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1.
Centromere locations and associated chromosome rearrangements in Arabidopsis lyrata and A. thaliana
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We analyzed linkage and chromosomal positions of genes in A. lyrata ssp. petraea that are located near the centromere (CEN) regions of A. thaliana, using at least two genes from the short and long arms of each chromosome. In our map, genes from all 10 A. thaliana chromosome arms are also tightly linked in A. lyrata. Genes from the regions on the two sides of CEN5 have distant map localizations in A. lyrata (genes on the A. thaliana short-arm genes are on linkage group AL6, and long-arm genes are on AL7), but genes from the other four A. thaliana centromere regions remain closely linked in A. lyrata. The observation of complete linkage between short- and long-arm centromere genes, but not between genes in other genome regions that are separated by similar physical distances, suggests that crossing-over frequencies near the A. lyrata ssp. petraea centromere regions are low, as in A. thaliana. Thus, the centromere positions appear to be conserved between A. thaliana and A. lyrata, even though three centromeres have been lost in A. thaliana, and the core satellite sequences in the two species are very different. We can now definitively identify the three centromeres that were eliminated in the fusions that formed the A. thaliana chromosomes. However, we cannot tell whether genes were lost along with these centromeres, because such genes are absent from the A. thaliana genome, which is the sole source of markers for our mapping. 相似文献
2.
Leister D 《Trends in genetics : TIG》2004,20(3):116-122
NBS-LRR genes are the major class of disease resistance genes in flowering plants, and are arranged as single genes and as clustered loci. The evolution of these genes has been investigated in Arabidopsis thaliana by combining data on their genomic organisation and position in phylogenetic trees. Tandem and segmental duplications distribute and separate NBS-LRR genes in the genome. It is, however, unclear by which mechanism(s) NBS-LRR genes from different clades are sampled into heterogeneous clusters. Once physically removed from their closest relatives, the NBS-LRR genes might adopt and preserve new specificities because they are less prone to sequence homogenization. 相似文献
3.
Evolution and ecology of antibiotic resistance genes 总被引:8,自引:0,他引:8
A new perspective on the topic of antibiotic resistance is beginning to emerge based on a broader evolutionary and ecological understanding rather than from the traditional boundaries of clinical research of antibiotic-resistant bacterial pathogens. Phylogenetic insights into the evolution and diversity of several antibiotic resistance genes suggest that at least some of these genes have a long evolutionary history of diversification that began well before the 'antibiotic era'. Besides, there is no indication that lateral gene transfer from antibiotic-producing bacteria has played any significant role in shaping the pool of antibiotic resistance genes in clinically relevant and commensal bacteria. Most likely, the primary antibiotic resistance gene pool originated and diversified within the environmental bacterial communities, from which the genes were mobilized and penetrated into taxonomically and ecologically distant bacterial populations, including pathogens. Dissemination and penetration of antibiotic resistance genes from antibiotic producers were less significant and essentially limited to other high G+C bacteria. Besides direct selection by antibiotics, there is a number of other factors that may contribute to dissemination and maintenance of antibiotic resistance genes in bacterial populations. 相似文献
4.
Background
Several aspects of microarray data analysis are dependent on identification of genes expressed at or near the limits of detection. For example, regression-based normalization methods rely on the premise that most genes in compared samples are expressed at similar levels and therefore require accurate identification of nonexpressed genes (additive noise) so that they can be excluded from the normalization procedure. Moreover, key regulatory genes can maintain stringent control of a given response at low expression levels. If arbitrary cutoffs are used for distinguishing expressed from nonexpressed genes, some of these key regulatory genes may be unnecessarily excluded from the analysis. Unfortunately, no accurate method for differentiating additive noise from genes expressed at low levels is currently available. 相似文献5.
LeGrand EK 《Perspectives in biology and medicine》2001,44(4):509-521
The benefits of apoptosis in the removal of unnecessary, damaged, or dangerous cells are dependent on the altruism resulting from the absence of genetic conflict between genes in cells. However, this altruism can be exploited by self-promoting or ultra-selfish genes. These self-promoting genes can be endogenous, as with neoplasia or germ cell mutations, or exogenous, as with cellular pathogens. The fundamental flaw of apoptosis is that its development and maintenance as a system is constantly opposed by the emergence of self-promoting genes. Since apoptotically impaired cells cannot be relied on to kill themselves, apoptotic input from other cells is required for controlling self-promoting genes. Certain unique features of germ cell development, such as linkage by cytoplasmic bridges and the requirement for granulosa or Sertoli cells, appear to serve this requirement for control of self-promoting genes. 相似文献
6.
转座子(transposable elements,TEs)是指在基因组上能从同一条染色体的一个位置转移到另一个位置或者从一条染色体转移到另一条染色体上的一段DNA序列。广泛存在于基因组中的转座子通过复制、动员、重组基因片段以及修改原基因结构形成的新基因,被称为转座子衍生基因。该文综述了转座子衍生基因与转座子和常规基因的异同以及转座子衍生基因的演变途径,归纳了转座子衍生基因对宿主基因进化,以及对生物生长发育的影响。 相似文献
7.
MOTIVATION: Several pattern discovery methods have been proposed to detect over-represented motifs in upstream sequences of co-regulated genes, and are for example used to predict cis-acting elements from clusters of co-expressed genes. The clusters to be analyzed are often noisy, containing a mixture of co-regulated and non-co-regulated genes. We propose a method to discriminate co-regulated from non-co-regulated genes on the basis of counts of pattern occurrences in their non-coding sequences. METHODS: String-based pattern discovery is combined with discriminant analysis to classify genes on the basis of putative regulatory motifs. RESULTS: The approach is evaluated by comparing the significance of patterns detected in annotated regulons (positive control), random gene selections (negative control) and high-throughput regulons (noisy data) from the yeast Saccharomyces cerevisiae. The classification is evaluated on the annotated regulons, and the robustness and rejection power is assessed with mixtures of co-regulated and random genes. 相似文献
8.
Abdourahamane Sangaré Jacques-Henry Weil Jean-Michel Grienenberger Christiane Fauron David Lonsdale 《Molecular & general genetics : MGG》1990,223(2):224-232
Summary Maize mitochondrial (mt) tRNA genes were localized on the mt master circles of two fertile lines (WF9-N and B37-N) and of one cytoplasmic male sterile line (B37-cmsT) of maize. The three genomes contain 16 tRNA genes with 14 different anticodons which correspond to 13 amino acids. Out of these 16 tRNA genes, 6 show a high degree of homology with the corresponding chloroplast (cp) tRNA genes and were shown to originate from cp DNA insertions and to be expressed in the mitochondria. The organization of the mt tRNA genes in both fertile lines is similar. The same genes are found, in the same environment, as judged from the restriction maps, in fertile and male sterile lines that have the same nuclear background, but the relative organization of the mt tRNA genes on the master circle is completely different. 相似文献
9.
About 25% of X-linked genes may escape inactivation at least to some degree. However, in vitro results from somatic cell hybrids may not reflect what happens in vivo. Therefore, we analyzed the female/male (F/M) gene fold expression ratio for 299 X-linked and 7795 autosomal genes from 11 different tissues from an existing in vivo microarray database. On average 5.1 and 4.9% of genes showed higher expression in females compared with 7.4 and 7.9% in males, respectively, for X-linked and autosomal genes. A trend was found for F/M gene fold ratios greater than 1.5 for several X-linked genes indicating overexpression in females among multiple tissues. Nine X-linked genes showed overexpression in females in at least 3 of the 11 studied tissues. Of the 9 genes, 6 were located on the short arm and 3 on the long arm of the X chromosome. Six of the 9 genes have previously been reported to escape X inactivation. However, in general, no consistent pattern was seen for the expression of X-linked genes between in vitro and in vivo systems. This study indicates that factors other than the X-inactivation process may impact on the expression of X-linked genes resulting in an overall similar gender expression for both X-linked and autosomal genes. 相似文献
10.
11.
Competitive hybridization: theory and application in isolation and quantification of differentially regulated genes 总被引:1,自引:0,他引:1
Competitive hybridization is a simple yet powerful method that was developed to screen cDNA libraries for differentially regulated genes. The method is based on competition between unlabeled cDNA from the mRNA of one sample and labeled cDNA from another sample. By manipulating the amount of competing unlabeled cDNA, background signals from the nonregulated genes can be increased or reduced, enabling the signals from differentially regulated genes to be contrasted and to be identified in a quantitative manner. To demonstrate the feasibility of the method, we screened a citrus cDNA library for ethylene-induced genes and identified three genes with different levels of ethylene induction. The mathematical basis of the method and its possible application in gene chip technology are discussed. 相似文献
12.
Horth L 《Genomics》2007,90(2):159-175
Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity--behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes' products are involved in the production, transmission, and receipt of crucial sensory mate-choice cues that affect fitness. This review exposes newfound evidence that alternative splicing, gene-expression pattern changes, and molecular genetic variation in sensory genes are crucial for both intra- and interspecific mate choice and mating success. Many sensory genes have arisen through gene duplications, and data amassed from studies conducted at scales ranging from individual genes to genomic comparisons show that strong, positive Darwinian selection acts on several mating-related genes and that these genes evolve rapidly. 相似文献
13.
14.
几个水稻品种抽穗期主效基因与微效基因的定位研究 总被引:18,自引:1,他引:17
在构建2张RFLP图谱的基础上,定位分析了控制水稻抽穗期的主效基因和微效基因。在特三矮2号/C.B.群体中定位到2个主效基因和2个微效基因。该2个主基因分别位于第3、8染色体上,累加贡献率约达50%,加性效应值分别为7天和6天,而分别位于第1、12染色体的2个微效基因的贡献率仅分别为8.3%和9.6%,加性效应值仅为3天和4天。在外引2号/C.B.群体中定位了2个连锁于第6染色体的主效基因和1个位于第8染色体的微效基因,该2个主效基因的贡献率分别为35.5%和27.4%,来自外引2号的该2个基因其效应均为明显推迟抽穗,因而可推测它们为感光性基因,微效基因的贡献率仅为8.9%,基因效应值较小。 相似文献
15.
《Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie》1998,321(10):805-817
This article aims to illustrate the potentialities of the Genatlas database, taking, as an example, the developmental genes and their associated diseases in man. These genes belong to several categories intervening from the first stages of embryonic life. They operate at all steps of developmental cascades from extracellular signaling to activation of target genes. Quite a number of those genes have been identified in man, which are the orthologs of genes previously described in lower species. These genes are mapped and an increasing number are associated with developmental anomalies. These studies shed light on the mechanisms of congenital malformations. They disclose a large array of genetic and phenotypic heterogeneity and a high degree of complexity. 相似文献
16.
MADS-box gene evolution-structure and transcription patterns 总被引:7,自引:0,他引:7
Johansen B Pedersen LB Skipper M Frederiksen S 《Molecular phylogenetics and evolution》2002,23(3):458-480
17.
Codon contexts in enterobacterial and coliphage genes 总被引:6,自引:0,他引:6
This investigation of the codon context of enterobacteria, plasmid, and
phage protein genes was based on a search for correlations between the
presence of one base type at codon position III and the presence of another
base type at some other position in adjacent codons. Enterobacterial genes
were compared with eukaryotic sequences for codon context effects. In
enterobacterial genes, base usage at codon position III is correlated with
the third position of the upstream adjacent codon and with all three
positions of the downstream codon. Plasmid genes are free of context
biases. Phage genes are heterogeneous: MS2 codons have no biased context,
whereas lambda genes partly follow the trends of the host bacterium, and T7
genes have biased codon contexts that differ from those of the host. It has
been reported that two successive third-codon positions tend to be occupied
by two purines or two pyrimidines in Escherichia coli genes of low
expression level. Here, the extent to which highly expressed protein genes
can modulate base usage at two successive codon positions III, given the
constraints on codon usage and protein sequence that act on them, was
quantified. This demonstrates that the above-mentioned favored patterns are
not a characteristic of weakly expressed genes but occur in all genes in
which codon context can vary appreciably. The correlation between
successive third-codon positions is a distinct feature of enterobacteria
and of some phages, one that may result from adaptation of gene structure
to translational efficiency. Conversely, codon context in yeast and human
genes is biased--but for reasons unrelated to translation.
相似文献
18.
19.
Robert L. Dorit Christopher M. Roy Sandra M. Robinson Margaret A. Riley 《Journal of molecular evolution》2013,76(6):388-393
The rise of antibiotic-resistant pathogens focuses our attention on the source of antibiotic resistance genes, on the existence of these genes in environments exposed to little or no antibiotics, and on the relationship between resistance genes found in the clinic and those encountered in non-clinical settings. Here, we address the evolutionary history of a class of resistance genes, the SHV β-lactamases. We focus on bla SHV genes isolated both from clinical and non-clinical sources and show that clinically important resistance determinants arise repeatedly from within a diverse pool of bla SHV genes present in the environment. While our results argue against the notion of a single common origin for all clinically derived bla SHV genes, we detect a characteristic selective signature shaping this protein in clinical environments. This clinical signature reveals the joint action of purifying and positive selection on specific residues, including those known to confer extended-spectrum activity. Surprisingly, antibiotic resistance genes isolated from non-clinical—and presumably antibiotic-free—settings also experience the joint action of purifying and positive selection. The picture that emerges undercuts the notion of a separate reservoir of antibiotic resistance genes confined only to clinical settings. Instead, we argue for the presence of a single extensive and variable pool of antibiotic resistance genes present in the environment. 相似文献
20.
Toll-interleukin-1 receptor (TIR)-encoding proteins represent one of the most important families of disease resistance genes in plants. Studies that have explored the functional details of these genes tended to focus on only a few limited groups; the origin and evolutionary history of these genes were therefore unclear. In this study, focusing on the four principal groups of TIR-encoding genes, we conducted an extensive genome-wide survey of 32 fully sequenced plant genomes and Expressed Sequence Tags (ESTs) from the gymnosperm Pinus taeda and explored the origins and evolution of these genes. Through the identification of the TIR-encoding genes, the analysis of chromosome positions, the identification and analysis of conserved motifs, and sequence alignment and phylogenetic reconstruction, our results showed that the genes of the TIR-X family (TXs) had an earlier origin and a wider distribution than the genes from the other three groups. TIR-encoding genes experienced large-scale gene duplications during evolution. A skeleton motif pattern of the TIR domain was present in all spermatophytes, and the genes with this skeleton pattern exhibited a conserved and independent evolutionary history in all spermatophytes, including monocots, that followed their gymnosperm origin. This study used comparative genomics to explore the origin and evolutionary history of the four main groups of TIR-encoding genes. Additionally, we unraveled the mechanism behind the uneven distribution of TIR-encoding genes in dicots and monocots. 相似文献