Comparison Of Gene Order Research Articles

Current approaches to whole genome phylogenetic analysis.

It has long been known that evolutionary trees (phylogenies) can be estimated by comparing the DNA or protein sequences of homologous genes across different organisms. More recently, attempts have been made to estimate phylogenies by comparing entire genomes. These attempts have focused largely on comparisons of gene content and gene order. Many different methods have been proposed for making these comparisons. These include primarily maximum parsimony and distance methods, although more recently maximum likelihood and Bayesian methods are being developed. This paper discusses each of these approaches in turn, including their merits and limitations, and any software which is available to make use of them.

Detailed chromosomal and radiation hybrid mapping in the proximal part of rat Chromosome 10 and gene order comparison with mouse and human.

The rat provides valuable and sometimes unique models of human complex diseases. To fully exploit the rat models in biomedical research, it is important to have access to detailed knowledge of the rat genome organization as well as its relation to the human genome. Rat Chromosome 10 (RNO10) harbors several important cancer-related genes. Deletions in the proximal part of RNO10 were repeatedly found in a rat model for endometrial cancer. To identify functional and positional candidate genes in the affected region, we used radiation hybrid (RH) mapping and single- and dual-color fluorescence in situ hybridization (FISH) techniques to construct a detailed chromosomal map of the proximal part of RNO10. The regional localization of 14 genes, most of them cancer-related ( Grin2a, Gspt1, Crebbp, Gfer, Tsc2, Tpsb1, Il9r, Il4, Irf1, Csf2, Sparc, Tp53, Thra1, Gh1), and of five microsatellite markers ( D10Mit10, D10Rat42, D10Rat50, D10Rat72, and D10Rat165) was determined on RNO10. For a fifteenth gene, Ppm1b, which had previously been assigned to RNO10, the map position was corrected to RNO6q12-q13.

Gene Arrangements and Phylogeny in the Class Proteobacteria

A simple method is presented for reconstructing phylogenetic trees on the basis of gene transposition. It is shown that differences in gene arrangements among genomes could allow us to determine whether a gene transposition event has occurred before or after species divergence from parsimonious considerations. The method is applied to evolutionary relationships among the bacterial class Proteobacteria, for which complete genomic sequences most densely accumulate and comprehensive gene order comparisons are possible. We were able to infer the emergence order of proteobacterial subclasses asε ⇒β⇒γ. This order is consistent with sequence-based inferences, which conversely confirms the usefulness of the approach presented here.

A Radiation Map of the Short Arm of Porcine Chromosome 2

In recent years, maps of mammalian genomes have been acquiring increasingly higher resolution. Integration of maps of different types has become possible. As a tool in integrating maps of mammalian genomes of different types, high-resolution mapping with radiation-induced hybrids (RH) is used. Here, we present an RH6000 map of the short arm of porcine chromosome 2. The map contains 15 microsatellites and five genes (for parathyroid hormone, lactate dehydrogenase A, myogenic factor, follicle-stimulating hormone beta, and calpain I). The RH panel was obtained on the basis of a hybrid cell line bearing the single porcine chromosome 2 against the background of mink chromosomes. The mean frequency of preserving markers examined in the panel was 18.3%. Integration of four genes in the panel and a comparison of gene order in homeologous regions of human and porcine chromosomes are presented.

Organization of specific genomic regions of Zygosaccharomyces rouxii and Pichia sorbitophila: comparison with Saccharomyces cerevisiae

The genomes of Zygosaccharomyces rouxii and Pichia sorbitophila were partially explored. The genome of Z. rouxii CBS 732 consists of seven chromosomes with an approximate size of 1.0–2.75 Mb, 12.8 Mb in total. Five of the chromosomes were labelled with specific probes. Three Z. rouxii genomic DNA fragments were sequenced; all 10 ORFs found were without introns and they have homologues in S. cerevisiae. Gene order comparison revealed that the organization is partially conserved in both species. The genome of P. sorbitophila CBS 7064 consists of seven chromosomes with an approximate size of 1.0–2.9 Mb, 13.9 Mb in total. Three of the chromosomes were labelled with specific probes. The sequencing of a 5.2 kb genomic DNA fragment revealed three ORFs, but no conservation of their organization was found, although all of them have their respective homologues in S. cerevisiae. According to our results, the presence of two overlapping ORFs in S. cerevisiae (YJL107c–YJL108c) could be interpreted as the result of a frameshift mutation. The Accession Nos of the sequenced DNA fragments are: Y18561, AJ25115, Y18560 and Y18559. Copyright © 2000 John Wiley & Sons, Ltd.

Analysis of the complete mitochondrial DNA sequence of the brachiopod terebratulina retusa places Brachiopoda within the protostomes.

Brachiopod phylogeny is still a controversial subject. Analyses using nuclear 18SrRNA and mitochondrial 12SrDNA sequences place them within the protostomes but some recent interpretations of morphological data support a relationship with deuterostomes. In order to investigate brachiopod affinities within the metazoa further, we compared the gene arrangement on the brachiopod mitochondrial genome with several metazoan taxa. The complete (15 451 bp) mitochondrial DNA (mtDNA) sequence of the articulate brachiopod Terebratulina retusa was determined from two overlapping long polymerase chain reaction products. All the genes are encoded on the same strand and gene order comparisons showed that.only one major rearrangement is required to interconvert the T. retusa and Katharina tunicata (Mollusca: Polvplacophora) mitochondrial genomes. The partial mtDNA sequence of the prosobranch mollusc Littorina saxatilis shows complete congruence with the T. rehtusa gene arrangement with regard to the ribosomal and protein coding genes. This high similarity in gene arrangement is the first to be reported within the protostomes. Sequence analyses of mitochondrial protein coding genes also support a close relationship of the brachiopod with molluscs and annelids, thus supporting the clade Lophotrochozoa. Though being highly informative, sequence analyses of the mitochondrial protein coding genes failed to resolve the branching order within the lophotrochozoa.

Comparative genetic mapping of allotetraploid cotton and its diploid progenitors

Allotetraploid cotton species (Gossypium) belong to a 1-2 million year old lineage that reunited diploid genomes that diverged from each other 5-10 million years ago. To characterize genome evolution in the diploids and allotetraploids, comparative RFLP mapping was used to construct genetic maps for the allotetraploids (AD genome; n = 26) and diploids (A and D genomes; n = 13). Comparisons among the 13 suites of homoeologous linkage groups permitted comparisons of synteny and gene order. Two reciprocal translocations were confirmed involving four allotetraploid At genome chromosomes, as was a translocation between the two extant A genome diploids. Nineteen locus order differences were detected among the two diploid and two allotetraploid genomes. Conservation of colinear linkage groups among the four genomes indicates that allopolyploidy in Gossypium was not accompanied by extensive chromosomal rearrangement. Many inversions include duplicated loci, suggesting that the processes that gave rise to inversions are not fully conservative. Allotetraploid At and Dt genomes and the A and D diploid genomes are recombinationally equivalent despite a nearly two-fold difference in physical size. Polyploidization in Gossypium is associated with enhanced recombination, as genetic lengths for allotetraploid genomes are over 50% greater than those of their diploid counterparts.Key words: restriction fragment length polymorphism (RFLP), Gossypium, evolution, polyploidy.

A Gene-Based Genetic Linkage and Comparative Map of the Rat X Chromosome

We have constructed a gene-based genetic linkage map of the rat X chromosome. Fifteen polymorphic microsatellite markers associated with 13 different X chromosome genes have been isolated and genotyped on F2progeny from five different intercrosses. These markers have been integrated with 23 further rat X chromosome markers, resulting in a single linkage group for the X chromosome containing 38 microsatellite markers associated with 21 different genes and spanning a genetic distance of 88 cM. Fluorescencein situhybridization was used to confirm the gene order obtained for the new markers and also placed 2 further genes, Hprt and Fmr1, on the map. Comparisons of gene order among rat, mouse, and human indicate homologous regions of conserved synteny and regions where evolutionary breakpoints have occurred. The genes from human Xq are conserved in order on the rat X chromosome, whereas those from human Xp have been rearranged into at least four conserved segments. The polymorphic markers and comparative map will be useful in studies on rat models of genetic disease.

Computational comparisons of model genomes

Complete genomes from model organisms provide new challenges for computational molecular biology. Novel questions emerge from the genome data obtained from the functional prediction of thousands of gene products. In this review, we present some approaches to the computational comparison of genomes, based on sequence and text analysis, and comparisons of genome composition and gene order.

Mapping of the OB receptor to 1p in a region of nonconserved gene order from mouse and rat to human.

As part of an effort to identify informative molecular markers for genetic analysis of human pedigrees segregating for obesity, we have developed a genetic map of human 1p in the region of the OB receptor (OBR), the gene that is defective in murine diabetes (Obrdb) and rat Zucker fatty (Obrfa) mutations located on mid-chromosome 4 and chromosome 5, respectively. OBR was mapped 0.9 cR centromeric to WI-9515 and 2.2 cR telomeric of WI-7249 by radiation hybrid (RH) mapping. Ten yeast artificial chromosomes (YACs) containing OBR were identified, confirming the location of OBR centromeric to WI-9515 and telomeric to WI-7249. Additionally, five P1 artificial chromosomes (PACs) were identified that comprised a contiguous series of overlapping clones spanning the length of OBR. WI-5182 was contained within the two PACs that are 3' of OBR. Using a panel of 68 individuals from a single three-generation family and an additional nuclear family, we have mapped 18 polymorphic markers including phosphoglucomutase 1 (PGM1), which is centromeric to Obrdb / Obrfa, and D1S85, which is telomeric to Obrdb / Obrfa in the mouse and rat. The following composite map integrates these radiation hybrid, genetic, and physical maps: Centromere-@WI-7249-[OBR; WI-5182]-D1S198-[WI-9515; WI-6550; D1S2866]-D1S2825-[WI-3077; D1S2886]-[D1S515; DS1613; PGM1]-[D1S312; D1S473; D1S230; D1S246; D1S203]-D2S1643-[D1S1669; D1S1596;]UNCJ-D1S476- D1S85-D1S220-C8B-GTAT1A7. Unresolvable markers are within brackets. A comparison of gene order on mouse chromosome 4, rat chromosome 5, and human 1p indicates that between rodents and humans, there has been a rearrangement of the gene order in the region surrounding OBR.

COLINEARITY OF CHLOROPLAST GENOMES IN DIVERGENT ECOTYYES OF THE MARINE DIATOM SKELETONEMA COSTATUM (BACILLARIOPHYTA)1

ABSTRACT The chloroplast genomes of three isolates of the marine diatom Skeletonema costatum (Grev.) Cleve were mapped and found to be 131 ± 2 kb with inverted repeats (IRs) of approximately 20 kb. In contrast to higher plants, the psbA gene mapped to the IR, and rbcS mapped to the same fragment as the rbcL gene in the large single‐copy region. The maps of the three isolates were colinear and revealed as many as 20 site mutations out of a total of 47 sites. The number of site mutations among isolates was consistent with previous data on their genetic diversity and physiology. Comparisons of gene order among our maps and those of three other diatom species showed that closely related genera retained similar gene orders but that more distantly related taxa exhibited extensive rearrangements. We conclude that simple restriction fragment analysis of chloroplast DNA is useful in comparative studies of diatom populations and species but that other analytical methods are more appropriate for phylogenetic studies at higher levels.

The histidine operon of Azospirillum brasilense: organization, nucleotide sequence and functional analysis

A 3457-base pair fragment of Azospirilum brasilense DNA which complemented mutations in the hisA and hisF genes of Escherichia coli was sequenced. The sequence analysis revealed the presence of six major contiguous open reading frames (ORF). The comparison of the predicted amino acid sequence of these ORF with those encoded by the eubacterial, archaebacterial and eukaryotic his genes sequenced thus far revealed that four of them have a significant degree of homology with the E. coli hisH, hisA, hisF and the C-terminal domain of the hisl gene products. S 1 mapping experiments indicated that the putative transcription start site coincided with the AUG translational initiation codon of the hisBd gene, the first gene of the A. brasilense his operon. Downstream from the last ORF, a sequence was identified which functions as a Rho-independent transcription terminator. Comparison of amino acid sequences, gene order and organization and evolutionary aspects of the A. brasilence his cluster are discussed.

Linkage, but not gene order, of homologous loci, including alpha-L-iduronidase (Idua), is conserved in the Huntington disease region of the mouse and human genomes.

alpha-L-iduronidase (IDUA), which when deficient causes mucopolysaccharidosis type I, is located near the Huntington disease locus (HD) on human Chromosome (Chr) 4p16.3, approximately 10(6) base pairs (bp) from the telomere. As part of our continuing efforts to define a detailed comparative map for this chromosomal segment in mice and humans, we have used an interspecific backcross between C57BL/6J and an inbred strain derived from Mus spretus to map Idua, the mouse homolog of IDUA. We also mapped the mouse homolog of D4S115, an anonymous locus approximately 250 kb proximal to IDUA. As expected, both Idua and D4S115h are located on the proximal portion of mouse Chr 5 near homologs for other loci on human Chr 4p. Comparison of gene order in mice and humans demonstrates, however, that a chromosomal rearrangement within this conserved synteny has occurred since divergence of lineages leading to mice and humans.

Chloroplast genome organization in Chlamydomonas

Summary Although the chloroplast genome of Chlamydomonas reinhardtii contains essentially the same complement of genes as chloroplast genomes of land plants, the arrangement of these genes within the circular DNA molecule is very different. Studies in several laboratories suggest that comparison of gene order, restriction fragment length polymorphisms, and sequences within chloroplast DNA may be valuable tools in phylogenetic analysis of Chlamydomonas species. We have found that six interfertile strains in the C. reinhardtii group differ by restriction fragment length polymorphisms throughout their chloroplast genomes. In two of these strains the chloroplast genomes are known to be colinear and the differences largely attributable to variations in the size and distribution of clusters of short dispersed repeat sequences occurring in intergenic regions. These repeats, which are marked by Aat II and Kpn I restriction sites, are present in the chloroplast genomes of all six interfertile strains of the C. reinhardtii group, but are absent from the chloroplast genomes of C. eugametos, C. moewusii, C. incerta and C. globosa. The latter two species, which are sensitive to the same vegetative cell autolysin as C. reinhardtii, do not appear to be interfertile with C. reinhardtii. Restriction fragment analysis of chloroplast DNA suggests that C. incerta and C. globosa are very similar to one another, but differ greatly from C. reinhardtii.