Mitochondrial DNA diversity and maternal origins of Pakistani donkey

Abstract Domestic donkey plays a key role as a draft animal in rural economy of Pakistan where its population is increasing every year. The complete mtDNA control region of forty randomly sampled donkeys was PCR- amplified and sequenced bi-directionally using specific primers. Distinct mtDNA haplotypes obtained in the current study (KY446001KY446011) were subjected to haplotype (h) and nucleotide diversity () measures using DnaS as well as to phylogenetic, Network, and AMOVA analyses. There were a total 27 polymorphic sites present within 11 unique mtDNA haplotypes from the studied 40 animals from different regions. Neighbor-joining network and median-joining network both illustrated the splitting of all these haplotypes into two well-defined Nubian and Somali lineages, confirming African maternal origin of Pakistani domestic donkey. Diversity parameters h (0.967± 0.037) and (0.02917± 0.00307) were found to reveal high levels of genetic diversity in Pakistani donkeys. AMOVA demonstrated only 1% of genetic differences between two mtDNA maternal lineages, pointing to lack of population substructure in Pakistani donkeys as is the case with worldwide domestic donkey population. Pakistani donkeys have African maternal origin and high levels of mtDNA diversity. High genetic diversity may be due to non-selective breeding and heteroplasmy. We herein provide the first report on mtDNA diversity of control region in Pakistani domestic donkey.

Resumo O burro doméstico possui um papel fundamental como animal de tração na economia rural do Paquistão, onde a população desse animal está aumentando a cada ano. A região de controle de mtDNA completa de 40 burros amostrados aleatoriamente foi ampliada por PCR e sequenciada bidirecionalmente por intermédio de primers específicos. Haplótipos distintos de mtDNA obtidos no estudo atual (KY446001 KY446011) foram submetidos a medidas de haplótipo (h) e diversidade de nucleotídeos () por meio de DnaS, bem como análises filogenéticas, de rede e AMOVA. Havia um total de 27 sítios polimórficos presentes em 11 haplótipos de mtDNA exclusivos dos 40 animais estudados de diferentes regiões. A rede de união de vizinhos e a rede de união mediana ilustram a divisão de todos esses haplótipos em duas linhagens núbias e somalis bem definidas, confirmando a origem materna africana do burro doméstico do Paquistão. Os parâmetros de diversidade h (0,967 ± 0,037) e (0,02917 ± 0,00307) revelaram altos níveis de diversidade genética em burros paquistaneses. AMOVA demonstrou apenas 1% de diferenças genéticas entre as duas linhagens maternas de mtDNA, apontando a falta de subestrutura populacional em burros paquistaneses, como é o caso da população mundial de burros domésticos. Os burros paquistaneses têm origem materna africana e altos níveis de diversidade de mtDNA. A alta diversidade genética pode ser por causa da reprodução não seletiva e de heteroplasmia. Aqui, fornecemos o primeiro relatório sobre a diversidade do mtDNA da região de controle em burros domésticos do Paquistão.

Mitochondrial DNA diversity and maternal origins of Pakistani donkey / Diversidade de DNA mitocondrial e origens maternas do burro do Paquistão

Domestic donkey plays a key role as a draft animal in rural economy of Pakistan where its population is increasing every year. The complete mtDNA control region of forty randomly sampled donkeys was PCR- amplified and sequenced bi-directionally using specific primers. Distinct mtDNA haplotypes obtained in the current study (KY446001−KY446011) were subjected to haplotype (h) and nucleotide diversity (π) measures using DnaS as well as to phylogenetic, Network, and AMOVA analyses. There were a total 27 polymorphic sites present within 11 unique mtDNA haplotypes from the studied 40 animals from different regions. Neighbor-joining network and median-joining network both illustrated the splitting of all these haplotypes into two well-defined Nubian and Somali lineages, confirming African maternal origin of Pakistani domestic donkey. Diversity parameters h (0.967± 0.037) and π (0.02917± 0.00307) were found to reveal high levels of genetic diversity in Pakistani donkeys. AMOVA demonstrated only 1% of genetic differences between two mtDNA maternal lineages, pointing to lack of population substructure in Pakistani donkeys as is the case with worldwide domestic donkey population. Pakistani donkeys have African maternal origin and high levels of mtDNA diversity. High genetic diversity may be due to non-selective breeding and heteroplasmy. We herein provide the first report on mtDNA diversity of control region in Pakistani domestic donkey.

O burro doméstico possui um papel fundamental como animal de tração na economia rural do Paquistão, onde a população desse animal está aumentando a cada ano. A região de controle de mtDNA completa de 40 burros amostrados aleatoriamente foi ampliada por PCR e sequenciada bidirecionalmente por intermédio de primers específicos. Haplótipos distintos de mtDNA obtidos no estudo atual (KY446001 − KY446011) foram submetidos a medidas de haplótipo (h) e diversidade de nucleotídeos (π) por meio de DnaS, bem como análises filogenéticas, de rede e AMOVA. Havia um total de 27 sítios polimórficos presentes em 11 haplótipos de mtDNA exclusivos dos 40 animais estudados de diferentes regiões. A rede de união de vizinhos e a rede de união mediana ilustram a divisão de todos esses haplótipos em duas linhagens núbias e somalis bem definidas, confirmando a origem materna africana do burro doméstico do Paquistão. Os parâmetros de diversidade h (0,967 ± 0,037) e π (0,02917 ± 0,00307) revelaram altos níveis de diversidade genética em burros paquistaneses. AMOVA demonstrou apenas 1% de diferenças genéticas entre as duas linhagens maternas de mtDNA, apontando a falta de subestrutura populacional em burros paquistaneses, como é o caso da população mundial de burros domésticos. Os burros paquistaneses têm origem materna africana e altos níveis de diversidade de mtDNA. A alta diversidade genética pode ser por causa da reprodução não seletiva e de heteroplasmia. Aqui, fornecemos o primeiro relatório sobre a diversidade do mtDNA da região de controle em burros domésticos do Paquistão

Microsatellite instability of D310 and D16184 located in mitochondrial D-loop region in acute leukemia / 白血病·淋巴瘤

Objective To study the microsatellite instability (MSD) of D310 and D16184 located in mitochondrial D-loop region in acute leukemia (AL). Methods The HV-1 and HV-2 regions in D-loop region of 100 persons with the untreated and treated acute leukemia was amplificated and screened by PCR-SSCP,then the abnormal samples was amplificated and sequenced directly and compared with revised Cambridge reference sequence (rCRS) and mtDB. The mutation rates of D310 and D16184 was measured by SPSS11.5 statistics software, x2-test. Results The total mutation rate of D310 was found in 49.0 % (49/100) of our patients. Its mutation rates in untreated group and treated group were 32.5 % (13/40) and 60.0 % (36/60)respectively. The mutation rate of treated group is higher than that in untreated group (P ＜ 0.05). The total mutation rate of D16184 was found in 32.0 % (32/100) of our patients. Its mutation rates in untreated group and treated group were 20.0 % (8/40) and 40.0 % (24/60) respectively. The mutation rate of treated group is higher than that in untreated group (P ＜ 0.05). Conclusion There was a high mutation rate with various types of mutations of microsatellite D310 and D16184 located in mitochondrial D-loop region in AL, which led to a doughty MSI. Chemotherapy could cause a more doughty MSI.

Relationship between HVRⅠ mutation of mitochondrial DNA and lung squamous carcinoma / 第三军医大学学报

Objective To investigate the relationship between hypervariable regionsⅠ(HVRⅠ) mutation of mitochondrial DNA (mtDNA) and lung squamous carcinoma and to explore its significance in carcinogenesis. Methods White blood cells and carcinoma tissues were obtained from 13 cases of lung squamous carcinoma patients and mtDNA were extracted by one step method. HVRⅠfragments were amplified by PCR. Mutations were determined by DNA sequencing. Results In 13 lung squamous carcinoma patients, 8 cases showed mutation in HVR Ⅰ, and 30 mutations were found in 25 different nucleotide sites, in which 17 were point mutations and 13 were insertions and deletions, including a 10-bp deletion in one patient. Conclusion These results suggest that the mutation rate of HVRⅠsequence in lung squamous carcinoma tissue was relatively high, and point mutation might play an important role in lung carcinogenesis.

Study on polymorphisms of mitochondrial DNA D-loop region in the Sala population in China / 西安交通大学学报(医学版)

Objective To investigate the mitochondrial DNA sequence polymorphisms in the Sala population from northwest China and to provide basic data for forensic purpose. Methods Genomic DNA was extracted from the whole blood of 100 unrelated individuals of the Sala population. The sequence polymorphic locus was determined by direct sequencing. Results 83 loci were observed in mtDNA np16 091-16 418 region, and 75 haplotypes were confirmed. The genetic diversity was estimated to be 0.991 2, and the random match probability was calculated to be 0.018 9. Conclusion There are some particular polymorphic loci in the Sala population. The results suggest that there are different genetic structures between Chinese and other Asian population in mitochondrial DNA D-loop region; mitochondrial DNA sequence polymorphism np16 091-16 418 can be used as a genetic marker for forensic individual identification.