindIII fragment and the 2.7-kb BamHI fragment have been shown to be capable of transforming the deletion mutant to prototrophy and ability to produce GDH. Analysis of one transformant showed that the am gene was integrated, together with a part of the long arm of the lambda vector, at an unusual locus. This transformant, in which the am gene does not show its normal linkage to the linkage group 5 marker inl, was found to produce GDH to about 20% of the normal level.     

小果野蕉(Musa acuminata)全基因组NBS抗病基因的鉴定与分析

为探讨小果野蕉(Musa acuminata)中NBS基因的功能,基于新近发表的小果野蕉全基因组序列,对NBS基因家族进行鉴定、分类和染色体定位,解析基因的复制特征、系统发育关系及上游启动子调控元件类别,推测这些基因在小果野蕉中可能的功能。结果表明,在小果野蕉全基因组中鉴定出125个NBS基因,包括78个标准和47个非标准NBS基因。多数NBS基因在染色体上以基因簇形式存在,串联复制是NBS基因家族扩张的主要动力。系统发育分析表明标准NBS基因形成两大分支,77个标准NBS基因有EST表达支持。这为群体水平的抗病基因型筛选提供了本底信息,促进栽培香蕉分子抗病育种进程。     

Babesia bovis: Genome size, number of chromosomes and telomeric probe hybridisation

Pulsed field gel electrophoresis of intact chromosomes of Babesia bovis revealed four chromosomes in the haploid genome. A telomere probe, derived from Plasmodium berghei, hybridised to eight SfiI restriction fragments of genomic B. bovis DNA digests indicating the presence of four chromosomes. A small subunit (18S) ribosomal RNA gene probe hybridised to the third chromsome only. The genome size of B. bovis is estimated to be 9.4 million base pairs. The sizes of chromosomes 1, 2, 3 and 4 are estimated to be 1.4, 2.0, 2.8 and 3.2 million base pairs, respectively.     

Characterization and mapping of sequence-tagged microsatellite sites in the chickpea ( Cicer arietinum L.) genome

A size-selected genomic library comprising 280,000 colonies and representing ≈18% of the chickpea genome, was screened for (GA)_n, (GAA)_n and (TAA)_n microsatellite-containing clones, of which 389 were sequenced. The majority (∼75%) contained perfect repeats; interrupted, interrupted compound and compound repeats were only present in 6%–9% of cases. (TAA)-microsatellites contained the longest repeats, with unit numbers from 9 to 131. For 218 loci primers could be designed and used for the detection of microsatellite length polymorphisms in six chickpea breeding cultivars, as well as in C. reticulatum and C. echinospermum, wild, intercrossable relatives of chickpea. A total of 174 primer pairs gave interpretable banding patterns, 137 (79%) of which revealed at least two alleles on native polyacrylamide gels. A total of 120 sequence-tagged microsatellite site (STMS) markers were genetically mapped in 90 recombinant inbred lines from an inter-species cross between C. reticulatum and the chickpea cultivar ICC 4958. Markers could be arranged in 11 linkage groups (at a LOD score of 4) covering 613 cM. Clustering as well as random distribution of loci was observed. Segregation of 46 markers (39%) deviated significantly (P ≥ 0.05) from the expected 1:1 ratio. The majority of these loci (73%) were located in three distinct regions of the genome. The present STMS marker map represents the most advanced co-dominant DNA marker map of the chickpea genome. Received: 14 January 1999 / Accepted: 29 April 1999     

植物内生链霉菌Streptomyces sp. SAT1的基因组测序和比较基因组分析

【背景】一直以来,链霉菌都是活性物质的主要生产者,近年来随着抗生素滥用引起的环境和微生物抗药性问题越发严重,挖掘高效生物防治因子和新型抗生素成为了解决以上问题的重要手段。【目的】通过获得植物内生链霉菌SAT1全基因组序列和次级代谢基因簇信息,利用比较基因组学和泛基因组学分析SAT1菌株的特殊性以及与其他链霉菌的共性,为阐明SAT1抑菌和内生机制提供理论基础,为揭示链霉菌的生态功能提供可靠数据。【方法】通过三代测序平台PacBio Sequel完成SAT1基因组测序,利用生物信息学技术进行注释和功能基因分类;分别利用RAxML和PGAP软件进行系统发育树的构建和泛基因组分析;次级代谢基因簇的预测和分析通过antiSMASH网站完成。【结果】获得SAT1菌株的全基因组完成图,该菌线性染色体长度约7.47 Mb,包含有4个质粒,GC含量近73%,共预测到7 550个蛋白编码基因,含有37个次级代谢基因簇,分属29个类型,其中默诺霉素基因簇与加纳链霉菌具有较高相似性。42株代表链霉菌中,单个菌株次级代谢基因簇数量为20-55个,主要类型为PKS类、Terpene类和Nrps类,而且含有大量杂合基因簇,各个菌株中特有基因数目较为庞大。【结论】链霉菌SAT1菌株在基因组特点以及次级代谢基因簇的数量和类型上与其余41株链霉菌具有一定的共性,其中潮霉素B基因簇和默诺霉素基因簇合成的相关物质可能与SAT1抑菌活性密切相关。42株链霉菌中次级代谢基因簇数量的多少与基因组大小成正相关,同时大量杂合基因簇以及庞大的特有基因数目的存在说明链霉菌在长期进化过程中存在了很高程度的水平基因转移现象,可能具有重要的生态功能。     

木贼镰孢基因功能注释及比较基因组学分析

为挖掘木贼镰孢(Fusarium equiseti (Corda) Sacc.)的产毒基因及明确其进化关系,通过BLAST软件与GO、KEGG、COG、E职NOG、CAZy等14个数据库结合的方法对其全基因组进行功能注释并挖掘产毒基因,进行系统进化分析及运用色谱技术研究产毒基因的分泌规律;以麦根腐平脐蠕孢、燕麦镰孢、尖...     

Molecular organisation of the malate synthase genes of Aspergillus nidulans and Neurospora crassa

Summary A soybean nodulin cDNA clone (E41) hybrid-selected mRNA for three in vitro translation products with apparent molecular weights of 26 kDa, 25 kDa and 24 kDa. Based on Southern analysis of soybean genomic DNA, combined with mapping and sequencing of genomic clones, we identified four genes that are related to E41, one of which was identified to be the previously characterized N-20 gene. Our data indicate the linkage of three of the genes, of which one is a truncated version and suggest that they originated by gene duplication combined with deletion and conversion. The genes are highly expressed and we postulate that the sequence conservation in the 5 and 3 flanking regions of all four genes, has a functional role in their expression. Hybrid-selected translation products of E41 are not immunoprecipitable with antibody to the soluble fraction of nodules suggesting that they are membrane associated. The N-20 gene, which is a member of this gene subfamily, showed sequence similarity to four previously characterized nodulin genes and a phylogenetic tree is proposed based on the extent of sequence similarity.     

枯草芽孢杆菌N2-10的基因组测序和比较基因组分析

【背景】枯草芽孢杆菌N2-10是一株具有较强抑菌能力且能产纤维素酶等多种水解酶的革兰氏阳性菌,在发酵饲料中具有较大的应用潜力。【目的】通过获得枯草芽孢杆菌N2-10的全基因组序列信息,进一步解析菌株次级代谢产物合成基因信息,并通过比较基因组学分析菌株N2-10与模式菌株的差异性,为阐明N2-10抑菌和益生机制提供理论基础。【方法】通过二代Illumina NovaSeq联合三代PacBio Sequel测序平台,对菌株N2-10进行全基因组测序,将测序数据进行基因组组装、基因预测与功能注释,并利用比较基因组学分析N2-10与其他菌株的差异。【结果】菌株N2-10基因组大小为4 036 899 bp,GC含量为43.88%;共编码4 163个编码基因,所有编码基因总长度为3594369bp,编码区总长度占基因组总长度的89.04%;含有85个tRNA、10个5S rRNA、10个16S rRNA、10个23S rRNA,以及2个CRISPR-Cas、1个前噬菌体和6个基因岛;在GO (gene ontolog)、COG (clusters of orthologous groups of...