Reconstructing Ancient DNA Sequences in Silico

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Reconstructing Ancient DNA Sequences in Silico

Jian Ma, University of California, Santa Cruz, California, USA

Published online: March 2008

DOI: 10.1002/9780470015902.a0020736

Full Article on Wiley Online Library

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The increasing number of mammalian genome sequences becoming available provides scientists with dramatic opportunities to computationally reconstruct ancestral mammalian genomic sequences by comparing the genomes of living descendants. In this article, we review computational genome reconstruction methods in different scales, from base-level reconstruction to chromosomal rearrangement reconstruction.

Keywords: genome reconstruction; substitution; insertion and deletion; rearrangement

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Web Links
	ePath http://genome.ucsc.edu/ UCSC genome browser, including sequences and alignments.
	ePath http://nbcr.sdsc.edu/GRIMM/mgr.cgi MGR, multiple genome rearrangements analysis.
	ePath http://www.bx.psu.edu/miller_lab/ CARs, partitioning genomes into synteny blocks and reconstructs ancestral order of them; TBA, multiple sequence alignment program.
	ePath http://evolutionhighway.ncsa.uiuc.edu/ Evolutionary Highway, genome structure visualization for multiple species.

Article Title:	Reconstructing Ancient DNA Sequences in Silico
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	Figure 1. The position of boreoeutherian common ancestor.
	Figure 2. A reconstructed region based on seven descendant species using armadillo and elephant as outgroups. The reconstructed ancestral sequences, including boreoeutherian, euarchontoglires, primate ancestor, ape ancestor, are shown above the multiple alignment. Position (1) is an ape-specific deletion. Position (2) corresponds to two deletion events in primate and rodent, respectively. Position (3) is a substitution happened before euarchontoglires ancestor.
	Figure 3. A microinversion happened on the branch leading from the boreoeutherian common ancestor to the euarchontoglires common ancestor (the primate–rodent ancestor). The corresponding human region is hg18.chr13:57 380 591–57 383 765. This snapshot from University of California at Santa Cruz (UCSC) genome browser clearly shows the relative orientations from which the ancestral orientation can be inferred by parsimony.

Reconstructing Ancient DNA Sequences in Silico

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