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Method: Contamination detection in sequencing studies using the mitochondrial phylogeny
- Hansi Weissensteiner,
- Lukas Forer,
- Liane Fendt,
- Azin Kheirkhah,
- Antonio Salas,
- Florian Kronenberg,
- and Sebastian Schoenherr
Genome Res. February 2021 31: 309-316; Published in Advance January 15, 2021, doi:10.1101/gr.256545.119
...the mtDNA and identify the mitochondrial copy number within a mixture as a critical component for the overall accuracy. The haplocheck tool is available both as a command-line tool and as a cloud web service producing interactive reports that facilitates the navigation through the phylogeny...
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Research: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution
- Amit Blumberg,
- Edward J. Rice,
- Anshul Kundaje,
- Charles G. Danko,
- and Dan Mishmar
Genome Res. March 2017 27: 362-373; Published in Advance January 3, 2017, doi:10.1101/gr.209924.116
...the possibility that a subset of the identified mtDNA reads reflect contamination by mtDNA-like pseudogenes that have been transferred to the cell nucleus during the course of evolution (NUMTs) (Hazkani-Covo et al. 2003; Mishmar et al. 2004). To control for this possibility, we focused our analyses on regions...
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Research: A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization
- Amit Blumberg,
- Charles G. Danko,
- Anshul Kundaje,
- and Dan Mishmar
Genome Res. August 2018 28: 1158-1168; Published in Advance July 12, 2018, doi:10.1101/gr.230409.117
...was not statistically significant (P = 0.32). Hence, analysis of mtDNA third codon silent SNPs that have accumulated during the course of human evolution did not reveal a significant difference between mt-DGFs and control simulations.Since evolutionary conservation reflects functional importance, we assessed...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...putative Y-linked duplicates with PCR, confirming male-specificity for 16 of 17 of tested duplications (Supplemental Tables S14, S15). We found that the Y Chromosomes of sim-complex species share an insertion derived from mtDNA that is absent in D. melanogaster.DiscussionHere we uncover novel structural...
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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...mitochondrial DNA (mtDNA) of the Puerto Rican population (Davies and Bermingham 2002). This implies that the indel diversity as estimated from the pseudohaplotypes of the single Puerto Rican H. charithonia individual in this study may be a general underestimate of indel proportions in other species...
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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
..., 30.7 Mb; base-pair accuracy QV score, 52; and BUSCO [Simão et al. 2015], 99.6%) (Supplemental Tables S2, S3). The vast majority of three telocentric autosomes (Chr 2, Chr 3, and Chr 4) and the dot chromosome, together with the complete circular mitochondrial DNA (mtDNA) are each assembled...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...-bound organellar genetic systems of eukaryotic cells (Ellis 1982), provides evidence for DNA transfer between organelles and the nucleus. Such transfers of mitochondrial DNA (mtDNA) or plastid DNA (ptDNA) to the nucleus result in formation of nuclear mitochondrial DNA (NUMT) and nuclear plastid DNA (NUPT), which...
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Resource: A calibrated human Y-chromosomal phylogeny based on resequencing
- Wei Wei,
- Qasim Ayub,
- Yuan Chen,
- Shane McCarthy,
- Yiping Hou,
- Ignazio Carbone,
- Yali Xue,
- and Chris Tyler-Smith
Genome Res. February 2013 23: 388-395; Published in Advance October 4, 2012, doi:10.1101/gr.143198.112
...base reads on self-assembling DNA nanoarrays. Science 327: 78–81. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29: 1969– 1973. Forster P, Harding R, Torroni A, Bandelt HJ. 1996. Origin and evolution of Native American mtDNA...
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Letter: mtDNA mutation pattern in tumors and human evolution are shaped by similar selective constraints
- Ilia Zhidkov,
- Erez A. Livneh,
- Eitan Rubin,
- and Dan Mishmar
Genome Res. April 2009 19: 576-580; Published in Advance February 10, 2009, doi:10.1101/gr.086462.108
...) phylogenetic tree using the Pan troglodytes (NC_001643) mtDNA sequence as an outgroup, utilizing the distance matrix program (PHYLIP package; http://evolution.genetics.washington.edu/phylip.html ). Manual inspection of the resulting tree showed no significant deviations from accepted human mtDNA phylogeny...
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Method: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
- Igor Rodrigues Costa,
- Francisco Prosdocimi,
- and W. Bryan Jennings
Genome Res. September 2016 26: 1257-1267; Published in Advance July 19, 2016, doi:10.1101/gr.203950.115
...In silico phylogenomics using complete genomes: a case study on the evolution of hominoids Igor Rodrigues Costa 1 , 3 , Francisco Prosdocimi 1 , 3 and W. Bryan Jennings 2 1Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica...

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