Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many mammals. These mtDNA related regions (called nuclear DNA sequences of mitochondrial origin or NUMTs) are pseudogenes derived from mtDNA fragments that have been integrated into the nuclear genome. Unintentionally amplified NUMTs can create biases in detecting true heteroplasmy and in phylogenetic analyses based on mtDNA as also demonstrated by the large fraction of mtDNA sequences available in GenBank/EMBL databases that are estimated to contain errors. In this study we obtained a detailed genome map of NUMTs in the Bos taurus genome and compared their distribution between the latest assembled versions, UMD3.1 and ARS-UCD1.2. These two genome versions were aligned with the reference linearized mtDNA sequence using LAST software. The highest proportion of NUMTs had an identity of about 70-80% with the modern mtDNA sequence, suggesting that most integration events occurred about 10 to 30 million of years before present in ancient genomes that evolved in the current Bos taurus species. A total of 422 and 441 NUMTs (for a total of 242,409 and 238,345 bp, which covered the whole mtDNA sequence) were identified in the two versions.These NUMT sequences could be grouped into 171 and 178 NUMT regions that represent putative unique insertional events. Two gff files were produced to support the annotation of the two cattle genome versions. There data will be helpful to plan studies based on mtDNA sequences in cattle and to interpret previous mtDNA sequence results obtained in this species.

A comparative genome landscape of mitochondrial DNA insertions into two cattle nuclear genome versions

Schiavo G.;Bovo S.;Ribani A.;Kazemi H.;Fontanesi L.
2020

Abstract

Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many mammals. These mtDNA related regions (called nuclear DNA sequences of mitochondrial origin or NUMTs) are pseudogenes derived from mtDNA fragments that have been integrated into the nuclear genome. Unintentionally amplified NUMTs can create biases in detecting true heteroplasmy and in phylogenetic analyses based on mtDNA as also demonstrated by the large fraction of mtDNA sequences available in GenBank/EMBL databases that are estimated to contain errors. In this study we obtained a detailed genome map of NUMTs in the Bos taurus genome and compared their distribution between the latest assembled versions, UMD3.1 and ARS-UCD1.2. These two genome versions were aligned with the reference linearized mtDNA sequence using LAST software. The highest proportion of NUMTs had an identity of about 70-80% with the modern mtDNA sequence, suggesting that most integration events occurred about 10 to 30 million of years before present in ancient genomes that evolved in the current Bos taurus species. A total of 422 and 441 NUMTs (for a total of 242,409 and 238,345 bp, which covered the whole mtDNA sequence) were identified in the two versions.These NUMT sequences could be grouped into 171 and 178 NUMT regions that represent putative unique insertional events. Two gff files were produced to support the annotation of the two cattle genome versions. There data will be helpful to plan studies based on mtDNA sequences in cattle and to interpret previous mtDNA sequence results obtained in this species.
Schiavo G.; Bovo S.; Ribani A.; Kazemi H.; Fontanesi L.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11585/742864
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