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Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Xiaosong Huang, Laurent-Philippe Albou, Tremayne Mushayahama, Anushya Muruganujan, Haiming Tang, Paul D Thomas
2018 Nucleic Acids Research  
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]

Matthieu Muffato, Alexandra Louis, Nga Thi Thuy Nguyen, Joseph Lucas, Camille Berthelot, Hugues Roest Crollius
2022 bioRxiv   pre-print
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

A. Siepel
2009 Genome Research  
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

R. E. Green, E. L. Braun, J. Armstrong, D. Earl, N. Nguyen, G. Hickey, M. W. Vandewege, J. A. St. John, S. Capella-Gutierrez, T. A. Castoe, C. Kern, M. K. Fujita (+43 others)
2014 Science  
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

Jorge Barriuso, María Jesús Martínez
2017 BMC Genomics  
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

Filipe Garrett Vieira, José Alfredo Samaniego Castruita, M. Thomas P. Gilbert
2020 Ecology and Evolution  
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]

Florent Lassalle, Remi Planel, Simon Penel, David Chapulliot, Valerie Barbe, Audrey Dubost, Alexandra Calteau, David Vallenet, Damien Mornico, Thomas Bigot, Laurent Gueguen, Ludovic Vial (+3 others)
2015 bioRxiv   pre-print
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]

Bob Zimmermann, Sofia M.C. Robb, Grigory Genikhovich, Whitney J. Fropf, Lukas Weilguny, Shuonan He, Shiyuan Chen, Jessica Lovegrove-Walsh, Eric M. Hill, Katerina Ragkousi, Daniela Praher, David Fredman (+3 others)
2020 bioRxiv   pre-print
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

Ferdinand Marlétaz, André Gilles, Xavier Caubit, Yvan Perez, Carole Dossat, Sylvie Samain, Gabor Gyapay, Patrick Wincker, Yannick Le Parco
2008 Genome Biology  
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

Adrian M Altenhoff, Clément-Marie Train, Kimberly J Gilbert, Ishita Mediratta, Tarcisio Mendes de Farias, David Moi, Yannis Nevers, Hale-Seda Radoykova, Victor Rossier, Alex Warwick Vesztrocy, Natasha M Glover, Christophe Dessimoz
2020 Nucleic Acids Research  
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

Ryan A. Folk, Jennifer R. Mandel, John V. Freudenstein
2016 Systematic Biology  
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

Clement Pichot, Anis Djari, Joseph Tran, Marion Verdenaud, William Marande, Cecile Huneau, Veronique Gautier, David Latrasse, Sandrine Arribat, Vivien Sommard, Christelle Troadec, Charles Poncet (+8 others)
2021 iScience  
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]

Angelino Carta, Gianni Bedini, Lorenzo Peruzzi
2020 bioRxiv   pre-print
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

Marijke J. van Baren, Charles Bachy, Emily Nahas Reistetter, Samuel O. Purvine, Jane Grimwood, Sebastian Sudek, Hang Yu, Camille Poirier, Thomas J. Deerinck, Alan Kuo, Igor V. Grigoriev, Chee-Hong Wong (+5 others)
2016 BMC Genomics  
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?

Federico Scossa, Alisdair R. Fernie
2021 Computational and Structural Biotechnology Journal  
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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