Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order

Qiaoji Xu,James H Leebens-Mack,Lingling Jin,David Sankoff

doi:10.3390/a14060160

Qiaoji Xu, James H Leebens-Mack + Show 2 more

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https://doi.org/10.3390/a14060160

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Abstract

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

Highlights

The reconstruction of ancestral gene orders proceeds through the identification of local commonalities—synteny blocks, “CARs”, contigs, microsyntenies—in the genomes of a number of extant descendant species through various merger, assembly and concatenation procedures to produce a set of chromosome fragments representing the ancestral genome
We have previously proposed an approach, RACCROCHE, to reconstruction that postpones the selection of gene adjacencies for reconstructing small ancestral segments [5]
To validate the accuracy of the reconstruction, this paper describes a simulation of the evolutionary processes giving rise to the gene content and order of a set of extant genomes

Summary

Introduction

The reconstruction of ancestral gene orders proceeds through the identification of local commonalities—synteny blocks, “CARs” (contiguous ancestral regions), contigs, microsyntenies—in the genomes of a number of extant descendant species through various merger, assembly and concatenation procedures to produce a set of chromosome fragments representing the ancestral genome. We have previously proposed an approach, RACCROCHE, to reconstruction that postpones the selection of gene adjacencies for reconstructing small ancestral segments [5]. Instead, it accumulates a very large number of syntenically validated candidate adjacencies to produce long ancestral contigs through maximum weight matching. It accumulates a very large number of syntenically validated candidate adjacencies to produce long ancestral contigs through maximum weight matching It does not construct chromosomes by successively piecing together contigs into larger segments, but instead counts all contig co-occurrences on the extant genomes and clusters these so that chromosomal assemblies of ancestral contigs can be recognized at each ancestral node of the phylogeny. We improve and automate the process of chromosome recovery through a more meaningful measure than raw contig co-occurrence, leading to the assignment of almost all contigs to clusters

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