Evidence of hybridization, mitochondrial introgression and biparental inheritance of the kDNA minicircles in Trypanosoma cruzi I

AbstractBackgroundGenetic Exchange in Trypanosoma cruzi is controversial not only in relation to its frequency but also in relation to its mechanism. A mechanism of parasexuality has been proposed based on laboratory hybrids, but population genomics strongly suggests meiosis. In addition, mitochondrial introgression has been reported several times in natural isolates although its mechanism is not clear. Moreover, hybrid DTUs (TcV and TcVI) have inherited at least part of the kinetoplastic DNA (kDNA = mitochondrial DNA) from both parents.Methodology/Principal findingsIn order to address such topics, we sequenced and analyzed fourteen nuclear DNA fragments and three kDNA maxicircle genes in three TcI stocks which are natural clones potentially involved in events of genetic exchange. We also deep-sequenced (a total of 6,146,686 paired-end reads) the hypervariable region of kDNA minicircles (mHVR) in such three strains. In addition, we analyzed the DNA content by flow cytometry to address cell ploidy. We observed that most polymorphic sites in nuclear loci showed a hybrid pattern in one cloned strain and the other two cloned strains were compatible as parental strains (or nearly related to the true parents). The three clones have almost the same ploidy and the DNA content was similar to the reference strain Sylvio (an almost diploid strain). Despite maxicircle genes evolve faster than nuclear housekeeping ones, we did not detect polymorphism in the sequence of three maxicircle genes showing mito-nuclear discordance. In addition, the hybrid stock shared 66% of its mHVR clusters with one putative parental and 47% with the another one. In contrast, the putative parental stocks shared less than 30% of the mHVR clusters among them.Conclusions/significanceThe results suggest a reductive division, a natural hybridization, biparental inheritance of the minicircles in the hybrid and maxicircle introgression. The models including such phenomena and that would explain the relationships between these three clones are discussed.Author summaryChagas disease, an important public health problem in Latin America, is caused by the parasite Trypanosoma cruzi. Despite it is a widely studied parasite, several questions about the biology of genetic exchange remain. Meiosis has not been yet observed in laboratory, although inferred from population genomic studies. In addition, previous results suggest that the mitochondrial DNA (called kDNA) may be inherited from both parents in hybrids. Here, we analyzed a hybrid strain and the potential parents to address about the mechanisms of genetic exchange at nuclear and mitochondrial level. We observed that the hybrid strain has heterozygous patterns and DNA content compatible with an event of meiosis. In addition, we observed that the evolutionary histories of nuclear DNA and maxicircles (a part of the kDNA) were discordant and the three strains share identical DNA sequences. Mitochondrial introgression of maxicircle DNA from one genotype to another may explain this observation. In addition, we detected that the hybrid strain shared minicircles (another part of the kDNA) with both parental strains. Our results suggest that hybridization implied meiosis and biparental inheritance of the kDNA. Further research is required to address such phenomena in detail.

Download Full-text

Range-wide genetic homogeneity in the California sea mussel (Mytilus californianus): a comparison of allozymes, nuclear DNA markers, and mitochondrial DNA sequences

Molecular Ecology ◽

10.1111/j.1365-294x.2008.03905.x ◽

2008 ◽

Vol 17 (19) ◽

pp. 4222-4232 ◽

Cited By ~ 48

Author(s):

JASON A. ADDISON ◽

BRIAN S. ORT ◽

KATHRYN A. MESA ◽

GRANT H. POGSON

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Dna Markers ◽

Nuclear Dna ◽

Genetic Homogeneity ◽

Mytilus Californianus ◽

Nuclear Dna Markers ◽

California Sea Mussel

Download Full-text

Nuclear DNA amount in pure species and hybrid willows (Salix): a flow cytometric investigation

Canadian Journal of Botany ◽

10.1139/b97-153 ◽

1998 ◽

Vol 76 (1) ◽

pp. 157-165 ◽

Cited By ~ 6

Author(s):

Jérôme Thibault

Keyword(s):

Flow Cytometry ◽

Ploidy Level ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Natural Hybridization ◽

Ploidy Levels ◽

Key Words Flow Cytometry ◽

Dna Values ◽

Dna Amounts

Flow cytometry (FCM) has been used to estimate the nuclear DNA content of 11 Salix species and 5 hybrids. One hundred and sixty nine individuals were studied including 159 individuals from a sequence of 32 communities along a stretch of river in France and 10 individuals from French and English collections for comparison. Isolated nuclei were stained with propidium iodide. FCM was a significantly more practical and rapid technique than that of establishing the karyotype to survey many samples of Salix for variation in ploidy. The 2C DNA amounts for diploid species ranged from 0.76 to 0.98 pg, and tetraploid values ranged from 1.62 to 1.80 pg. The DNA values were consistent with the known ploidy levels. With the exception of a doubtful Salix xquercifolia, ploidy levels and DNA amounts of hybrids were intermediate compared with those of their parents. Intraspecific variation of nuclear DNA values including instrumental variation was low (i.e., 6-11% at the same ploidy level). FCM appeared to be an accurate tool for determination of Salix triploid hybrids. However, it remains limited concerning hybrids from crosses between species of the same ploidy level. Results suggest that natural hybridization might not be frequent in the communities studied, although they have been subject to disturbance. Previous overestimates of hybridization frequency in willows were probably due to misinterpretation of the effects of the environment on Salix spp. morphology; however, the extent and mechanisms of introgression in the genus remain to be further investigated. Key words: flow cytometry, Salix, hybridization, nuclear DNA content, riparian vegetation, disturbance.

Download Full-text

B-chromosome and C-band heterochromatin variation in Arizona maize populations adapted to different altitudes

Genome ◽

10.1139/g90-097 ◽

1990 ◽

Vol 33 (5) ◽

pp. 659-662 ◽

Cited By ~ 22

Author(s):

H. L. Porter ◽

A. Lane Rayburn

Keyword(s):

Dna Sequences ◽

Dna Content ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

B Chromosome ◽

Chromosomal Dna ◽

Dna Amount ◽

Maize Populations ◽

Dna Content Variation ◽

Band Number

The B-chromosome and C-band numbers were determined in 12 Arizona Indian maize populations. These populations were originally collected from altitudes ranging from 100 to 5300 ft (1 ft = 0.3048 m). In addition, the total nuclear DNA amounts of these populations have been observed to vary by as much as 20%. The number of B-chromosomes was not significantly correlated with altitude, C-band number, or nuclear DNA amount. C-band number was significantly correlated with both altitude and genome size. It does not appear that the amount of C-band variation can account for the large nuclear DNA variation observed in these accessions. Additional A-chromosomal DNA sequences may be involved in the nuclear DNA content variation that exists among these accessions.Key words: heterochromatin, DNA content, evolution, repeated DNA.

Download Full-text

Increase of Cell-Free Nuclear and Mitochondrial DNA Content in the Urine of Rats after X-ray Irradiation or Bleomycin Administration

Medical Radiology and radiation safety ◽

10.12737/1024-6177-2019-64-5-5-8 ◽

2019 ◽

Vol 64 (5) ◽

pp. 5-8

Author(s):

Г. Минкабирова ◽

G. Minkabirova ◽

С. Абдуллаев ◽

S. Abdullaev

Keyword(s):

Mitochondrial Dna ◽

Linear Dependence ◽

Dna Content ◽

Nuclear Dna ◽

The Body ◽

Male Rats ◽

Cytostatic Drug ◽

Rat Urine ◽

X Ray ◽

Potential Biomarker

Purpose: To study the content of cell-free mitochondrial DNA (cf-mtDNA) and cell-free nuclear DNA (cf-nDNA) in urine of rats exposed to ionizing radiation, and after injection of a cytostatic drug bleomycin. Material and methods: Wistar male rats aged 3 months were used in the experiments. Rats were irradiated at a doses of 3, 5, and 8 Gy. Bleomycin was administered intraperitoneally in concentrations of 3, 7, and 10 mg/kg. The DNA content was measured by real-time PCR. Results: The results showed an increase in the level of the number of cf-nDNA and cf-mtDNA fragments in urine of irradiated rats. It was shown that the content of cf-nDNA and cf-mtDNA has a linear dependence on the X-ray dose. Thus, the maximum number of mtDNA and nDNA copies was recorded for 12–24th hours after irradiation. The number of PCR amplification products of cf-mtDNA is 2–3 times higher than those of cf-nDNA. Data analysis of the content of cf-nDNA and cf-mtDNA in rat urine after introduction of bleomycin also showed elevated levels compared with control animals. It was shown that the content of cf-nDNA and cf-mtDNA has a linear dependence on the dose of the chemotherapeutic drug. Conclusion: Thus, it has been shown that it is possible to overcome the transrenal (renal) barrier in animals with cf-mtDNA and cf-nDNA and pass them into the urine after X-ray irradiation, as well as after the administration of bleomycin. The dose dependence of the identified effects was found. The increased content of cell-free DNA in the urine can be considered as a potential biomarker for assessing the level of genotoxic load during radiation damage to the body, as well as when exposed to other genotoxic agents.

Download Full-text

Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions

Molecular Biology of the Cell ◽

10.1091/mbc.e15-05-0260 ◽

2016 ◽

Vol 27 (2) ◽

pp. 223-235 ◽

Cited By ~ 62

Author(s):

Satish Kumar Tadi ◽

Robin Sebastian ◽

Sumedha Dahal ◽

Ravi K. Babu ◽

Bibha Choudhary ◽

...

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Nuclear Dna ◽

Ex Vivo ◽

Strand Break ◽

Mitochondrial Disorders ◽

Dna Lesions ◽

End Joining ◽

Dsb Repair

Mitochondrial DNA (mtDNA) deletions are associated with various mitochondrial disorders. The deletions identified in humans are flanked by short, directly repeated mitochondrial DNA sequences; however, the mechanism of such DNA rearrangements has yet to be elucidated. In contrast to nuclear DNA (nDNA), mtDNA is more exposed to oxidative damage, which may result in double-strand breaks (DSBs). Although DSB repair in nDNA is well studied, repair mechanisms in mitochondria are not characterized. In the present study, we investigate the mechanisms of DSB repair in mitochondria using in vitro and ex vivo assays. Whereas classical NHEJ (C-NHEJ) is undetectable, microhomology-mediated alternative NHEJ efficiently repairs DSBs in mitochondria. Of interest, robust microhomology-mediated end joining (MMEJ) was observed with DNA substrates bearing 5-, 8-, 10-, 13-, 16-, 19-, and 22-nt microhomology. Furthermore, MMEJ efficiency was enhanced with an increase in the length of homology. Western blotting, immunoprecipitation, and protein inhibition assays suggest the involvement of CtIP, FEN1, MRE11, and PARP1 in mitochondrial MMEJ. Knockdown studies, in conjunction with other experiments, demonstrated that DNA ligase III, but not ligase IV or ligase I, is primarily responsible for the final sealing of DSBs during mitochondrial MMEJ. These observations highlight the central role of MMEJ in maintenance of mammalian mitochondrial genome integrity and is likely relevant for deletions observed in many human mitochondrial disorders.

Download Full-text

Phylogeny of Triatomine Vectors of Trypanosoma cruzi Suggested by Mitochondrial DNA Sequences

Genetica ◽

10.1023/b:gene.0000039842.82574.02 ◽

2004 ◽

Vol 121 (3) ◽

pp. 229-240 ◽

Cited By ~ 31

Author(s):

Andrés C. Sainz ◽

Laura V. Mauro ◽

Etsuko N. Moriyama ◽

Beatriz A. García

Keyword(s):

Mitochondrial Dna ◽

Trypanosoma Cruzi ◽

Dna Sequences

Download Full-text

Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)

ZooKeys ◽

10.3897/zookeys.763.21252 ◽

2018 ◽

Vol 763 ◽

pp. 1-111 ◽

Cited By ~ 6

Author(s):

Tricia C. Goulding ◽

Munawar Khalil ◽

Shau Hwai Tan ◽

Benoît Dayrat

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Dna Analysis ◽

Nuclear Dna ◽

Comparative Anatomy ◽

Morphological Characters ◽

Integrative Taxonomy ◽

The Philippines ◽

Coral Triangle ◽

Yellow Orange

A new genus of onchidiid slugs,WallaconchisGoulding & Dayrat,gen. n., is described, including ten species. Five species were previously described but known only from the type material:Wallaconchisater(Lesson, 1830),W.graniferum(Semper, 1880),W.nangkauriense(Plate, 1893),W.buetschlii(Stantschinsky, 1907), andW.gracile(Stantschinsky, 1907), all of which were originally classified inOnchidiumBuchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new:WallaconchisachleitneriGoulding,sp. n.,W.comendadoriGoulding & Dayrat,sp. n.,W.melanesiensisGoulding & Dayrat,sp. n.,W.sinanuiGoulding & Dayrat,sp. n., andW.uncinusGoulding & Dayrat,sp. n.Nine of the tenWallaconchisspecies are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia).Wallaconchisis distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify allWallaconchisspecies. The copulatory organs ofWallaconchisspecies are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed,nomina dubiaare discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.

Download Full-text