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PubMed2003

The mitochondrial genome of Strongyloides stercoralis (Nematoda) - idiosyncratic gene order and evolutionary implications.

The complete mitochondrial genome sequence of the parasitic nematode Strongyloides stercoralis was determined, and its organisation and structure compared with other nematodes for which complete mitochondrial sequence data were available. The mitochondrial genome of S. stercoralis is 13,758 bp in size and contains 36 genes (all transcribed in the clockwise direction) but lacks the atp8 gene. This genome has a high T content (55.9%) and a low C content (8.3%). Corresponding to this T content, there are 16 (poly-T) tracts of >/=12 Ts distributed across the genome. In protein-coding genes, the T bias is greatest (76.4%) at the third codon position compared with the first and second codon positions. Also, the C content is higher at the first (9.3%) and second (13.4%) codon positions than at the third (2%) position. These nucleotide biases have a significant effect on predicted codon usage patterns and, hence, on amino acid compositions of the mitochondrial proteins. Interestingly, six of the 12 protein-coding genes are predicted to employ a unique initiation codon (TTT), which has not yet been reported for any other animal mitochondrial genome. The secondary structures predicted for the 22 transfer RNA (trn) genes and the two ribosomal RNA (rrn) genes are similar to those of other nematodes. In contrast, the gene arrangement in the mitochondrial genome of S. stercoralis is different from all other nematodes studied to date, revealing only a limited number of shared gene boundaries (atp6-nad2 and cox2-rrnL). Evolutionary analyses of mitochondrial nucleotide and amino acid sequence data sets for S. stercoralis and seven other nematodes demonstrate that the mitochondrial genome provides a rich source of phylogenetically informative characters. In conclusion, the S. stercoralis mitochondrial genome, with its unique gene order and characteristics, should provide a resource for comparative mitochondrial genomics and systematics studies of parasitic nematodes.

Amino Acid Sequence↗

PubMed1988

Translation mapping with the flavivirus Kunjin: gene order and anomalies in translation of Ns5.

Kunjin (KUN) virus-infected cells were synchronized in translation by reversal of hypertonic inhibition; cells were then pulse-labelled with [35S]methionine. Electrophoretic analyses defined the sequence of incorporation of label into all the known KUN gene products shown previously to be unique and unrelated. GP44 or NS1 was inadequately labelled for analysis and was assumed to be translated sequentially after E in the polyprotein sequence. The relationship of the KUN gene order obtained by translation mapping to that proposed by Rice et al. Science (1985) 229, 726-733 based on the nucleotide sequence of yellow fever virus is as follows: KUN: 5'-C.GP20.E.GP44.P19.P10.P71. (?).P21.P98-3' YF: 5'-C.prM.E.NS1.ns2a.ns2b.NS3.ns4a.ns4b. NS5-3'. These results eliminate the ambiguities in identities of the previously hypothetical ns2a, ns2b and ns4b. Although ns4a was not positively identified, a labelled protein of Mr 12,000 to 14,000 was observed in one experiment and it mapped in the appropriate position for ns4a. Variation occurred in translation of NS5 when the hypertonic treatment of 40 min at 37 degrees C was reduced in time or in temperature.

Animals↗

PubMed2001

Radiation hybrid comparative mapping between human chromosome 17 and porcine chromosome 12 demonstrates conservation of gene order.

A comparative study of human chromosome 17 (HSA17) and pig chromosome 12 (SSC12) was conducted using both somatic cell hybrid panel (SCHP) and radiation hybrid (RH) panel analysis. Sequences from an expressed sequence tag (EST) project in pig reproduction were examined and six genes and ESTs originally believed to map to HSA17 were selected for this study. The genes/ESTs were TATA box binding protein-associated factor (TAF2N/RBP56), alpha-2-plasmin inhibitor (SERPINF2/PLI), H3 histone family 3B (H3F3B), aminopeptidase puromycin sensitive (NPEPPS), an expressed sequence tag (ESTMI015) and P311 protein (P311). The SCHP analysis mapped five genes/ESTs (TAF2N, H3F3B, SERPINF2, NPEPPS and ESTMI015) to SSC12q11-q15 and SSC12p11-p15 with 100% concordance, and assigned P311 to SSC2 (1/2q24)-q29 with 100% concordance. Radiation hybrid analysis of all six genes confirmed the SCHP mapping results, with average retention frequency of 25%. Recent human sequence data demonstrated that P311 is actually located on HSA5q. As HSA5q and SSC2q show conserved syntenic regions predicted from bi-directional painting, our P311 mapping data is consistent with these results. An expanded comparative SSC12 RH map integrating the five new type I markers and 23 previously mapped loci was established using a LOD score threshold of 4.8. The gene order of the five genes/ESTs on the SSC12 framework RH map (H3F3B-ESTMI015-NPEPPS-TAF2N-SERPINF2) is identical to the HSA17 GB4 map but with inversion of the map as conventionally drawn.

Animals↗

PubMed1995

Linear chromosomes of Lyme disease agent spirochetes: genetic diversity and conservation of gene order.

We have constructed physical and genetic maps of the chromosomes of 21 Lyme disease agent spirochetes from geographically diverse locations. All have linear chromosomes whose lengths range from 935 to 955 kbp, and all contain multiple linear plasmids in the 16- to 175-kbp size range. The locations of 11 gene clusters on the chromosomes of these different isolates are indistinguishable at the resolution achieved in this study, indicating that the members of this related group of species have highly conserved chromosomal gene orders. However, chromosomal restriction endonuclease cleavage site maps are unique for nearly all isolates. The 22 chromosomal maps currently available define eight classes of Lyme disease agents. Four of these correspond to the previously proposed species Borrelia burgdorferi, Borrelia garinii, Borrelia afzelii, and Borrelia japonica. In addition, the North American isolates 21038, DN127 c19-2, 25015, and CA55 typify four additional chromosomal types that are as phylogenetically distinct as the species listed above. These findings support the idea that comparison of restriction maps is currently the most robust and definitive method for determining overall chromosomal relationships among closely related bacteria. In the course of this work, we located on the chromosome the previously unmapped outer surface protein-encoding LA7 gene and genes homologous to the Escherichia coli priA, plsC, parE, and parC genes, and we have substantially refined the locations of the recA, fla, p22A, and flgE genes.

Animals↗

PubMed2003

A DNA region of Torulaspora delbrueckii containing the HIS3 gene: sequence, gene order and evolution.

We cloned a genomic DNA fragment of the yeast Torulaspora delbrueckii by complementation of a Saccharomyces cerevisiae his3 mutant strain. DNA sequence analysis revealed that the fragment contained two complete ORFs, which share a high similarity with S. cerevisiae His3p and Mrp51p, respectively. The cloned TdHIS3 gene fully complemented the his3 mutation of S. cerevisiae, confirming that it encodes for the imidazoleglycerol-phosphate dehydrate of T. delbrueckii. Two additional ORFs, with a high homology to S. cerevisiae PET56 and DED1 genes, were mapped upstream and downstream from TdHIS3 and TdMRP51, respectively. This genetic organization is analogous to that previously found in Saccharomyces kluyveri and Zygosaccharomyces rouxii. The evolutionary significance of gene order in this chromosomal region is analysed and discussed.

Amino Acid Sequence↗

PubMed2002

Conservation of gene order between horse and human X chromosomes as evidenced through radiation hybrid mapping.

A radiation hybrid (RH) map of the equine X chromosome (ECAX) was obtained using the recently produced 5000(rad) horse x hamster hybrid panel. The map comprises 34 markers (16 genes and 18 microsatellites) and spans a total of 676 cR(5000), covering almost the entire length of ECAX. Cytogenetic alignment of the RH map was improved by fluorescent in situ hybridization mapping of six of the markers. The map integrates and refines the currently available genetic linkage, syntenic, and cytogenetic maps, and adds new loci. Comparison of the physical location of the 16 genes mapped in this study with the human genome reveals similarity in the order of the genes along the entire length of the two X chromosomes. This degree of gene order conservation across evolutionarily distantly related species has up to now been reported only between human and cat. The ECAX RH map provides a framework for the generation of a high-density map for this chromosome. The map will serve as an important tool for positional cloning of X-linked diseases/conditions in the horse.

Animals↗

PubMed1981

Gene order in the major histocompatibility complex of the rat.

The loci in the major histocompatibility complex (MHC) of the rat which code for class I and class II antigens--RT1.A and RT1.B, respectively--have previously been separated by laboratory-derived recombinants and by observations in inbred and wild rats. Closely linked to the MHC is the growth and reproduction complex (Grc) which contains genes influencing body size (dw3) and fertility (ft). These phenotypic markers were used in this study to orient the A and B loci of the MHC. Two recombinants were used for mapping. The BIL(R1) animal is a recombinant between the MHC and Grc, and it carries the haplotype RT1.AlBlGrc+. The r10 animal is an intra-MHC recombinant, and it has the haplotype RT1.AnB1Grc. These recombinants were characterized serologically, by mixed lymphocyte reactivity, by immune responsiveness to poly (Glu52Lys33Tyr15) and by the presence of the dw-3 gene. The data demonstrate that the gene order of the loci is: dw-3--RT1.B--RT1.A.

Animals↗

PubMed1985

Molecular cloning of the six mRNA species of infectious hematopoietic necrosis virus, a fish rhabdovirus, and gene order determination by R-loop mapping.

Plasmids carrying cDNA sequences to the mRNA species of infectious hematopoietic necrosis virus were constructed and cloned into Escherichia coli. Characterization of 21 cloned plasmids by hybridization to mRNA blots identified sets of plasmids with homology to each of the six viral mRNA species. R-loop mapping with these cDNA plasmids determined that the gene order on the infectious hematopoietic necrosis virus genome is (3')N-M1-M2-G-NV-L(5').

Animals↗

PubMed1978

Tryptic peptide analyses of polypeptides generated by premature termination of cell-free protein synthesis allow a determination of the Rauscher leukemia virus gag gene order.

Translation of Rauscher murine leukemia virus (R-MuLV) 35S RNA in an mRNA-dependent cell-free protein-synthesizing system yields polypeptides identical to authentic Pr65gag, the R-MuLV gag precursor, and Pr200gag-pol, the precursor to the R-MuLV reverse transcriptase. In addition to these polypeptides, the cell-free product contains a family of polypeptides of less than 65,000 molecular weight which appear to be generated by premature termination of protein synthesis within the viral gag gene. We compared the tryptic maps of several of these less than 65,000-molecular-weight premature termination polypeptides with that of full-size Pr65gag and found a progressive loss of tryptic peptides which could be assigned to known R-MuLV gag proteins. A 40,000-molecular-weight fragment, P40gag, lacked p10 and part of p30, placing p10 at the C terminus pf Pr65gag and p30 ajacent to it. Fragments of 33,000 (P33gag) and 27,000 to 28,000 (P27/28gag) molecular weight showed a successive loss of additional p30 tryptic peptides, but no loss of either p15 or p12. An 18,000-molecular-weight fragment lost p12 but retained p15. These data suggest an R-MuLV gag gene order of NH2-p15-p12-p30-p10-COOH.

Genes, Viral↗

PubMed1988

Molecular cloning and characterization of six genes, determination of gene order and intergenic sequences and leader sequence of mumps virus.

mRNA isolated from mumps virus-infected Vero cells was converted into cDNA and cloned into the PstI site of the plasmid pBR322. After screening with 32P-labelled cDNA synthesized from poly(A)+ RNA of uninfected or mumps virus-infected Vero cells, five different groups of virus-specific clones were obtained. The virus specificity of the clones was confirmed by Northern blot analysis, in which the cDNA inserts from the five different groups hybridized to mRNAs of about 2100, 1500, 1450, 2000 and 2200 nucleotides. By the use of oligonucleotides synthesized on the basis of sequences obtained from the five cDNA clones and mRNAs, the sequence of the intergenic and surrounding areas was determined. During genome sequencing, a separate gene was identified between the fusion protein (F) gene and the haemagglutinin-neuraminidase protein (HN) gene. Using oligonucleotides synthesized on the basis of the new gene sequence, cDNA clones with poly(A) were isolated from the cDNA library. The gene order was determined to be 3' NC-P-M-F-SH-HN-L 5' (where NC, P, M, SH, and L represent the genes for the nucleocapsid, phosphoprotein or polymerase-associated, matrix or membrane, small hydrophobic and large proteins respectively). There is one nucleotide between the P and M (A), M and F (A), and HN and L genes (G), two between the NC and P (AA) and SH and HN (3'-CG) genes, and seven between the F and SH genes (3' GAUUUUA) as intergenic sequence. The leader sequence at the 3' end of the genome has been determined by sequencing the dicistronic leader-NC mRNA using oligonucleotide primers. The sequence from the 3' terminus to the NC gene start of the mumps virus genome is similar in length (55 nucleotides) to that present in Sendai virus, Newcastle disease virus and parainfluenza virus type 3, and the first five nucleotides are conserved in all negative-stranded RNA virus genomes sequenced to date.

Base Sequence↗

PubMed1995

Comparative mapping reveals extensive linkage conservation--but with gene order rearrangements--between the pig and the human genomes.

A porcine comparative map based on 83 coding loci was constructed. Comparisons to the human and mouse genetic maps revealed linkage conservation between humans and pigs more extensive than that between any of these and the mouse. The average lengths of conserved chromosome segments between pig and human and between pig and mouse were estimated at 37 and 21 cM, respectively. Rearrangements of gene orders within homologous chromosome segments were found to be common among these distantly related mammals. The development of a comparative map is an advance in pig genome analysis and contributes to the dissection of mammalian genome evolution.

Animals↗

PubMed2006

A second-generation integrated map of the silkworm reveals synteny and conserved gene order between lepidopteran insects.

A second-generation linkage map was constructed for the silkworm, Bombyx mori, focusing on mapping Bombyx sequences appearing in public nucleotide databases and bacterial artificial chromosome (BAC) contigs. A total of 874 BAC contigs containing 5067 clones (22% of the library) were constructed by PCR-based screening with sequence-tagged sites (STSs) derived from whole-genome shotgun (WGS) sequences. A total of 523 BAC contigs, including 342 independent genes registered in public databases and 85 expressed sequence tags (ESTs), were placed onto the linkage map. We found significant synteny and conserved gene order between B. mori and a nymphalid butterfly, Heliconius melpomene, in four linkage groups (LGs), strongly suggesting that using B. mori as a reference for comparative genomics in Lepidotera is highly feasible.

Animals↗

PubMed1988

The Ig kappa L chain allelic groups among the Ig kappa haplotypes and Ig kappa crossover populations suggest a gene order.

The Ig kappa complex locus of inbred mice found on chromosome 6 contains one constant (C kappa), five joining (J kappa), and 100 to 300 variable (V kappa) exons and spans an estimated 500 to 2000 kbp of DNA. The V kappa exons are organized into groups of highly homologous coding regions (approximately 300 bp) separated by approximately 10 kbp of intervening sequence. A group contains from 1 to 30 or more exons (exon refers to uninterrupted coding region DNA which is capable of encoding all or part of V kappa gene) that can be detected with specific DNA probes in conjunction with restriction endonuclease fragments (REF) from genomic DNA. Thirteen DNA probes specific for different V kappa exon groups and one DNA probe specific for J kappa and C kappa exons were used in conjunction with 55 inbred strains in an attempt to detect RFLP that could be used to establish Ig kappa allelic groups and Ig kappa haplotypes. Each probe detected two to four different REF patterns (allelic groups) among the panel of inbred mice examined. Size estimates of the REF were made, and each probe detected 4.2 to 107.7 kbp of DNA, including faint REF, 675.6 to 723.6 kbp of DNA could be detected within a single haplotype. Based on these allelic groups, seven haplotypes were identified among the 55 inbred strains of mice. No subline differences were detected, and the distribution of allelic groups implied common ancestry among many of the inbred strains examined. The DNA probes were also used in conjunction with recombinant inbred, congenic strains and backcross populations of mice. By using the analysis of known Ig kappa r populations, and assuming a common ancestry among the inbred strains, a gene order was predicted: Centromere-Hd-(Ig kappa-V11, Ig kappa-V24, Ig kappa-V9-26)-(Ig kappa-V1, Ig kappa-V9)-(Ig kappa-V4, Ig kappa-V8, Ig kappa-V10, Ig kappa-V12, 13, Ig kappa-V19)-(Ig kappa-V28, Rn7s-6)-Ig kappa-V23-(Ig kappa-V21, Ig kappa-J, Ig kappa-C)-(Ly2, Ly3)-wa-1.

Alleles↗

PubMed1975

Studies on bacteriophage M13 DNA. 2. The gene order of the M13 genome.

The double-stranded replicative form DNA of bacteriophage M13 was cleaved into 13 specific fragments by the restriction endonuclease from Haemophilus aphirophilus. The individual DNA fragments from wild-type replicative form molecules were then annealed to circular, single-stranded DNAs of phage M13, bearing amber mutations as genetic markers. When such DNA hybrids infected competent Escherichia coli cells, only those duplexes which were genetically heterozygous gave rise to wild-type phages in the progeny. In this way, the genetic markers carried on the individual DNA fragments could be determined. In addition, marker rescue in each gene was obtained with the 10 specific fragments of M13 replicative form DNA, produced by cleavage with the restriction endonuclease from Haemophilus aegyptius. From these results and the enzyme cleavage maps of both types of restriction fragments a distribution of genetic markers along the physical map could be obtained, which allowed an arrangement of M13 genes into a genetic map. Evidence is presented that the gene order of M13 is: IV-(I,VI)-III-VIII-VII-V-II with II and IV being contiguous on the circular map.

Chromosome Mapping↗

PubMed1988

Linkage relationships and gene order around the locus for X-linked retinoschisis.

X-linked recessive retinoschisis (RS) is a hereditary disorder with variable clinical features. The main symptoms are poor sight; radial, cystic macula degeneration; and peripheral superficial retinal detachment. The disease is quite common in Finland, where at least 300 hemizygous males have been diagnosed. We used nine polymorphic DNA markers to study the localization of RS on the short arm of the X chromosome in 31 families comprising 88 affected persons. Two-point linkage results confirmed close linkage of the RS gene to the marker loci DXS43, DXS16, DXS207, and DXS41 and also revealed close linkage to the marker loci DXS197 and DXS9. Only one recombination was observed between DXS43 and RS in 59 informative meioses, giving a maximum lod score of 13.87 at the recombination fraction .02. No recombinations were observed between the RS locus and DXS9 and DXS197 (lods between 3 and 4), but at neither locus was the number of informative meioses sufficient to provide reliable estimates of recombination fractions. The most likely gene order on the basis of multilocus analysis was Xpter-DXS85-(DXS207,DXS43)-RS-DXS41-DXS 164-Xcen. Because multilocus linkage analysis indicated that the most probable location of RS is proximal to DXS207 and DXS43 and distal to DXS41, these three flanking markers are the closest and most informative markers currently available for carrier detection.

Female↗

PubMed2006

The complete mitochondrial genome of the orbiniid polychaete Orbinia latreillii (Annelida, Orbiniidae)--A novel gene order for Annelida and implications for annelid phylogeny.

Relationships of annelid subtaxa are controversially discussed and additional markers are necessarily needed to get further insights into their evolution. Due to their high content of information, mitochondrial genomes have been proven very useful in phylogenetic analyses. Whereas many complete mitochondrial genomes of arthropods are available, lophotrochozoan taxa are only scarcely represented and this is especially true for annelids. Here we present the complete mitochondrial genome of the orbiniid polychaete Orbinia latreillii. The circular genome is 15,558 bp in size and contains the same 37 genes as found in most other metazoans. As in the case for all studied annelids all genes are transcribed from the same strand. Compared with the known data from other annelids at least five gene translocations must be hypothesized for O. latreillii. A comparison of the available data shows that gene translocations within Annelida seem to be less frequent than in molluscs, but more frequent as previously assumed. Phylogenetic analyses of mitochondrial DNA sequence data and amino acid data support an inclusion of Sipuncula within Annelida and a closer relationship to orbiniids is recovered for this taxon.

Animals↗

PubMed1993

Partial inversion of gene order within a homologous segment on the X chromosome.

The locus for the erthyroid transcription factor, GATA1, has been positioned in the small interval between DXS255 and TIMP on the proximal short arm of the human X Chromosome (Chr) by use of a partial human cDNA clone and a well-characterized somatic cell hybrid panel. Analysis of selected recombinants from 108 Mus musculus x Mus spretus backcross progeny with the same clone confirmed that the homologous murine locus (Gf-1) lies between Otc and the centromere of the mouse X Chr. These data imply that a partial inversion of gene order has occurred within the conserved segment that represents Xp21.1-Xp11.23 in human (CYBB-GATA1) and the proximal 6 cM of the mouse X Chr (Gf-1-Timp). Furthermore, they indicate that the mouse mutant scurfy and the human genetic disorder Wiskott-Aldrich syndrome, which have been mapped to the same regions as GATA1/Gf-1 in both species, may indeed be homologous disorders.

Animals↗

PubMed1985

Gene order and recombination rates in the linkage group S-Phi-Hal-H-(Po2)-Pgd in pigs.

Families of Czech Landrace (94 litters and 636 offspring) were tested for halothane sensitivity, A-O (S), H, PHI and PGD phenotypes. Informative matings for the estimation of recombination rates between marker loci were selected. The following recombination frequencies were established: S - Phi = 4.8% (2.5%-10.7%); S - H = 6.8% (4.3%-11.7%); Phi - H = 2.6% (0.9%-5.3%); H - Pgd = 4.4% (1.6%-8.0%). Cross-overs were observed also between S - Hal, Hal - H and Hal - Pgd, but were not found between Phi - Hal. On the basis of these results it has been possible to revise the position of the S locus in this linkage group. The most probable gene order would be: S - Phi - Hal (or Hal - Phi) - H - (Po2) - Pgd. A striking difference was found between the number of halothane-sensitive pigs (87) and HalnHaln genotypes determined by haplotyping (123). Segregation rates in 19 backcross matings and experimental matings of the animals proved that this difference is mostly due to incomplete penetrance or low expression of halothane sensitivity.

Alleles↗