Rabbit mitochondrial DNA: preliminary comparison between some domestic and wild animals (original) (raw)
Related papers
DNA Sequence Variation in the Mitochondrial Control Region of Oryctolagus cuniculus from Croatia
2017
800x600 Normal 0 21 false false false HR X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Calibri",sans-serif;} In Croatia, w ild rabbits ( Oryctolagus cuniculus ) are present in several East Adriatic islands, while their origin is not known (documented). To characterize their maternal origin, we have analysed p artial mitochondrial DNA control region (CR-mtDNA) sequence (317-bp) in 36 wild rabbits sampled in three Croatian islands ( 11 in Dolin, 10 in Dugi otok and 15 in Trstenik). After comparison with other worldwide distributed wild and domestic rabbit sequences (208), two distinguished haplotypes (H1 and H2) were found in Croatian rabbits. H1...
Genetics, 1981
Restriction endonuclease analysis has revealed extensive mtDNA polymorphism in two species of rats, Rattus rattus and Rattus norvegicus. Sequence divergence values for the eight detected R. norvegicus variants range from 0.2% to 1.8% and for the eight R. rattus variants, from 0.2% to 9.6%. Three of the most closely related R. norvegicus mtDNA's appear to differ by deletions/insertions of about 4 base pairs apiece. Restriction sites for seven enzymes have been mapped for 11 of these variants. The 31 intraspecific and 41 interspecific variant sites appear to be evenly distributed on the mtDNA molecule outside of the rRNA cistrons. The location of sites present in all the DNAs suggests that the rRNA genes and possibly the light strand origin of replication may be more highly evolutionarily conserved than other parts of the molecule. The sequence divergences among the mtDNAs of animals whose geographic origins are separated by major barriers, such as oceans, were significantly great...
Development and application of long‐PCR for the assay of full‐length animal mitochondrial DNA
Molecular Ecology, 1996
Native mitochondria1 (mt) DNA in higher animals exists as a closed-circular molecule typically 1&20 kilobase pairs (kb) in length. For nearly two decades, this cytoplasmically housed genetic system has been employed to estimate matrilineal phylogeny within and among species (Avise 1994). Beginning in the late-lWOs, a primary assay method involved restriction analyses of whole mtDNA molecules that had been physically isolated from nuclear DNA. In the late-l980s, many studies moved to PCR-based (Saiki et al. 1988) restriction-site or sequence assays of particular mtDNA regions typically a few hundred to lo00 bp in length. Here we document successful 'long-PCR amplification (Cohen 1994) of hll-length animal mtDNA, using cmserved 16s ribosomal gene sequences. Heretofore, PCR amplification of full-length mtDNA has been reported only for humans, and in a clinical context (Cheng et al. 1994b; Li et al. 1995). Assays were focused primarily on armadillos (Mammalia, Edentata, Dasypodidae): Dasypus norwncinctus (n = 12 specimens from scattered sites in the south-eastem United States); and Tolypeutes rnatacus (nl), Zoedyus pichiy (n = 2), Chaetophrnctus wlIerOsus (n-2), and C. villosus (n = 2) collected in northern Argentina. From the non-Dnsypus species, total genomic DNA was prepared from blood by standard methods involving phenol chloroform extraction and ethanol precipitation. For the other specimens, mtDNA was purified from heart and liver by conventional CsCl gradient centrifugation (Lansman et al. 1981). Total genomic DNA also was prepared from 20 additional specimens of Dasypus according to Taggart et nl. (1992), using clips of ear tissue preserved in 90% ethanol. Sequences (c. 500 bp long) within the mtDNA 16s ribosomal RNA gene were PCR-amplified using the 'universal' primers 16sar-L and 16sbr-H (Palumbi et al. 1991). Templates for these amplifications were CsCl gradient
Molecular Biology and Evolution
Initial amplification and sequencing of a 366-bp fragment of the cytochrome b gene by a conserved primer pair (MVZ 03 and MVZ 04) revealed a nonfunctional copy of the gene with two deletions (one of which is 17 bp in length and the other of which is 3 bp in length) in Chroeomys jelskii, a South American akodontine rodent. By means of an alternative primer to MVZ 03-namely, MVZ 05-from the region of the tRNA for glutamic acid, a functional copy of cytochrome b was subsequently amplified. Both primer pairs amplify functional sequence when applied to purified mitochondrial DNA (mtDNA). Restriction-endonuclease digestion of purified mtDNA from C. jelskii did not reveal any additional sets of bands that would suggest heteroplasmy in the mitochondrial genome. When probed with both functional and nonfunctional gene fragments, Mb01 restriction digests revealed the same pattern, providing further evidence that the nonfunctional copy must be located in the nucleus. Observed differences in the mitochondrial and nuclear sequences from two populations are consistent with a faster rate of change in mtDNA than in nuclear DNA.
Proceedings of the National Academy of Sciences, 1980
ABSTRACr Restriction enzyme analysis of mtDNAs for the purpose of determining sequence divergence rests on the assumption that variant recognition sites differ with respect to sequence and not methylation. This assumption was tested on two mtDNAs, A and B, which are distributed throughout the laboratory rat population and which can be distinguished by a number of restriction enzymes. The mtDNAs were cloned and the nucleotide sequences of corresponding small HindIII fragments, in which a variant EcoRI site occurs, were determined. Evidence that the fragments differ in sequence and not methylation is as follows: (i) The cloned mtDNA yielded the same fragment pattern as did native mtDNA when treated with EcoRI, Hha I, Hinfl, and Hae Im; (ii) three nucleotide replacements were found in the 169-base pair fragment, A T site in the type A and its absence in the type B mtDNA. Examination of the sequence leads to the suggestion that these three nucleotide replacements are silent; i.e., they would not lead to amino acid substitutions in a possible encoded protein. The phenomenon of intraspecific mtDNA polymorphism in mammals as detected by restriction endonucleases is well established (1-11) and is proving valuable as an approach to a number of important problems. For example, the discovery of two types of mtDNA in the laboratory rat population (3) was used to conclusively prove the operation of maternal inheritance in mammals (5, 6, 12, 13). Also, the high degree of this intraspecific mtDNA variation in all the species that have been studied, and particularly in Rattus rattus (ref. 11; unpublished data), suggests a rapid rate of evolution for mtDNA, and this has been proposed previously in an interspecific comparison of mtDNAs. Thus, the restriction enzyme analysis of this rapidly evolving DNA offers an approach at high resolution to the study of the evolution of closely related species and even of the population genetics within a species (refs. 10 and 11; unpublished data).
The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the oppositeonly the head enters the eggbecame fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra-and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.
Nucleic Acids Research, 1983
Three closely related variants of rat (Rattus norvegicus) mtDNA have been shown to differ in the number of T residues found in a run of Ts (light strand) which spans the junction between the tRNACYS and tRNATyr genes. The number of Ts in the repeat varies from 6 to 8 in these DNAs. Another, less closely related, R. norvegicus variant has a run of 5 Ts at this site and in the related species, Rattus rattus, a run of 4 Ts is found. In R. norvegicus mtDNA runs of 5 As and 5 Gs are found just to the 3' side of the variable T repeat, and it is suggested that the three runs of repeated nucleotides may stabilize heteroduplexes which result from strand slippage and which give rise to the insertions and/or deletions. Among 17 mtDNA clones derived from an individual with the 8T repeat, one clone was found which possessed a 9T repeat. This variant may represent an additional DNA type originally present within the individual.
Rabbit mitochondrial DNA diversity from prehistoric to modern times
Journal of Molecular Evolution, 1995
The mitochondrial genetic variability in European rabbit (Oryctolagus cuniculus) populations present in Europe and North Africa from 11,000 years ago to the present day has been analyzed using ancient DNA techniques. DNA was extracted from 90 rabbit bones found in 22 archaeological sites dated between the Mesolithic and recent times. Nucleotide sequences present in a variable 233-bp domain of the cytochrome b gene were compared to those present in modern-day rabbits. The results show that the structure of ancient populations of wild rabbit exhibited remarkable stability over time until the Middle Ages. At this time, a novel type of mtDNA molecule abruptly appears into most wild populations studied from France. This mtDNA type corresponds to that currently present in the domestic breeds of rabbit examined so far. The relative rapidity by which this mtDNA type established and its absence in all sites examined before 1,700 years ago lend support to the hypothesis that between 2,000 and 1,000 years ago, man may have favored the development, into all regions of France, of animals carrying this particular mtDNA molecule. The origin of such animals has still to be found: animals previously living outside of France or within France but in very restricted areas? This event was concomitant with the documented establishment of warrens after the tenth century A.D. in Europe.
Genome, 2008
In a previous phylogeographic study of the rodent Calomys musculinus, 24 haplotypes of the mitochondrial DNA D-loop region were detected using the restriction fragment length polymorphism technique (PCR-RFLP). Seven percent of the individuals showed patterns in which the sum of the sizes of the restriction fragments exceeded the size of the original PCR product. In the present paper we analyze possible causes of these atypical haplotypes. PCR products were cloned, and two or three different clones from a single individual were detected by their RFLP patterns. Nine clones with different restriction patterns were selected for sequence analyses. A maximum parsimony phylogenetic analysis revealed two well-supported paraphyletic groups. One group comprised sequences showing low nucleotide divergence compared with the most common haplotypes detected in the phylogeographic study. The other group was basal to the three species of Calomys other than C. musculinus included in the study; the mutations in the short portion of the cytochrome b gene amplified corresponded to 12 amino acid substitutions. The results suggest that two independent insertions of mtDNA sequences into the nucleus occurred; these sequences would co-amplify in the PCR procedure. Identification of pseudogenes is crucial to obtain reliable reconstruction of the intraspecific genealogy in phylogeographic studies.