Author:
Xu Qiaoji,Jin Lingling,Zheng Chunfang,Zhang Xiaomeng,Leebens-Mack James,Sankoff David
Abstract
AbstractTo reconstruct the ancestral genome of a set of phylogenetically related descendant species, we use the raccroche pipeline for organizing a large number of generalized gene adjacencies into contigs and then into chromosomes. Separate reconstructions are carried out for each ancestral node of the phylogenetic tree for focal taxa. The ancestral reconstructions are monoploids; they each contain at most one member of each gene family constructed from descendants, ordered along the chromosomes. We design and implement a new computational technique for solving the problem of estimating the ancestral monoploid number of chromosomes x. This involves a “g-mer” analysis to resolve a bias due long contigs, and gap statistics to estimate x. We find that the monoploid number of all the rosid and asterid orders is $$x=9$$
x
=
9
. We show that this is not an artifact of our method by deriving $$x\approx 20$$
x
≈
20
for the metazoan ancestor.
Funder
Natural Sciences and Engineering Research Council of Canada
Publisher
Springer Science and Business Media LLC
Cited by
3 articles.
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