Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms

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Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms. / Hawash, Mohamed Bayoumi Fahmy; Al-Jubury, Azmi; Sengupta, Mita Eva; Hansen, Tina Vicky Alstrup; Thamsborg, Stig Milan; Nejsum, Peter.

In: Infection, Genetics and Evolution, Vol. 86, 104627, 12.2020.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Hawash, MBF, Al-Jubury, A, Sengupta, ME, Hansen, TVA, Thamsborg, SM & Nejsum, P 2020, 'Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms', Infection, Genetics and Evolution, vol. 86, 104627. https://doi.org/10.1016/j.meegid.2020.104627

APA

Hawash, M. B. F., Al-Jubury, A., Sengupta, M. E., Hansen, T. V. A., Thamsborg, S. M., & Nejsum, P. (2020). Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms. Infection, Genetics and Evolution, 86, [104627]. https://doi.org/10.1016/j.meegid.2020.104627

CBE

Hawash MBF, Al-Jubury A, Sengupta ME, Hansen TVA, Thamsborg SM, Nejsum P. 2020. Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms. Infection, Genetics and Evolution. 86:Article 104627. https://doi.org/10.1016/j.meegid.2020.104627

MLA

Vancouver

Hawash MBF, Al-Jubury A, Sengupta ME, Hansen TVA, Thamsborg SM, Nejsum P. Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms. Infection, Genetics and Evolution. 2020 Dec;86. 104627. https://doi.org/10.1016/j.meegid.2020.104627

Author

Hawash, Mohamed Bayoumi Fahmy ; Al-Jubury, Azmi ; Sengupta, Mita Eva ; Hansen, Tina Vicky Alstrup ; Thamsborg, Stig Milan ; Nejsum, Peter. / Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms. In: Infection, Genetics and Evolution. 2020 ; Vol. 86.

Bibtex

@article{7089fe615f804c50a50261366660d543,
title = "Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms",
abstract = "Trichuris trichiura and T. suis are whipworms of humans and pigs, respectively, but it has recently been suggested that humans may be infected with multiple genotypes or species of Trichuris and cross-infection with Trichuris of pig origin has also been reported. In addition, the species status of Trichuris in non-human primates is unsettled and it is unknown how many whipworm species we share with other primates. Herein, we inferred the phylogeny of Trichuris collected from human, baboon and pig based on nuclear (18S and beta-tubulin) and mitochondrial (cox1) genes and evaluated the use of three PCR linked restriction fragment length polymorphism (PCR-RFLP) to identify worms. We found that all baboon worms clustered with human worms and that all these primate worms are different from T. suis. In general, there was an agreement between the phylogeny established based on the nuclear and mtDNA genes. However, we found evidence for non-targeted cox1 gene amplification for a subset of the human worms and suggest the presence of mitochondrial pseudogenes (numts) of pig cox1 gene in the human Trichuris genome. In conclusion, phylogenetic characterization of human whipworm based on the cox1 gene alone may be problematic without suitable preceded measures to avoid the numts amplification.",
keywords = "Baboon, Humans, Numts, Phylogeny, Pigs, Trichuris, Whipworms",
author = "Hawash, {Mohamed Bayoumi Fahmy} and Azmi Al-Jubury and Sengupta, {Mita Eva} and Hansen, {Tina Vicky Alstrup} and Thamsborg, {Stig Milan} and Peter Nejsum",
year = "2020",
month = dec,
doi = "10.1016/j.meegid.2020.104627",
language = "English",
volume = "86",
journal = "Infection, Genetics and Evolution",
issn = "1567-1348",
publisher = "Elsevier BV",

}

RIS

TY - JOUR

T1 - Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms

AU - Hawash, Mohamed Bayoumi Fahmy

AU - Al-Jubury, Azmi

AU - Sengupta, Mita Eva

AU - Hansen, Tina Vicky Alstrup

AU - Thamsborg, Stig Milan

AU - Nejsum, Peter

PY - 2020/12

Y1 - 2020/12

N2 - Trichuris trichiura and T. suis are whipworms of humans and pigs, respectively, but it has recently been suggested that humans may be infected with multiple genotypes or species of Trichuris and cross-infection with Trichuris of pig origin has also been reported. In addition, the species status of Trichuris in non-human primates is unsettled and it is unknown how many whipworm species we share with other primates. Herein, we inferred the phylogeny of Trichuris collected from human, baboon and pig based on nuclear (18S and beta-tubulin) and mitochondrial (cox1) genes and evaluated the use of three PCR linked restriction fragment length polymorphism (PCR-RFLP) to identify worms. We found that all baboon worms clustered with human worms and that all these primate worms are different from T. suis. In general, there was an agreement between the phylogeny established based on the nuclear and mtDNA genes. However, we found evidence for non-targeted cox1 gene amplification for a subset of the human worms and suggest the presence of mitochondrial pseudogenes (numts) of pig cox1 gene in the human Trichuris genome. In conclusion, phylogenetic characterization of human whipworm based on the cox1 gene alone may be problematic without suitable preceded measures to avoid the numts amplification.

AB - Trichuris trichiura and T. suis are whipworms of humans and pigs, respectively, but it has recently been suggested that humans may be infected with multiple genotypes or species of Trichuris and cross-infection with Trichuris of pig origin has also been reported. In addition, the species status of Trichuris in non-human primates is unsettled and it is unknown how many whipworm species we share with other primates. Herein, we inferred the phylogeny of Trichuris collected from human, baboon and pig based on nuclear (18S and beta-tubulin) and mitochondrial (cox1) genes and evaluated the use of three PCR linked restriction fragment length polymorphism (PCR-RFLP) to identify worms. We found that all baboon worms clustered with human worms and that all these primate worms are different from T. suis. In general, there was an agreement between the phylogeny established based on the nuclear and mtDNA genes. However, we found evidence for non-targeted cox1 gene amplification for a subset of the human worms and suggest the presence of mitochondrial pseudogenes (numts) of pig cox1 gene in the human Trichuris genome. In conclusion, phylogenetic characterization of human whipworm based on the cox1 gene alone may be problematic without suitable preceded measures to avoid the numts amplification.

KW - Baboon

KW - Humans

KW - Numts

KW - Phylogeny

KW - Pigs

KW - Trichuris

KW - Whipworms

UR - http://www.scopus.com/inward/record.url?scp=85096636112&partnerID=8YFLogxK

U2 - 10.1016/j.meegid.2020.104627

DO - 10.1016/j.meegid.2020.104627

M3 - Journal article

C2 - 33181334

AN - SCOPUS:85096636112

VL - 86

JO - Infection, Genetics and Evolution

JF - Infection, Genetics and Evolution

SN - 1567-1348

M1 - 104627

ER -