Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

Froenicke, Lutz; Caldés, Montserrat Garcia; Graphodatsky, Alexander S.; Müller, Stefan; Lyons, Leslie A.; Robinson, Terence J.; Volleth, Marianne; Yang, Fengtang; Wienberg, Johannes

doi:10.1101/gr.3955206

Cited by 73 publications

(81 citation statements)

References 28 publications

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“…However, bioinformatic analyses of genome sequences often deviate from more traditional cytogenetic views of chromosomal evolution (Bourque et al 2006;Froenicke et al 2006). Here, a combination of bioinformatic and cytological approaches is used to determine the correct rearrangement phylogeny of D. buzzatii.…”

Section: Discussionmentioning

confidence: 99%

Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila

González¹,

Casals²,

Ruíz

2007

Genetics

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A combination of cytogenetic and bioinformatic procedures was used to test the chromosomal phylogeny relating Drosophila buzzatii with D. repleta. Chromosomes X and 2, harboring most of the inversions fixed between these two species, were analyzed. First, chromosomal segments conserved during the divergence of the two species were identified by comparative in situ hybridization to the D. repleta chromosomes of 180 BAC clones from a BAC-based physical map of the D. buzzatii genome. These conserved segments were precisely delimited with the aid of clones containing inversion breakpoints. Then GRIMM software was used to estimate the minimum number of rearrangements necessary to transform one genome into the other and identify all possible rearrangement scenarios. Finally, the most plausible inversion trajectory was tested by hybridizing 12 breakpoint-bearing BAC clones to the chromosomes of seven other species in the repleta group. The results show that chromosomes X and 2 of D. buzzatii and D. repleta differ by 12 paracentric inversions. Nine of them are fixed in chromosome 2 and entail two breakpoint reuses. Our results also show that the cytological relationship between D. repleta and D. mercatorum is closer than that between D. repleta and D. peninsularis, and we propose that the phylogenetic relationships in this lineage of the repleta group be reconsidered. We also estimated the rate of rearrangement between D. repleta and D. buzzatii and conclude that rates within the genus Drosophila vary substantially between lineages, even within a single species group.

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Section: Discussionmentioning

confidence: 99%

Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila

González¹,

Casals²,

Ruíz

2007

Genetics

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“…Recently, Froenicke et al (2006) expressed a concern about some differences between the rearrangement-based and cytogenetics-based approaches to ancestral genome reconstruction. The problem is that some important insights developed by the cytogenetics community still did not find their way into the genome rearrangement tools like MGR, GRAPPA, inferCARs, and EMRAE.…”

Section: Discussionmentioning

confidence: 99%

“…However, even with a small increase in the number of the genomes from three to four (as in Bourque et al 2004Bourque et al , 2005 to six to seven (as in Murphy et al 2005;Ma et al 2006), there are very few discrepancies between the cytogeneticsbased and the genomics-based approaches (Rocchi et al 2006). Despite a recent debate (Bourque et al 2006;Froenicke et al 2006), the cytogenetics-based and genomics-based approaches are converging and benefiting from the higher resolution of the genomics-based approaches. However, the key condition for such convergence is the availability of algorithms that improve on the existing heuristics for separating between strong and weak associations.…”

Section: Breakpoint Graphs and Ancestral Reconstructionsmentioning

confidence: 99%

“…Since genomic distances lead to more accurate ancestral reconstructions (Moret et al 2002;Tang and Moret 2003), GRAPPA has been modified for genomic distances as well. While MGR has been used in several phylogenomic studies Murphy et al 2005;Bulazel et al 2007;Pontius et al 2007;Xia et al 2007;Cardone et al 2008;Deuve et al 2008), both MGR and GRAPPA have limited ability to distinguish reliable from unreliable rearrangements and to address the ''weak associations'' problem in ancestral reconstructions (Bourque et al 2004(Bourque et al , 2006Froenicke et al 2006).…”

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Breakpoint graphs and ancestral genome reconstructions

Alekseyev¹,

Pevzner²

2009

Genome Res.

122

130

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Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.

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“…These methods address the problem at a much higher resolution, although with much less available genomes. The first results have been obtained on mammalian genomes [4,20,16], and several reviews have been published [9,19], analyzing the divergences with earlier cytogenetics results [10,5,22]. These methods can be divided into model-based methods, that compute complete evolutionary scenarios [4,20] and model-free approaches that do not consider a precise rearrangement model, which are used by cytogeneticians and currently receive a lot of attention from computational biology (see [16,6] and references there).…”

Section: Introductionmentioning

confidence: 99%

Prediction of Contiguous Regions in the Amniote Ancestral Genome

Ouangraoua

Boyer

McPherson

et al. 2009

Bioinformatics Research and Applications

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Abstract. We investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes, based on the currently sequenced and assembled amniote genomes as ingroups and three teleost fish genomes as outgroups. We combine a methodological framework using conserved syntenies computed from whole genome alignments of amniote species together with double conserved syntenies (DCS) using gene families from amniote and fish genomes, to take into account the whole genome duplication that occurred in the teleost lineage. From these comparisons, ancestral genome segments are computed using techniques inspired by physical mapping. Due to the difficulty caused by the whole genome duplication and the large evolutionary distance to the closest assembled outgroup, very few methods have been published with a reconstruction of the amniote ancestral genome. This one is the first which is founded on a simple and formal methodological framework, whose good stability is shown and whose CARs cover large regions of the human and chicken genomes.

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Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

Cited by 73 publications

References 28 publications

Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila

Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila

Breakpoint graphs and ancestral genome reconstructions

Prediction of Contiguous Regions in the Amniote Ancestral Genome

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