Department of Evolutionary Biology, Zoological Institute, University of Copenhagen, Copenhagen, Denmark
Mitochondrial genomes are believed to gradually transfer DNA fragments (numts) into the nuclear chromosomes of eukaryotic cells during evolution (reviewed in Zhang and Hewitt 1996
). This assumption relies on hybridization studies of mitochondrial DNA sequences (mtDNA) (Tsuzuki et al. 1983
), sequencing of numts (e.g., Lopez et al. 1994
; Arctander 1995
; Zischler et al. 1995
; Herrnstadt et al. 1999
), and similarity searches in sequence databases (Blanchard and Schmidt 1996
; Bensasson et al. 2001
). Here we present the first extensive analysis of numts in the human nuclear genome. Through a combination of conventional BLAST alignment (Altschul et al. 1997
) and a DNA block aligning (DBA) algorithm (Jareborg, Birney, and Durbin 1999
), we searched roughly 93.5% of the human genome (http://www.ncbi.nlm.nih.gov/genome/seq/) for numts. This approach revealed three notable findings. First, several numts exceed the size of the longest human numt reported to date (Herrnstadt et al. 1999
). Second, all parts of the mitochondrial DNA are represented in the nuclear genome. Finally, the integration of mtDNAs into the nucleus is a continuous evolutionary process, thereby verifying previous beliefs (Zhang and Hewitt 1996
; Wallace et al. 1997
; Herrnstadt et al. 1999
).
Through the web service provided by NCBI (http://www.ncbi.nlm.nih.gov/), we compared the complete human mitochondrial DNA and the working draft of the human nuclear genome (as of mid-April 2001) using BLAST. This procedure was followed by alignment using the DBA algorithm (Jareborg, Birney, and Durbin 1999
), which found collinear blocks of conserved sequence allowing for indels between blocks. The rationale for this twofold alignment procedure stems from the assumption that two mechanisms may obscure the BLAST alignment. First, the extant mtDNA will have diverged from the ancestral sequence. Second, as the numts are presumably released from selection, larger deletions and insertions may take place.
Hits from the BLAST search (default settings) in the same sense and within the vicinity (46,128 bp) of each other were assessed to potentially stem from a single insertion event. If such a group of hits involved more than 100 identical positions, the genomic sequence covering all the hits and their intervening sequences were retrieved. This sequence was aligned to the corresponding mtDNA sequence using the DBA algorithm. The sequences were considered a result of a single insertion event if the DBA algorithm was able to align more than 80% of the mtDNA sequence in a collinear way.
Following the above criteria, we found 296 numts ranging between 106 and 14,654 bp in size (table
1
). Fifteen of these were found to be longer than 5,842 bp, previously reported by Herrnstadt et al. (1999)
as the length of the longest human numt.
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To estimate the time of insertion of the numts, we collected all numt-mitochondria alignments longer than 2,000 bp (i.e., either complete numts, if they were completely alignable, or subsets of numts of which DBA blocks exceeded 2,000 bp) and aligned these with the corresponding mtDNA sequences from a variety of mammals. The phylogenetic analysis supported the general conviction that numt DNAs are continually integrated into the nuclear genome as a result of several independent evolutionary events (fig. 2 ).
|
This study presents the first extensive large-scale survey of human numts based on the human genome projectan initial step on the way to a complete catalog of human numts.
As previously stated (Perna and Kocher 1996
), human numts may serve as both obstacles and tools in understanding the evolution of the human mitochondria. For example, the large number of long numts can confound studies on mitochondrial heteroplasmy as well as phylogenetic and population studies using mtDNA markers. For these studies, decisive knowledge of human numts may be crucial in detecting erroneous results due to false amplification of nuclear homologs.
On the contrary, since numts may be regarded as "molecular fossils" of mtDNA (Zischler, Geisert, and Castresana 1998
), they may provide fruitful insight into the evolution of modern human mitochondria and help to uncover the evolutionary basis of contemporary human diseases related to the genetics of the mitochondria.
Supplementary Materials
A table of all 296 human numts is provided on the Molecular Biology and Evolution web site.
Acknowledgements
We thank Douda Bensasson, Kasi B. Desfor, Sylvia Mathiasen, and Seirian Sumner for help and discussions. A.J.H. and E.W. were supported by the VELUX foundation of 1981, Denmark. A.J.H. and E.W. contributed equally to this work and should be regarded as joint authors.
Footnotes
Pekka Pamilo, Reviewing Editor
1 Keywords: mitochondrial DNA
nuclear insertions
human genome
2 Address for correspondence and reprints: Tobias Mourier, Department of Evolutionary Biology, Zoological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. tmourier{at}zi.ku.dk
.
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