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Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
2018
Nucleic Acids Research
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Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life. ...
(GO) annotations, and a 'proxy gene' for each ancestral gene, defined as the least-diverged descendant of the ancestral gene in a given extant genome. ...
CONCLUSIONS We have created a new resource for exploring reconstructed Ancestral Genomes across the tree of life. ...
doi:10.1093/nar/gky1009
pmid:30371900
pmcid:PMC6323951
fatcat:7fnve3dahjgt5gdxufdzfjbt4i
Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom
[article]
2022
bioRxiv
pre-print
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Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies, and can trace small-scale sequence modifications through the evolution of genomes and species. ...
Here we reconstruct the detailed gene contents and organisations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal reconstructions. ...
Acknowledgements We thank Pierre Vincens for the coordination of computing resources and Amélie Peres for computer code engineering. ...
doi:10.1101/2022.02.17.480882
fatcat:fc3vmrsc6baddptw73ztqfushu
Phylogenomics of primates and their ancestral populations
2009
Genome Research
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In particular, local genealogies can vary considerably across loci, which can produce biases and diminished power in many phylogenomic analyses of interest, including phylogeny reconstruction, the identification ...
Genome assemblies are now available for nine primate species, and large-scale sequencing projects are underway or approved for six others. ...
I thank Phil Green and Graham McVicker for stimulating my interest in incomplete lineage sorting and background selection; Vikas Taliwal for many helpful discussions about the ancestral recombination graph ...
doi:10.1101/gr.084228.108
pmid:19801602
pmcid:PMC2775601
fatcat:cxu3cnodlvb7dn2jzdksxydmd4
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
2014
Science
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Vandewege, 4 John A. St. John, 1 § Salvador Capella-Gutiérrez, 5, 6 Todd A. Castoe, 7, 8 Colin Kern, 9 Matthew K. Fujita, 8 Juan C. Opazo, 10 Jerzy Jurka, 11 † Kenji K. ...
Platt, 4,13 Christine A. Lavoie, 4 Meganathan P. Ramakodi, 4,13 ‡ John W. Finger Jr., 14 Alexander Suh, 15, 16 Sally R. Isberg, 17, 18, 19 Lee Miles, 18 # Amanda Y. ...
Because crocodilians are the sister group of birds, these three genomes also provide a critical resource for examining the ancestral state of var-ious genomic features for birds, for which multiple genomes ...
doi:10.1126/science.1254449
pmid:25504731
pmcid:PMC4386873
fatcat:mb3cuxtsfzeutptxgbdcycpg4e
Evolutionary history of versatile-lipases from Agaricales through reconstruction of ancestral structures
2017
BMC Genomics
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Here we carried out a bioinformatic screening to find these proteins in genomes from Agaricales, by means of searching for conserved motifs, sequence and phylogenetic analysis, and three-dimensional modeling ...
Moreover, we reconstructed the molecular evolution of these enzymes along the time by inferring and analyzing the sequence of ancestral intermediate forms. ...
We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI). ...
doi:10.1186/s12864-016-3419-2
pmid:28049436
pmcid:PMC5209871
fatcat:4njhakorjnabxncje7ne3snlqe
Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction
2020
Ecology and Evolution
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genome as reference for mapping DNA sequences of ancient samples. ...
Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral ...
This has been revolutionary across the fields of biology, enabling researchers to not only introduce genomic approaches to model organisms, but across the tree of life (Ellegren, 2014) . ...
doi:10.1002/ece3.6925
pmid:33304488
pmcid:PMC7713980
fatcat:pzssu7c5bzbrray6hp53cjy5o4
Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium
[article]
2015
bioRxiv
pre-print
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We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial ...
The acquisition of these synapomorphic blocks of co-functioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently ...
and by AGROMICS grant from the ENVIROMICS challenge of the Interdisciplinary Mission of the French National Centre for Scientific Research (CNRS). ...
doi:10.1101/034843
fatcat:v3sg26w5xra47d2j2kswqyp6gq
Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny
[article]
2020
bioRxiv
pre-print
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Accordingly, there is a lack of evidence for topologically associated domains, which have been implicated in the evolutionary pressure to retain tight microsyntenic gene clusters. ...
Within this clade, the sea anemone Nematostella vectensis has emerged as a slow evolving model for investigating characteristics of the cnidarian-bilaterian common ancestor, which diverged near the Cambrian ...
Steinmetz and Hanna Kraus for the photo of Nematostella vectensis (Fig. 1 ). Special thanks to Tatiana Bagaeva for the cartoon drawings of animals used in this study. ...
doi:10.1101/2020.10.30.359448
fatcat:cx25mpmsh5g4lopebsppzndsle
Chætognath transcriptome reveals ancestral and unique features among bilaterians
2008
Genome Biology
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Conclusion: These findings reveal both shared ancestral and unique derived characteristics of the chaetognath genome, which suggests that this genome is likely the product of a very original evolutionary ...
These features promote chaetognaths as a pivotal model for comparative genomics, which could provide new clues for the investigation of the evolution of animal genomes. ...
We also thank Eliane Alivon for her help in the molecular biology experiments, Susan Cure and Andy Saurin for correcting the manuscript. ...
doi:10.1186/gb-2008-9-6-r94
pmid:18533022
pmcid:PMC2481426
fatcat:74s7hpx3gnaxxkxrm2ry4dbwje
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more
2020
Nucleic Acids Research
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OMA is an established resource to elucidate evolutionary relationships among genes from currently 2326 genomes covering all domains of life. ...
This update paper describes the reorganisation of the database into gene-, group- and genome-centric pages. ...
ACKNOWLEDGEMENTS We thank Andries Hannaart for his creative vision and execution of the new logo and design of the OMA website. ...
doi:10.1093/nar/gkaa1007
pmid:33174605
fatcat:se6xvgi7i5afjdo676xqvcfxkm
Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms
2016
Systematic Biology
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observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). ...
We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (∼400,000 bp), plastid (∼160,000 bp), and mitochondrial ...
ACKNOWLEDGMENTS We would like to acknowledge the Ohio Supercomputer Center and Ohio Biodiversity Conservation Partnership Cluster for resources to perform analyses, L. Kubatko ...
doi:10.1093/sysbio/syw083
pmid:27637567
fatcat:achjtwb6mfh5vouurnpuepjcre
Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral Cucurbitaceae karyotype
2021
iScience
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To assess the paleohistory of the Cucurbitaceae, we reconstructed the ancestral Cucurbitaceae karyotype and compared it to sequenced cucurbit genomes. ...
We provide comprehensive genomic resources and new insights in the diversity of melon horticultural groups and evolution of cucurbits. ...
The second step consists of clustering or chaining groups of conserved and duplicated genes into ancestral protochromosomes (also referred to as CARs for Contiguous Ancestral Regions) corresponding to ...
doi:10.1016/j.isci.2021.103696
pmid:35059606
pmcid:PMC8760558
fatcat:w74lhpppg5ekxlupekaossvkzm
A deep dive into the ancestral chromosome number of flowering plants
[article]
2020
bioRxiv
pre-print
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Significantly, while dysploidy is equally distributed early and late across the whole phylogeny, polyploidy is detected mainly towards the tips of the tree. ...
Chromosome fusion (loss) and duplication (polyploidy) are the predominant transition types inferred along the phylogenetic tree, emphasising the importance of both dysploidy and genome duplication in chromosome ...
Acknowledgements
313 The authors thank Marcial Escudero and Itay Mayrose for their help with ChromEvol analyses. ...
doi:10.1101/2020.01.05.893859
fatcat:bd3lxrzo4nbwfnw3qdtvsari3i
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants
2016
BMC Genomics
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Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution. ...
Results: We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. ...
We thank N Turland for guidance on the International Code of Nomenclature (http://www.iapt-taxon.org/nomen/main.php) protocol for species naming and N Simon for proof reading it. ...
doi:10.1186/s12864-016-2585-6
pmid:27029936
pmcid:PMC4815162
fatcat:5slonocucjgsvjq6av6dsxbee4
Ancestral sequence reconstruction - an underused approach to understand the evolution of gene function in plants?
2021
Computational and Structural Biotechnology Journal
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Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. ...
We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. ...
A well supported gene tree, which has been reconciled with the tree of the species under examination, representing a phylogeny which is coherent with the larger tree of life, is of course an essential ...
doi:10.1016/j.csbj.2021.03.008
pmid:33868595
pmcid:PMC8039532
fatcat:mnhmboq3zngj5nnrxff3o2huda
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