Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-Occurrences

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

doi:10.1089/cmb.2021.0340

Cited by 6 publications

(9 citation statements)

References 27 publications

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“…9 ). The two proposed AMK ancestors show a perfect chromosome-to-chromosome relationship for chromosomes 1-5, 3-4 and 5-6 between, respectively, the current n = 6 AMK and the n = 7 AMK from Xu et al 36 . Differences are observed between the proposed AMK ancestors for chromosomes 2-(2-6), 4-(3-4) and 6-(5-7) between, respectively, the current n = 6 AMK and the n = 7 AMK from Xu et al, corresponding to different alternative scenarios proposed to explain the transition between the proposed AMKs and the modern genomes (Extended Data Fig.…”

Section: Resultsmentioning

confidence: 89%

“…Recently, Xu et al suggested an n = 7 AMK before and after the ancestral τ-WGD event from the comparison of Acorus ( A. americanus ), Spirodela , Colocasia, Ananas (pineapple) and Elaeis (palm) 36 . We then compared our proposed n = 6 AMK structure with that of the seven chromosomes from Xu et al (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“… The figure illustrates the ancestral monocot karyotypes with all the proposed rearrangements (fusions, fissions) that shaped the modern genomes with the evolution of the number of chromosomes (in green circles) compared to what proposed in Xu et al 36 (in red circles). …”

Section: Extended Datamentioning

confidence: 97%

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The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution

et al. 2022

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Monocots are one of the most diverse groups of flowering plants, and tracing the evolution of their ancestral genome into modern species is essential for understanding their evolutionary success. Here, we report a high-quality assembly of the Acorus tatarinowii genome, a species that diverged early from all the other monocots. Genome-wide comparisons with a range of representative monocots characterized Acorus as a slowly evolved genome with one whole-genome duplication. Our inference of the ancestral monocot karyotypes provides new insights into the chromosomal evolutionary history assigned to modern species and reveals the probable molecular functions and processes related to the early adaptation of monocots to wetland or aquatic habitats (that is, low levels of inorganic phosphate, parallel leaf venation and ephemeral primary roots). The evolution of ancestral gene order in monocots is constrained by gene structural and functional features. The newly obtained Acorus genome offers crucial evidence for delineating the origin and diversification of monocots, including grasses.

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Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 99%

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The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution

et al. 2022

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“…There are various methods for detecting the inflection point of a curve transitioning from one trend to another. The intersection of linear fits to the gap statistic for first few values of k , and for the last few k [10], proves to be unstable and misleading estimate, largely due to the variable concavity of the first trend. The method known as “kneedles” [18], based on finding the point of maximum curvature in the plot, is biased towards low values of k , also because of the template concavity of the initial trend.…”

Section: Methodsmentioning

confidence: 99%

“…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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confidence: 99%

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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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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Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-Occurrences

Cited by 6 publications

References 27 publications

The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution

The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution

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

Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo

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