RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences

Xu, Qiaoji; Jin, Lingling; Zheng, Chunfang; Leebens‐Mack, James H.; Sankoff, David

doi:10.1007/978-3-030-79290-9_9

Cited by 4 publications

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References 18 publications

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“…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].…”

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

Jin

Zheng

et al. 2022

Preprint

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To 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. We show that this is not an artifact of our method by deriving x = 20 for the metazoan ancestor.

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

Jin

Zheng

et al. 2022

Preprint

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Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo

Sankoff

2023

Lecture Notes in Computer Science

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We present a proof of principle for a new kind of stepwise algorithm for unrooted binary gene-order phylogenies. This method incorporates a simple look-ahead inspired by Dollo’s law, while simultaneously reconstructing each ancestor (sometimes referred to as hypothetical taxonomic units “HTU”). We first present a generic version of the algorithm illustrating a necessary consequence of Dollo characters. In a concrete application we use generalized oriented gene adjacencies and maximum weight matching (MWM) to reconstruct fragments of monoploid ancestral genomes as HTUs. This is applied to three flowering plant orders while estimating phylogenies for these orders in the process. We discuss how to improve on the extensive computing times that would be necessary for this method to handle larger trees.

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

Jin

Zheng

et al. 2023

Sci Rep

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To 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.

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RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences

Cited by 4 publications

References 18 publications

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

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

Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo

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

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