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.
I: Infection, Genetics and Evolution, Bind 86, 104627, 2020.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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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
Y1 - 2020
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
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 -
ID: 252680394