Meiotic Recombination, Noncoding DNA and Genomic Organization in Caenorhabditis Elegans

The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.     

Evolution of the CYP2ABFGST gene cluster in rat, and a fine-scale comparison among rodent and primate species

The evolution of gene families can be best understood by studying the modern organization and functions of family members, and by comparing parallel families in different species. In this study, the CYP2ABFGST gene cluster has been characterized in rat and compared to the syntenic clusters in mouse and human, providing an interesting example of gene family evolution. In the rat, 18 loci from six subfamilies have been identified by specifically amplifying and sequencing gene fragments from cloned DNA, and have been exactly placed on chromosome 1. The overall organization of the gene cluster in rat is relatively simple, with genes from each subfamily in tandem, and is more similar to the mouse than to the human cluster. We have reconstructed the probable structure of the CYP2ABFGST cluster in the common ancestor of primates and rodents, and inferred a model of the evolution of this gene cluster in the three species. Numerous nontandem and block duplications, inversions, and translocations have occurred entirely inside the cluster, indicating that pairing between duplicate genes is keeping the rearrangements within the cluster region. The initial tandem duplication of a CYP2 gene in an early mammalian ancestor has made this region particularly subject to such localized rearrangements. Even if duplicated genes do not have a large-scale effect on chromosomal rearrangements, on a local level clustered gene families may have contributed significantly to the genomic complexity of modern mammals.     

A Radiation Hybrid Map of BTA23: Identification of a Chromosomal Rearrangement Leading to Separation of the Cattle MHC Class II Subregions

Bovine chromosome 23 (BTA23) contains the bovine major histocompatibility complex (MHC) and is thus of particular interest because of the role of MHC genes in immunity. Previous studies have shown cattle MHC class II genes to be subdivided into two distinct subregions separated by a variable genetic distance of 15–30 cM. To elucidate the genetic events that resulted in the present organization of the class II and other MHC genes, a framework radiation hybrid (RH) map of BTA23 was developed by testing DNA samples from a 5000 rad whole genome RH panel. Twenty-six markers were screened with an average retention frequency of 0.27, ranging from 0.14 to 0.42. Total length of the chromosome was 220 cR₅₀₀₀, with 4.1 cR₅₀₀₀/cM when compared to linkage data. Gene orders for the markers common to both the RH framework map and the consensus framework linkage map are identical. Large centiray intervals,D23S23–D23S7, DYA–D23S24andCYP21–D23S31,were observed compared to linkage distances. These data may indicate a much larger physical distance or suppression of recombination in the interval separating the class II subregions and also within the class I region than previously estimated. Comparison of 13 Type I genes conserved between BTA23 and the human homolog HSA6p suggests the occurrence of an inversion encompassing the centromeric half of the bovine chromosome, thus explaining the large distance between the bovine class IIa and IIb clusters. These results exemplify the power of RH mapping in solving problems in comparative genomics and evolution. Furthermore, noncongruence of the genetic and physical RH map distances indicates that caution must be observed in using either resource alone in searching for candidate genes controlling traits of economic importance.     

Linear chromosomal physical and genetic map of Borrelia burgdorferi, the Lyme disease agent

A physical map of the 952kbp chromosome of Borrelia burgdorferi Sh-2-82 has been constructed. Eighty-three intervals on the chromosome, defined by the cleavage sites of 15 restriction enzymes, are delineated. The intervals vary in size from 96kbp to a few hundred bp, with an average size of 11.5 kbp. A striking feature of the map is its linearity; no other bacterial groups are known to have linear chromosomes. The two ends of the chromosome do not hybridize with one another, indicating that there are no large common terminal regions. The chromosome of this strain was found to be stable in culture; passage 6, 165 and 320 cultures have identical chromosomal restriction maps. We have positioned all previously known Borrelia burgdorferi chromosomal genes and several newly identified ones on this map. These include the gyrA/gyrB/dnaA/dnaN gene cluster, the rRNA gene cluster, fla, flgE, groEL (hsp60), recA, the rho/hip cluster, the dnaK (hsp70)/dnaJ/grpE cluster, the pheT/pheS cluster, and the genes which encode the potent immunogen proteins p22A, p39 and p83. Our electrophoretic analysis detects five linear and at least two circular plasmids in B. burgdorferi Sh-2-82. We have constructed a physical map of the 53 kbp linear plasmid and located the operon that encodes the two major outer surface proteins ospA and ospB on this plasmid. Because of the absence of functional genetic tools for this organism, these maps will serve as a basis for future mapping, cloning and sequencing studies of B. burgdorferi.     

Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae,Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location

The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species.     

Conserved organization of an avian histone gene cluster with inverted duplications of H3 and H4 genes

Summary The organization of histone gene clusters of the duckCairina moschata was studied in the DNA inserts of two recombinant phage that overlap and feature identical histone gene arrangements but differ in sequence details and in the extent of repetition of an AT-rich motif in one of the nontranscribed spacer regions. These few but substantial differences between otherwise nearly identical histone gene groups suggest that we have independently isolated alleles of the same site of the duck genome or that this gene arrangement occurs (with slight variations) more than once per haploid genome. Within the histone gene cluster described, H3 and H4 genes are duplicated (with inverted orientation), whereas one H1 gene is flanked by single H2A and H2B genes. The arrangement of duck histone genes described here is identical to a subsection of the chicken genome but differs from any other published histone gene cluster.     

The recent origin of the Sdic gene cluster in the melanogaster subgroup

Gene families are composed of closely related genes and are an important part of eukaryotic genomes. In the proximal region of the X chromosome of Drosophila melanogaster there is a cluster of four tandem Sdic genes, located between the gene Cdic and the gene AnnX. Sdic is a chimeric gene that encodes a novel protein with sperm-specific expression. It had been hypothesized that the Sdic gene cluster was formed after the split of D. melanogaster and D. simulans. To study the evolution of this cluster, the sequence of this region was studied in several Drosophilidae species. In all species analyzed, Sdic genes are absent and AnnX and Cdic are adjacent to each other. The results allowed the inference of the ancestral situation and the reconstruction of the evolution of the cluster, and confirm that the Sdic cluster was indeed formed in the lineage that gave rise to D. melanogaster, being one of the youngest gene clusters known. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

小麦基因组研究进展

本文从小麦遗传图谱、物理图谱、比较基因组、基因组测序和EST 5个方面,介绍国内外小麦基因组的研究进展。我们利用W7984×Opata重组近交系的RFLP作图群体,对33个与小麦水分利用效率有关的性状进行了QTL遗传图谱比较分析,结果显明：在第一部分同源群染色体（1A,1B）上的着丝粒周围,分布有控制光合作用和根系特性的基因簇。在第二部分同源染色体上,有控制单株水分利用效率、根冠形态和生长发育的基因簇存在。在第六部分同源染色体上,6A和6B上都分别有由控制根系多个QTL组成的基因簇,6D染色体着丝粒周围有一个大的基因簇,由7个控制叶片和单株水分利用效率的QTL组成,说明第六部分同源染色体在小麦水分利用效率遗传方面起重要作用。 Abstract:Research development of genetic mapping,physics mapping,genome sequencing and expressed sequence tags in wheat have been reviewed in this paper.RFLP genetic linkage map of wheat recombinant inbred lines derived from W7984×Opata,was used to study QTL of 33 traits associated with water use efficiency.Compared with QTL map of 7 group homeologues chromosomes,the results were showed as follows:nearby the centromeric region of 1A and 1B chromosome,the gene cluster of controlling photosynthetic and root traits were located.The gene clusters of controlling water use efficiency per plant,root and plant height and growth rate were located on the 2 group chromosomes.The gene clusters of controlling root traits were located on the 6A an 6B chromosome,there was a big gene cluster mad up by 7 QTLs controlling water use efficiency of wheat leaf and per plant nearby the centromeric region of 6D chromosome.It showed that 6th homeologous chromosomes play an important role in controlling water use efficiency in wheat.     

Genetic analysis of two tomato mutants affected in the regulation of iron metabolism

Iron is one of the most important micronutrients for plants. Like other organisms, plants have developed active mechanisms for the acquisition of sufficient iron from the soil. Nevertheless, very little is known about the genetic mechanisms that control the active uptake. In tomato, two spontaneously derived mutants are available, which are defective in key steps that control this process. The recessive mutationchloronerva (chln) affects a gene which controls the synthesis of the non-protein amino acid nicotianamine (NA), a key component in the iron physiology of plants. The root system of the recessive mutantfer is unable to induce any of the characteristic responses to iron deficiency and iron uptake is thus completely blocked. We present a characterization of the double mutant, showing that thefer gene is epistatic over thechln gene and thus very likely to be one of the major genetic elements controlling iron physiology in tomato. In order to gain access to these two genes at the molecular level, both mutants were precisely mapped onto the high density RFLP map of tomato. Thechln gene is located on chromosome 1 and thefer gene is on chromosome 6 of tomato. Using this high-resolution map, a chromosome walk has been started to isolate thefer gene by map-based cloning. The isolation of thefer gene will provide new insights into the molecular mechanisms of iron uptake control in plants.     

The density distribution of gene loci over the genetic map ofEscherichia coli: Its structural,functional and evolutionary implications

Summary A quantitative analysis was carried out on the dispersion of gene loci over theE. coli genetic map. Therefore, the map was divided into regions characterized by an homogeneous gene density. This created a distribution pattern of gene loci that contained a symmetry axis located near to the origin of DNA replication. The pattern could be subdivided into a set of 22 functional domains containing gene loci whose products revealed a biochemical or functional relatedness. A correlation was found between the boundary positions of these domains and the distribution of F plasmid- and DNA insertion sites over theE. coli chromosome. The structural, functional and evolutionary implications of these findings are discussed.     

Genome analysis of Agrobacterium tumefaciens: linkage map and genetic features of the left region of the linear chromosome

In addition to a unique tumor-inducing (Ti) plasmid, the plant pathogenic bacterium Agrobacterium tumefaciens has an unconventional chromosomal organization. Our previous studies on A. tumefaciens MAFF301001 revealed that it possesses a 2 Mb linear and a 2.8 Mb circular chromosome plus a 206.479 kbp Ti plasmid (pTi-SAKURA). In this study, a linkage map for the left half of its linear chromosome covering a 900 kbp region was constructed and the number of potential genes existing in the region was estimated. The linkage map consists of 31 BAC and 8 lambda phage recombinants without any gaps. It confirmed the size and all the structural landmarks indicated in the corresponding region of our previously constructed physical map for the linear chromosome. Sequencing analysis of the end-regions of each linking clone led to the identification of 6 genes and another 27 potential genes or ORFs, including genes and/or gene clusters responsible for homologous recombination (ruvB), trehalose/maltose sugar transport (thuR, thuG) and alanine catabolism (dadR). Two virulence-related gene homologues (attK and celB), previously reported in the circular chromosome of a different strain of A. tumefaciens were found in this region. These findings will provide a ready-to-use linkage map for further functional analysis of the linear chromosome.     

Recombination events suggest potential sites for the Huntington's disease gene

The Huntington's disease gene (HD) maps distal to the D4S10 marker in the terminal 4p16.3 subband of chromosome 4. Directed cloning has provided several DNA segments that have been grouped into three clusters on a physical map of approximately 5 X 10(6) bp in 4p16.3. We have typed RFLPs in both reference and HD pedigrees to produce a fine-structure genetic map that establishes the relative order of the clusters and further narrows the target area containing the HD gene. Despite the large number of meiotic events examined, the HD gene cannot be positioned relative to the most distal cluster. One recombination event with HD suggests that the terminal-most markers flank the disease gene; two others favor a telomeric location for the defect. Efforts to isolate the HD gene must be divided between these two distinct intervals until additional genetic data resolve the apparent contradiction in localization.     

Hemoglobins of Kiefferulus,sister genus of Chironomus (Diptera: Insecta): Evolution of the Hb VIIB cluster

A genomic clone containing hemoglobin genes was isolated from a species of the chironomid genus Kiefferulus. Eight genes, including an apparent pseudogene, were sequenced and the amino acid sequences of the putative proteins were determined. By comparison to the previously described hemoglobins in the sister-genus Chironomus, they were identified as members of the dimeric Hb VIIB group. The results indicate that the existence of clusters of hemoglobin genes may be a common feature in chironomids and not just confined to Chironomus. The Kiefferulus genes show greatest similarity of amino acid sequence to Hb VIIB-7 from the Chironomus cluster. The results suggest that the ancestral cluster contained at least two gene types, one of which gave rise to VIIB-7 and the Kiefferulus genes while the other gave rise to the other Chironomus VIIB genes. Both clusters appear to have increased in size by duplication or unequal crossing over since the separation of the genera. It also appears that an unrelated gene present in the Chironomus cluster, Hb-Y, arose from a completely independent origin with no apparent equivalent gene anywhere in the genome of Kiefferulus or some other Chironomus species. Correspondence to: J. Martin     

A 2-Mb YAC/BAC-based physical map of the ovum mutant (Om) locus region on mouse chromosome 11

The embryonic lethal phenotype observed when DDK females are crossed with males from other strains results from a deleterious interaction between the egg cytoplasm and the paternal pronucleus soon after fertilization. We have previously mapped the Om locus responsible for this phenotype, called the DDK syndrome, to an approximately 2-cM region of chromosome 11. Here, we report the generation of a physical map of 28 yeast and bacterial artificial chromosome clones encompassing the entire genetic interval containing the Om locus. This contig, spanning approximately 2 Mb, was used to map precisely genes and genetic markers of the region. We determined the maximum physical interval for Om to be 1400 kb. In addition, 11 members of the Scya gene family were found to be organized into two clusters at the borders of the Om region. Two other genes (Rad51l3 and Schlafen 2) and one EST (D11Wsu78e) were also mapped in the Om region. This integrated map provides support for the identification of additional candidate genes for the DDK syndrome.     

An 18-locus linkage map of the pericentromeric region of the human X chromosome: Genetic framework for mapping X-linked disorders

We report a high-resolution genetic linkage map of the region Xp11.4 to Xq13.3, spanning the centromere of the X chromosome and encompassing approximately 30 cM. This 18-locus map is composed of 11 intervals that are spaced on average about 3 cM apart. Markers incorporated into the map together detect 19 distinct polymorphisms and include five genes (TIMP, SYP, AR, CCG1, PGK1), the OATL1 cluster, the hypervariable locus DXS255, the centromeric locus DXZ1, and 10 other anonymous DNA segments. Given that this map spans roughly one-fifth of the length of the X chromosome and includes many loci currently used in both diagnosis and mapping of X-linked disorders, it should be useful for genetic counseling and for guiding efforts to clone disease genes in this region.