Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.
| Autor: | Anselmetti Y; ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.; Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France., Duchemin W; Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France.; INRIA Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France., Tannier E; Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France.; INRIA Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France., Chauve C; Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, V5A1S6, BC, Canada., Bérard S; ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France. Severine.Berard@umontpellier.fr. |
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| Jazyk: | angličtina |
| Zdroj: | BMC genomics [BMC Genomics] 2018 May 09; Vol. 19 (Suppl 2), pp. 96. Date of Electronic Publication: 2018 May 09. |
| DOI: | 10.1186/s12864-018-4466-7 |
| Abstrakt: | Background: Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. Results: We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADSEQ provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADSEQ to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. Conclusions: We demonstrate the method's ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression. |
| Databáze: | MEDLINE |
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