Length Heteroplasmy Research Articles

Doubly uniparental transmission of mitochondrial DNA length variants in the mussel Mytilus trossulus

Doubly uniparental inheritance of mitochondrial DNA (mtDNA) is an unusual feature found in marine mussels and a few other bivalve species. In addition to a mitochondrial genome (F) inherited through the female line, heteroplasmic individuals (males) contain a second highly diverged genome (M) that is inherited through the paternal line. The Baltic mussel Mytilustrossulus is characterized by the presence of two phylogenetically close female and male genomes. We examined M. trossulus sampled from the Gulf of Gdansk, southern Baltic. Somatic tissues and gametes were surveyed for the presence of different types of mtDNA. Length variants were identified using PCR (polymerase chain reaction) amplification of the mtDNA fragment containing the major noncoding region. Seventeen length variants present in homo- and heteroplasmic individuals were found in a sample of 343 individuals analyzed. Two length variants of the major noncoding region (PCR product lengths: 1520 and 1370 bp) were the most frequent. Length heteroplasmy was found in 46.8% of males, and was mostly caused by the presence of the short length variant (PCR product length: 1370 bp) of the major noncoding region. MtDNA variants were also detected by restriction analysis of a 1.3 kb segment of coding region (ND2–COIII) amplified by PCR. This study provides evidence that the short length variant is always transmitted to sperm and has taken over the role of the M genome. The remaining length variants were present in both males and females. Longer length variants were transmitted mainly through the female line. A possibility of much higher incidence of genome role reversals in Baltic M. trossulus, in comparison with other populations of mussels is discussed.

Sequencing of mitochondrial HV1 and HV2 DNA with length heteroplasmy

This study presents a fast method for sequencing the poly C/G regions in HV1 and HV2 in the mitochondrial DNA (mtDNA).

Sequencing strategy of mitochondrial HV1 and HV2 DNA with length heteroplasmy

We describe a method to obtain reliable mitochondrial DNA (mtDNA) sequences downstream of the homopolymeric stretches with length heteroplasmy in the sequencing direction. The method is based on the use of junction primers that bind to a part of the homopolymeric stretch and the first 2–4 bases downstream of the homopolymeric region. This junction primer method gave clear and unambiguous results using samples from 21 individuals with length heteroplasmy in the hypervariable regions HV1, HV2 or both. The method is of special value for forensic casework, because sequencing of both strands of an mtDNA region is preferable in order to reduce ambiguities in sequence determination.

Evolution of heteroplasmy at a mitochondrial tandem repeat locus in cultured rabbit cells.

Surveys of animal mitochondrial DNA (mtDNA) polymorphism reveal that mtDNA length variation is common. Much of this variation involves non-coding tandem repeat arrays in the main control region of the molecule. Despite a high mutation rate, generating systematic individual mtDNA length heteroplasmy, the number of repeats in a tandem array is maintained within a narrow range in lagomorphs. To investigate the basis for this apparent paradox, we studied the evolution of mtDNA length polymorphism in several rabbit cell clones containing different proportions of mtDNA, with four or five 153-bp repeats. Our data show that equivalent amounts of two mtDNA molecular types are not stable (evolution towards a predominant type being the rule) and that other types remain represented, maintaining the length polymorphism. The data suggest that mtDNA molecules with a longer array of repeats have a replicative advantage that could depend on the nuclear background.

Evolution of length variation and heteroplasmy in the chloroplast rDNA of symbiotic dinoflagellates (Symbiodinium, Dinophyta) and a novel insertion in the universal core region of the large subunit rDNA

Marine dinoflagellates are a diverse and ecologically important group of unicellular protists responsible for events such as ‘red tides’ and for forming mutualistic symbioses with various invertebrates. However, little is known about the evolution of organellar DNA in these organisms. We analysed domain V of the chloroplast large subunit ribosomal DNA (cp23S-rDNA) from a variety of symbiotic dinoflagellates and uncovered several unique features. These included length heteroplasmy of cp23S-rDNA that resulted from deletion mutations and the presence of a 1–13 bp nucleotide insertion in the universal core region. The insertion in the large subunit rDNA is novel across all kingdoms and appears to be a unique derived state for the symbiotic genus Symbiodinium. In addition, analysis of expansion segments (ES) revealed that the cp23S-rDNA domain V of symbiotic dinoflagellates is the most size variable of any known plastid-harbouring organism. Our results demonstrate that the universal core secondary structure and the chloroplast rDNA ES are less constrained in size than previously thought.

Nuclear mitochondrial interplay in the modulation of the homopolymeric tract length heteroplasmy in the control (D-loop) region of the mitochondrial DNA.

We have studied the genetic characteristics of a homopolymeric tract length heteroplasmy associated with the 16189C variant in the mtDNA D-loop control region to identify the factor(s) involved in the generation of the length heteroplasmy. The relative proportion of the various lengths of the polycytosines (i.e., the pattern of the length heteroplasmy) is maintained in an individual, and previous evidence shows that it is regenerated de novo following cell divisions. The pattern is maintained in maternally related individuals, suggestive of mtDNA determinants. Of the 38 individuals with the 16189C variant studied, 39% were found to exhibit the (16180)AAACCCCCCCCCCC(16193) variant associated with A16183C polymorphism [(11C)-group], while 53% showed the (16180)AACCCCCCCCCCCC(16193) variant associated with a further A16182C polymorphism [(12C)-group]. Haplotype analysis of the mtDNA revealed a specific association of the longer mean length of the poly[C] in the (12C)-group with haplogroup B. A similar association was also observed in the (11C)-group, but with a novel haplogroup. Cybrid constructions revealed that the involvement of nuclear factor(s) in the generation of the length heteroplasmy is prominent in homopolymeric tract of eight cytosines. The nuclearly coded factor(s) is/are presumably related to the fidelity of the nuclearly coded components of the mitochondrial DNA replication machinery.

A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals.

A database of mitochondrial DNA (mtDNA) hypervariable region 1 (HV1) and region 2 (HV2) sequences of the mtDNA control region was established from 162 unrelated Japanese individuals. The random match probability and the genetic diversity for this database were 0.96% and 0.997, respectively. Length heteroplasmy in the C-stretch regions located around position 16189 in HVI and 310 in HV2 was observed in 37% and 38% of the samples, respectively. A strategy using internal sequencing primers was devised to obtain confirmed sequences in these length heteroplasmic individuals. This database, combined with other mtDNA sequence databases from the Japanese population, will permit the significance of mtDNA match results to be properly reported in mtDNA typing casework in Japan.

Evidence for the de novo regeneration of the pattern of the length heteroplasmy associated with the T16189C variant in the control (D-loop) region of mitochondrial DNA.

We have investigated the genetics of the length heteroplasmy associated with the T16189C variant of mitochondrial DNA (mtDNA), and report here definitive evidence that the pattern of the length heteroplasmy is not simply the outcome of drift related to the random segregation of the mtDNA population during cell division, but is actively maintained and regenerated de novo following each cell division. The pattern of the length heteroplasmy was maintained in a fibroblast cell line during an extensive mtDNA depletion experiment by ethidium bromide treatment, and following the subsequent repopulation of the cells with mtDNA. The investigation of the pattern of the length heteroplasmy by single cell pick up shows a similar pattern in sister cells despite the evidence of the randomness of mtDNA segregation, providing definitive evidence for the de novo regeneration of the pattern following cell division. Consistent with this conclusion is the observation that similar patterns of length heteroplasmy are found in tissues of single individuals.

Length Variation in HV2 of the Human Mitochondrial DNA Control Region

Hair samples were typed from three individuals who exhibited length heteroplasmy in the homopolymeric cytosine stretches (C-stretch) in hypervariable region 2 (HV2). The study demonstrated that for different hairs within an individual, the HV2 C-stretch region can vary with respect to the number of cytosines and/or proportion of C-stretch length variants. Length heteroplasmy may occur regardless of the prominent length variant present in this region. Differences in the number of cytosines at the C-stretch region, or a variation in the relative amounts of heteroplasmic length variants, cannot be used to support an interpretation of exclusion.

Polymorphism of the mitochondrial DNA control region in Italians.

Mitochondrial DNA sequences of the hypervariable regions HVI and HVII were analysed in 83 Caucasians living in central Italy to expand the database for forensic identification purposes, and 75 different haplotypes resulting from 62 polymorphic positions in HVI and 44 in HVII were observed. The most frequent haplotype (263G, 309.1C, 315.1C) was shared by 7 individuals, 2 haplotypes were shared by 2 individuals, and 72 were unique. The genetic diversity was found to be 0.99 and the random match probability 1.9%. A condition of sequence heteroplasmy was found in only one case at nt 16311, whereas a length heteroplasmy was found in the homopolymeric stretch of cytosines 303-315. Our results indicate that in direct sequencing beyond the poly-cytosine stretch, the overlap is due to length heteroplasmy, whereas the blurred signal occurs when the stretch is composed of more than 10 cytosines.

The 1998–1999 collaborative exercises and proficiency testing program on DNA typing of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG)

A total of 28 laboratories (labs) submitted results for the 1998 collaborative exercise and the proficiency testing program of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG) group. This number increased to 46 labs in 1999. Six bloodstains were submitted, each one with 200 μl soaked in cotton except the sample no. 6 submitted for DNA quantification which had 2 μl. One of the samples was a mixed stain. A paternity testing case and a criminal case in the 1998 trial (GEP’98) and two paternity testing cases in 1999 (GEP’99) were included and the statistical evaluation of the evidence was requested in both cases. In the GEP’99 trial, a theoretical paternity testing case was included. A total of 52 DNA genetic markers were used by the participants in the GEP’98 trial, which increased to 101 in GEP’99. Despite this increasing number of participating labs, results remained quite satisfactory. All the labs used PCR-based DNA polymorphisms with an increasing number of markers, obtaining good results. SLPs were used by a decreasing number of labs but the results indicated a good level of expertise despite the different protocols used. Good results were also obtained for mtDNA despite the difficulties presented by the samples due to the presence of length heteroplasmy in some samples in both trials. The detection of heteroplasmy should, however, be improved. Similar conclusions were reached for both, the paternity and the criminal case by all the labs. Common methodologies for the statistical evaluation of the paternity case were used and the paternity index and the probability of paternity (with an a priori value of 0.5) reported by most of the labs. Also, a great uniformity was found in the evaluation of the criminal case despite the lack of a specific hypothesis in the design of the exercise. Some errors in statistical programs or in calculations were detected in a theoretical paternity case included in the GEP’99 trial for statistical analysis.

MtDNA substitution rate and segregation of heteroplasmy in coding and noncoding regions

The mitochondrial DNA (mtDNA) substitution rate and segregation of heteroplasmy were studied for the non-coding control region (D-loop) and 500 bp of the coding region between nucleotide positions 5550 and 6050, by sequence analysis of blood samples from 194 individuals, representing 33 maternal lineages. No homoplasmic nucleotide substitutions were detected in a total of 292 transmissions. The estimated substitution rate per nucleotide per million years for the control region (micro>0.21, 95% CI 0-0.6) was not significantly different from that for the coding region (micro>0.54, 95% CI 0-1.0). Variation in the length of homopolymeric C streches was observed at three sites in the control region (positions 65, 309 and 16,189), all of which were in the heteroplasmic state. Segregation of heteroplasmic genotypes between generations was observed in several maternal pedigrees. At position 309, a longer poly C tract length was strongly associated with a higher probability for heteroplasmy and rapid segregation between generations. The length heteroplasmy at positions 65 and 16,189 was found at low frequency and was confined to a few families.

Mitochondrial heteroplasmy among maternally related individuals.

The second hypervariable segment of the human mtDNA control region contains a homopolymeric tract of cytidines between nucleotides (nt) 303 and 315, interrupted by a thymidine at position 310, according to the Cambridge reference sequence. By direct sequencing, some individuals show blurred sequence chromatograms in this region which are not caused by a sequencing artefact but by high levels of length heteroplasmy. With respect to this length heteroplasmy ten maternally related individuals and two unrelated probands were examined. The relative proportions of length variants in the homopolymeric tract in selected individuals were determined by cloning and sequencing of multiple independent clones. All ten family members examined were heteroplasmic while the proportions of each genotype varied widely in different individuals. The size of a possible mitochondrial bottleneck during embryonic development of the offspring is discussed with respect to the changes in mitochondrial haplotypes within mother-offspring pairs. Our data are consistent with both slow and rapid segregation of mtDNAs between the generations, which would implicate a tight as well as a wide bottleneck. Therefore, a common bottleneck size in all individuals from this lineage seems to be very unlikely.

Mitochondrial DNA Length Variation and Heteroplasmy in Natural Populations of the European Sea Bass, Dicentrarchus labrax

Mitochondrial DNA length variation in Dicentrarchus labrax is the outcome of the simultaneous variation in the copy number of two tandem repeat arrays located in the D-loop region. The repeated sequences, named R17 and R48, are 17 and 48 bp long, respectively. On the basis of 209 individuals collected in eight Mediterranean localities, length variation and its partitioning between the two repeat arrays have been characterized and quantified by means of frequency distributions of repeat copy number and genetic diversity estimates. The median copy numbers are 4 and 11 for the R17 and R48 repeat arrays, respectively. For both repeat arrays, continuity in step variation and the occurrence of both frequent and rare arrangements was observed. More than 50% of the individuals are heteroplasmic for up to four variants. Within populations, heteroplasmy ranges between 33.3% and 70.0% of the individuals. A large proportion of the total gene diversity (29.1%) occurs within individuals and the greatest proportion (66.6%) is found between individuals within populations, while only 4.3% is due to variation between populations. Although the interpopulation component of the diversity is rather low, the significant differentiation of the two Eastern populations from all the other Western samples suggests the occurrence of a phylogeographic component of the genetic divergence between the Mediterranean populations, which is only recognizable on a large geographic scale.

The generation of transplasmic Drosophila simulans by cytoplasmic injection: effects of segregation and selection on the perpetuation of mitochondrial DNA heteroplasmy.

Experimental transplasmic Drosophila simulans were obtained through cytoplasm microinjection between eggs carrying different mitochondrial genomes. These genomes (siII and siIII) show a 1.5% difference in their sequences. They produced a large number of heteroplasmic flies in their F1 progeny and several flies were still heteroplasmic at the eighth generation. The distribution of frequencies of mitochondrial genotypes in the offspring of heteroplasmic females suggests that the stochastic processes involved in the evolution of experimental heteroplasmy of multiple nucleotide sites are very similar to those previously described for spontaneous length heteroplasmy. In addition, the siII genome has a noticeable advantage over the siIII genome in both directions of injection. This advantage is estimated at 58% per fly generation and 5% per cell generation.