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

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.

From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes

“…To group contigs into clusters reflecting ancient chromosomes, we match each contig against the chromosomes of the extent genomes, and count the number of times any two contigs match the same chromosome, taking account of their ordering, possibly twice or more within a single genome. The resulting co-occurrence matrix, smoothed by a correlation analysis of pairs of contigs [8], is then submitted to a complete-link clustering analysis to distinguish the contigs, and hence the gene content, appropriate to each hypothetical ancestral chromosome. Once contig content of each chromosome is posited, the data on relative order of each pair of contigs on a chromosome is submitted to a Linear template Ordering Problem routine to locate them along the chromosome.…”

“…The focus on monoploidy in our method, however, permits a single-step reconstruction of ancestral chromosomal fragments, contigs , without any recourse to information external to the given set of phylogenetically-related genomes. The maximum weight matching (mwm) algorithm embedded in the Raccroche pipeline [7,8] assures a robust monoploid reconstruction; each ancestor contains at most one representative of each gene family, organized into a number x of ancestral chromosomes, the “basic number”, and ordered along the chromosomes in a way most consistent with the gene order in their extant descendants. Somewhat unexpectedly, as illustrated in Figure 1, the method produces more clear-cut inferences on clades of more remotely related species, such as six genomes each from a different monocot order [8], or six eudicot species from different orders [9], than sampling of lineages within orders or families, where the results are degraded by high levels of noise [10].…”

“…The maximum weight matching (mwm) algorithm embedded in the Raccroche pipeline [7,8] assures a robust monoploid reconstruction; each ancestor contains at most one representative of each gene family, organized into a number x of ancestral chromosomes, the "basic number", and ordered along the chromosomes in a way most consistent with the gene order in their extant descendants. Somewhat unexpectedly, as illustrated in Figure 1, the method produces more clear-cut inferences on clades of more remotely related species, such as six genomes each from a different monocot order [8], or six eudicot species from different orders [9], than sampling of lineages within orders or families, where the results are degraded by high levels of noise [10]. In this paper, we trace the origin of this noise to a severe bias that arises when analyzing a clade of closely related genomes.…”

From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes

“…Somewhat unexpectedly, as illustrated in Fig. 1, the method produces more clear-cut inferences on clades of more remotely related species, such as six genomes each from a different monocot order 8 , or six eudicot species from different orders 9 , than sampling of lineages within orders (here Fagales) or families, where the results are degraded by high levels of noise 10 .…”

“…In contrast, the focus on monoploidy in our method permits a single-step reconstruction of ancestral chromosomal fragments, contigs, without any recourse to information external to the given set of phylogenetically-related annotated genome sequences. The maximum weight matching (mwm) algorithm embedded in the raccroche pipeline 7,8 assures a robust monoploid reconstruction; each ancestor contains at most one representative of www.nature.com/scientificreports/ each gene family. These gene family representatives are organized into a number x of ancestral chromosomes, the "basic number", and ordered along the chromosomes in a way most consistent with the gene order in their extant descendants.…”