DPKQDFMRFamide expression is similar in two distantly related Drosophila species

Drosophila melanogaster DPKQDFMRFamide was isolated and its expression reported. Distribution of DPKQDFMRFamide immunoreactivity is now described in Drosophila virilis. DPKQDFMRFamide antibody stained a cell in the subesophageal ganglion in embryo. DPKQDFMRFamide antibody stained cells in the superior protocerebrum, subesophageal ganglion, thoracic ganglia, and an abdominal ganglion in larva, pupa, and adult. DPKQDFMRFamide antibody stained an additional pair of cells in the optic lobe and a cell in the lateral protocerebrum in adult. Structure identity and similar distribution of DPKQDFMRFamide in D. virilis and D. melanogaster, two distantly related Drosophila species, suggests an important and conserved activity for the peptide.     

DNA sequences repaired at pachytene exhibit strong homology among distantly related higher plants

Moderately repetitive DNA sequences in Lilium (cv Enchantment) which undergo a meiotic-specific repair synthesis during pachytene (P-DNA) were previously shown to exist as families of very low internal sequence divergence. The present study concerns P-DNA sequence preservation among higher plants. The relative abundance of these sequences in a variety of plant species and their divergence relative to Enchantment P-DNA was determined through C₀t analysis and thermal denaturation of hybrid duplexes. Nearly all of the P-DNA sequence families of Enchantment were found to be present in the genomes of a number of monocot species and the dicot Vicia faba. Sequence content is highly conserved, with less than 6% divergence between Lilium and distantly related species such as Zea mays and Secale cereale. However, the number of repeats per P-DNA family varies considerably in different species, being particularly low among the Poales. P-DNA differs from most high thermal stability (HTS) sequence families of Enchantment which, although exhibiting a high degree of internal homology, are not present as repetitive DNA in the genomes of the other species examined. For most HTS families, the lack of internal divergence probably reflects their fairly recent introduction into the moderately repetitive DNA class, while P-DNA sequences represent evolutionarily ancient families which are the products of strong selective pressure for an indispensable meiotic function.     

Detecting homology of distantly related proteins with consensus sequences

A simple protocol is described that is suitable for the detection of distantly related members of a protein family. In this procedure, similarity to a consensus sequence is used to distinguish chance similarity from similarity due to common ancestry. The consensus sequence is constructed from the sequences of established members of a protein family and it incorporates features characteristic of the protein fold of this family: conserved residues, the pattern of variable and conserved segments, preferred location of gaps etc. The database is searched with the consensus sequence, using the unitary matrix or log odds matrix for scoring the alignments, with variable gap penalty. The advantage of the method is that it weights key residues, ignores sequence similarity in variable segments (thus partially eliminating "background noise" coming from chance similarity), distinguishes gaps disrupting conserved segments from those occurring in positions known to be tolerant of gap events. The utility of the method was demonstrated in the case of the protein family homologous with the internal repeats of complement B as well as the internal repeats identified in fibroblast proteoglycan PG40. The consensus sequence method succeeded in finding some new members of these protein families that could not be detected by earlier methods of sequence comparison.     

The actin loci in the genus Drosophila: establishment of chromosomal homologies among distantly related species by in situ hybridization

We have mapped by in situ hybridization the actin genes in selected, distantly related Drosophila species, using the 5C actin gene of D. melanogaster as a probe. In all species six dispersed actin loci were observed, probably corresponding to six genes, and they were similarly distributed among the chromosomes. In conjunction with previously available genetic and cytogenetic evidence, this consistent pattern of actin gene distribution reinforces the hypothesis that the chromosomal elements have maintained their essential identities throughout Drosophila evolution, and permits identification of these elements in very diverse species. Conservation of the actin loci also offers fixed points for the analysis of chromosomal inversions and other rearrangements.     

DNA homologies among Drosophila species and a related genus.

Deoxyribonucleic acids of members of the family Drosophilidae; e.g., D. melanogaster, D. robusta, D. pellewae, D, immigrans, D. mcclintockae, D. calloptera, C. procnemis and from a tissue culture cells of D. melanogaster have been compared with respect to base composition, heterogenecity, and nucleotide sequence homology. Considerable heterogeneity exists in DNA's from 3rd instar larvae and tissue culture cells. The DNA base composition of adult species ranges from 33-42 moles percent GC; in addition a polydAT component is apparent in larval DNA's. There are about 21 and 29 percent intragenomic homology in DNA's of D. melanogaster and D. immigrans, respectively. Relatively large differences were revealed in the nucleotide sequences of several species by DNA hybridization and thermal stability studies.     

Conservation of capR (lon) DNA of Escherichia coli K-12 between distantly related species.

Mutations in the capR gene of Escherichia coli K-12 are responsible for a wide variety of phenotypic changes, including defects in cell division. Since this gene plays a critical role in cell division, it might be evolutionarily conserved. Of the DNAs examined by Southern analysis, capR probe sequences were found not only in other enterics but also in Caulobacter crescentus CB13 and the distantly related archebacterium Halobacterium halobium R1.     

Quantitative in situ hybridization reveals extent of sequence homology between related DNA sequences in Drosophila melanogaster

Cloned DNA from the larval serum protein one (LSP-1) genes was hybridized to polytene chromosomes of D. melanogaster. The ratio of grains deposited over any two of the three LSP-1 genes with any one LSP-1 subunit probe was constant. Varying the gene dose of any one LSP-1 subunit relative to the others by up to six fold gave a linear relationship of grain ratios to gene ratios. We show that these constant ratios closely reflect the extent of sequence homology between the genes as determined by heteroduplex mapping (Smith et al., 1981) and thermal denaturation studies. The results obtained demonstrate that the LSP-1 subunit genes are present in equal copies in the genome.     

Comparative mapping of cosmids and gene clones from a 1.6 Mb chromosomal region of Drosophila melanogaster in three species of the distantly related subgenus Drosophila

The successful hybridization of cosmid clones from Drosophila melanogaster (Sophophora subgenus) to the salivary gland chromosomes of other species as distantly related as those in the Drosophila subgenus attests their great potential for unravelling genome evolution. We have carried out, using 28 cosmids and 13 gene clones, a study of the organization of the D. melanogaster 95A-96A chromosomal region in three Drosophila subgenus species: D. repleta, D. buzzattii and D. virilis. These clones were first used to built an accurate map of this 1.6 Mb region of D. melanogaster chromosome 3R (Muller’s element E). Then, they were hybridized and mapped to the homologous chromosome 2 of the other three distantly related species. The studied region is disseminated over 13 different sites of chromosome 2 in the Drosophila subgenus species, which implies a minimum of 12 inversion breakpoints fixed between the two subgenera. Extrapolation to the entire chromosome gives 90 fixed inversions. The D. melanogaster Pp1-96A-Acr96Aa segment conserved in D. repleta and D. buzzatii is longer than previously thought and is also conserved in D. virilis. In addition, three other D. melanogaster segments conserved in the three Drosophila subgenus species were found. Finally, our data indicate significant statistical differences in the evolution rate of Muller’s element E among lineages, a result that agrees well with the previous cytogenetic data. Received: 22 July 1998; in revised form: 11 November 1998 / Accepted: 12 November 1998     

Microsatellite DNA in Actinidia chinensis: isolation, characterisation, and homology in related species

 We have isolated and sequenced 263 microsatellite-containing clones from two small insert libraries of Actinidia chinensis enriched for (AC/GT) and (AG/CT) repeats, respectively. Primer pairs were designed for 203 microsatellite loci and successfully amplified from both plasmid and A. chinensis genomic DNA. In this paper we report the sequences of 40 primer pairs for which we have demonstrated Mendelian segregation in the progeny from controlled crosses. The polymorphism of ten microsatellites of each type was evaluated in four diploid and six tetraploid genotypes of A. chinensis. All microsatellites proved to be polymorphic, the number of alleles per locus detected in polyacrylamide sequencing gels ranging from 9 to 17. The high degree of polymorphism in Actinidia renders these markers useful either for mapping in A. chinensis or for fingerprinting cultivars of both domesticated kiwifruit species (A. chinensis and A. deliciosa). While most primer pairs produced single amplification products, about 20% generated banding patterns consistent with the amplification of two different loci. This supports the hypothesis that diploid species of Actinidia (2n=2x=58) are polyploid in origin with a basic chromosome number x=14/15 and that chromosome duplication may have occurred during the evolution of the genus. Finally, we have assayed the cross-species transportability of primer pairs designed from A. chinensis sequences and have found extensive cross-species amplification within the genus Actinidia; 75% of primer pairs gave successful amplification in the eight species assayed (A. arguta, A. rufa, A. polygama, A. chrysantha, A. callosa, A. hemsleyana, A. eriantha, and A. deliciosa), which are representative of the four sections into which the genus is currently split. Received: 14 February 1998 / Accepted: 26 May 1998     

Mitochondrial DNA variation in Drosophila pseudoobscura and related species in Pacific northwest populations

We have analysed mitochondrial DNA (mtDNA) from Pacific Northwest populations of Drosophila pseudoobscura, D. persimilis, and D. miranda using six restriction enzymes. We find that HpaII restriction sites are hypervariable compared to the other enzymes used. This hypervariability allows construction of a maximum parsimony map linking each mtDNA genotype. Small insertions, possibly tandem duplications, appear to have arisen concomitantly with, or subsequent to, speciation events, perhaps within the A + T rich region. Convergence of mtDNA genotypes is also evident. Unlike findings for other populations of these species, we find little evidence of mitochondrial introgression between D. pseudoobscura and D. persimilis, despite their ability to produce fertile hybrid females.     

Vitellogenin genes and their products in closely and distantly related species of Xenopus

Plasma vitellogenins from two closely related species of Xenopus, X. laevis and X. borealis, and a more ancient species, X. tropicalis, exhibited the same size on gel electrophoresis and were immunologically related. Partial peptide maps of 125I-labelled plasma vitellogenins, however, revealed marked differences in th structure and organisation of vitellogenin in the three Xenopus species. Northern blot hybridisation of liver RNA from oestrogen-treated males and females, probed with cloned vitellogenin cDNA, revealed the presence of mRNA of the same size in the three species of Xenopus, which was absent in untreated male liver. Cell-free translation of total liver RNA showed the presence of functional mRNA coding for vitellogenin subunit of the same size (Mr congruent to 210,000). Restriction endonuclease digestion patterns of genomic DNA from the three Xenopus species, using cloned X. laevis vitellogenin cDNA as the hybridisation probe, revealed significant differences in the organisation of these genes, which occur at a higher multiplicity in X. laevis and X. borealis than in X. tropicalis. Thus, despite a high degree of conservation of size, overall sequence and immunological identity of vitellogenin genes and their products in the three species of Xenopus, there is a substantial structural rearrangement during evolution of Xenopus within this multigene family.     

PCR-RFLP and total DNA homology revealed three related genomic species among broad-host-range Frankia strains

Abstract: Restriction fragment length polymorphism (RFLP) analysis of the PCR amplified nif D-K intergenic spacer (IGS) region was used to cluster 22 Frankia strains of the Elaeagnus host specificity group into seven genomic groups and to measure the degree of genetic similarity among them. This PCR-RFLP analysis could assign freshly isolated strains to described genomic species and revealed genomic groups not yet described among Frankia strains of the Elaeagnus specificity group. Six broad-host-range Frankia strains, infective on both Alnus and Elaeagnus , fell into three closely related PCR-RFLP clusters. DNA-DNA hybridization was then used to establish the correlations between PCR-RFLP clusters and total DNA relatedness groups. The three PCR-RFLP clusters agreed with two new and one reference genomic species, indicating that Frankia ability to nodulate with Alnus and Elaeagnus is a monophyletic trait shared by three genomic species.     

A comparative study of the short term cold resistance response in distantly related Drosophila species: the role of regucalcin and frost

The molecular basis of short term cold resistance (indexed as chill-coma recovery time) has been mostly addressed in D. melanogaster, where candidate genes (Dca (also known as smp-30) and Frost (Fst)) have been identified. Nevertheless, in Drosophila, the ability to tolerate short term exposure to low temperatures evolved several times independently. Therefore, it is unclear whether variation in the same candidate genes is also responsible for short term cold resistance in distantly related Drosophila species. It should be noted that Dca is a candidate gene for cold resistance in the Sophophora subgenus only, since there is no orthologous gene copy in the Drosophila subgenus. Here we show that, in D. americana (Drosophila subgenus), there is a north-south gradient for a variant at the 5' non-coding region of regucalcin (a Dca-like gene; in D. melanogaster the proteins encoded by the two genes share 71.9% amino acid identities) but in our D. americana F2 association experiment there is no association between this polymorphism and chill-coma recovery times. Moreover, we found no convincing evidence that this gene is up-regulated after cold shock in both D. americana and D. melanogaster. Size variation in the Fst PEST domain (putatively involved in rapid protein degradation) is observed when comparing distantly related Drosophila species, and is associated with short term cold resistance differences in D. americana. Nevertheless, this effect is likely through body size variation. Moreover, we show that, even at two hours after cold shock, when up-regulation of this gene is maximal in D. melanogaster (about 48 fold expression change), in D. americana this gene is only moderately up-regulated (about 3 fold expression change). Our work thus shows that there are important differences regarding the molecular basis of cold resistance in distantly related Drosophila species.     

Chemotactic transducer proteins of Escherichia coli exhibit homology with methyl-accepting proteins from distantly related bacteria.

Transducers are transmembrane, methyl-accepting proteins central to the chemotactic systems of the enteric bacteria Escherichia coli and Salmonella typhimurium. Methyl-accepting proteins have been reported in a number of species in addition to these enteric bacteria. Those species include Bacillus subtilis and Spirochaeta aurantia, representatives of groups that diverged from ancestral enteric bacteria and from each other very early in bacterial evolution. An antiserum that reacts with all transducers of E. coli precipitated specifically methyl-accepting proteins from B. subtilis and S. aurantia, indicating that these proteins share antigenic determinants with transducers of E. coli. In addition, analysis of tryptic peptides by high-pressure liquid chromatography revealed similarities in the regions of methyl-accepting sites for proteins from all three species. These observations imply that structural features have been preserved in the three species from transducers contained in a common ancestor of eubacteria. It is thus reasonable to predict that other flagellated, chemotactic bacteria will be found to contain methyl-accepting proteins homologous to transducers of enteric bacteria.