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The genome of the medieval Black Death agent (extended abstract) [article]

Ashok Rajaraman and Eric Tannier and Cedric Chauve
2013 arXiv   pre-print
the contig set of the Black Death agent genome, providing a full chromosome sequence, at the nucleotide scale, of this ancient bacteria.  ...  We show that recent computational paleogenomics methods, aiming at reconstructing the organization of ancestral genomes from the comparison of extant genomes, can be used to correct, order and complete  ...  ., a PIMS IGTC Fellowship to A.R. and ANR-10-BINF-01-01 Ancestrome to E.T. We are thankful to Laurent Duret, Vincent Daubin, Annie Chateau, Eric Rivals, Hendrik Poinar for useful discussions.  ... 
arXiv:1307.7642v1 fatcat:qwyph37zmzhq5jfotc3priq55e

Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

Nina Luhmann, Daniel Doerr, Cedric Chauve
2017 Microbial Genomics  
We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal.  ...  We describe an optimization-based method AGapEs (ancestral gap estimation) to fill in intercontig gaps using a combination of a template obtained from related extant genomes and aDNA reads.  ...  Acknowledgements We thank the group of Hendrik Poinar for help with the processing of the raw reads and discussions during a visit in Hamilton.  ... 
doi:10.1099/mgen.0.000123 pmid:29114402 pmcid:PMC5643016 fatcat:zcpve6v37ra6rdalrqdj23yyre

Improved assemblies and comparison of two ancient Yersinia pestis genomes [article]

Nina Luhmann, Daniel Doerr, Cedric Chauve
2016 bioRxiv   pre-print
We describe an optimization-based method AGapEs (Ancestral Gap Estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads.  ...  We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and evolutionary parsimony signal.  ...  We thank the group of Hendrik Poinar for help with the processing of the raw reads and 343 discussions during a visit in Hamilton.  ... 
doi:10.1101/073445 fatcat:c4ndlbja45btdoxqrmrb3iq2bi

Ancestral gene synteny reconstruction improves extant species scaffolding

Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, Sèverine Bérard
2015 BMC Genomics  
We present a method, called ARt-DeCo that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context.  ...  We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding.  ...  We thank Yann Ponty for technical help for patching DeClone to integrate the scaffolding and the exploration of the solution space.  ... 
doi:10.1186/1471-2164-16-s10-s11 pmid:26450761 pmcid:PMC4603332 fatcat:pzvhkdso3vatfjblvlwx66ym4u

Ancestral gene synteny reconstruction improves extant species scaffolding [article]

Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, Severine Berard
2015 bioRxiv   pre-print
We present a method, called \decopp\ that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context.  ...  We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding.  ...  It suggests a methodological link with ancestral genome reconstructions: if ancestral genes are considered as contigs, scaffolding extant or ancestral contigs in a phylogenetic context differs only in  ... 
doi:10.1101/023085 fatcat:s7gkuqzszrfdvkq4rrkb2xie44

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

Virpi Ahola, Rainer Lehtonen, Panu Somervuo, Leena Salmela, Patrik Koskinen, Pasi Rastas, Niko Välimäki, Lars Paulin, Jouni Kvist, Niklas Wahlberg, Jaakko Tanskanen, Emily A. Hornett (+35 others)
2014 Nature Communications  
Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n ¼ 31 for  ...  Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which  ...  K.Q. was supported by the Viikki Doctoral Programme in Molecular Biosciences (VGSB) at the University of Helsinki, and R.M.W. by Marie Curie International Outgoing Fellowship PIOF-GA-2011-303312.  ... 
doi:10.1038/ncomms5737 pmid:25189940 pmcid:PMC4164777 fatcat:i7eb6q7tobalbp243hyedjv7cq

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

Charles Y. Feigin, Axel H. Newton, Liliya Doronina, Jürgen Schmitz, Christy A. Hipsley, Kieren J. Mitchell, Graham Gower, Bastien Llamas, Julien Soubrier, Thomas N. Heider, Brandon R. Menzies, Alan Cooper (+2 others)
2017 Nature Ecology & Evolution  
Baldur Hlidberg for the animal paintings in Fig. 2a and Supplementary Fig. 4 .  ...  of Melbourne) for operating the micro-CT scanner and processing data; K.  ...  Resulting contigs were named for their scaffold of origin with an additional numerical suffix (for example, the 12th contig in scaffold GL834412.1 was named GL834412.1.12).  ... 
doi:10.1038/s41559-017-0417-y pmid:29230027 fatcat:dwzcturanrhqppc7zz3rwjwo4m

Organellar Genomes from a ∼5,000-Year-Old Archaeological Maize Sample Are Closely Related to NB Genotype

Bernardo Pérez-Zamorano, Miguel Vallebueno-Estrada, Javier Martínez González, Angel García Cook, Rafael Montiel, Jean-Philippe Vielle-Calzada, Luis Delaye
2017 Genome Biology and Evolution  
As shown here, the inclusion of ancient genomes on phylogenetic trees greatly improves our understanding of the domestication process of maize, one of the most important crops worldwide.  ...  Here, we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacá n, Mé xico.  ...  This research was supported by a grant from CONACyT (CB256826) and the Instituto Nacional de Antropología e Historia (INAH), through the CINVESTAV-INAH collaboration.  ... 
doi:10.1093/gbe/evx048 pmid:28338960 pmcid:PMC5387994 fatcat:fra3udzrjngxli5lqqdxllqzsy

The Amborella Genome and the Evolution of Flowering Plants

V. A. Albert, W. B. Barbazuk, C. W. dePamphilis, J. P. Der, J. Leebens-Mack, H. Ma, J. D. Palmer, S. Rounsley, D. Sankoff, S. C. Schuster, D. E. Soltis, P. S. Soltis (+136 others)
2013 Science  
Genome structure and phylogenomic analyses indicate that the ancestral angiosperm was a polyploid with a large constellation of both novel and ancient genes that survived to play key roles in angiosperm  ...  123 kb, an N50 length of 4.9 Mb, and a maximum scaffold length of 16 Mb (table S2) .  ... 
doi:10.1126/science.1241089 pmid:24357323 fatcat:w4xthgghrnejfiomneqsrjh7pu

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Jan E. Janečka, Brian W. Davis, Sharmila Ghosh, Nandina Paria, Pranab J. Das, Ludovic Orlando, Mikkel Schubert, Martin K. Nielsen, Tom A. E. Stout, Wesley Brashear, Gang Li, Charles D. Johnson (+8 others)
2018 Nature Communications  
Multiple sequence alignment of horse ETSTY7 and ETSTY7-like sequences from donkey, Przewalski's horse and Parascaris were used to reconstruct a phylogenetic tree (Fig. 6) .  ...  that eMSY has retained a unique set of ancestral genes (Supplementary Table 3 ).  ...  To view a copy of this license, visit http://creativecommons.org/ licenses/by/4.0/.  ... 
doi:10.1038/s41467-018-05290-6 pmid:30054462 pmcid:PMC6063916 fatcat:slkkhxrhijarxe4suuhneiqlmm

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

Carlos W Nossa, Paul Havlak, Jia-Xing Yue, Jie Lv, Kimberly Y Vincent, H Jane Brockmann, Nicholas H Putnam
2014 GigaScience  
Comparison to other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient  ...  They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of "living fossils."  ...  , the Department of Biology, and the UF Marine Laboratory at Seahorse Key.  ... 
doi:10.1186/2047-217x-3-9 pmid:24987520 pmcid:PMC4066314 fatcat:37qpu5hcfbef3fkuoptbu4nvea

The comparative genomics and complex population history of Papio baboons

Jeffrey Rogers, Muthuswamy Raveendran, R. Alan Harris, Thomas Mailund, Kalle Leppälä, Georgios Athanasiadis, Mikkel Heide Schierup, Jade Cheng, Kasper Munch, Jerilyn A. Walker, Miriam K. Konkel, Vallmer Jordan (+30 others)
2019 Science Advances  
Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression.  ...  These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.  ...  A set of 323 scaffolds (a total of 217 Mb) were identified this way and therefore split. The N50 of the contigs in the Panu_2.0 assembly is 40.3 kb, and the N50 of the scaffolds is 529 kb.  ... 
doi:10.1126/sciadv.aau6947 pmid:30854422 pmcid:PMC6401983 fatcat:lefjx5bukbhyzka77j2mis4xba

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

Yue Hao, Makenzie E. Mabry, Patrick P. Edger, Michael Freeling, Chunfang Zheng, Lingling Jin, Robert VanBuren, Marivi Colle, Hong An, R. Shawn Abrahams, Jacob D. Washburn, Xinshuai Qi (+9 others)
2021 Genome Research  
interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep.  ...  We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.  ...  We thank A. Platts for assistance with our analyses and J.A. Birchler, R. Roberts, J. Thorne, and H. Ashrafi for helpful discussions.  ... 
doi:10.1101/gr.270033.120 pmid:33863805 pmcid:PMC8092008 fatcat:jer3vfzcrvd23a722vlp3dyifa

Major Histocompatibility Complex Genes Map to Two Chromosomes in an Evolutionarily Ancient Reptile, the Tuatara Sphenodon punctatus

Hilary C. Miller, Denis O'Meally, Tariq Ezaz, Chris Amemiya, Jennifer A. Marshall-Graves, Scott Edwards
2015 G3: Genes, Genomes, Genetics  
Major histocompatibility complex (MHC) genes are a central component of the vertebrate immune system and usually exist in a single genomic region.  ...  Reptiles occupy a key evolutionary position for understanding how variation in MHC structure evolved in vertebrates, but information on the structure of the MHC region in reptiles is limited.  ...  gap in reconstructing the evolutionary history of the amniote MHC.  ... 
doi:10.1534/g3.115.017467 pmid:25953959 pmcid:PMC4502378 fatcat:3dov32xqkzaevhwtbgijtm7mim

Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex

Katherine Belov, Janine E Deakin, Anthony T Papenfuss, Michelle L Baker, Sandra D Melman, Hannah V Siddle, Nicolas Gouin, David L Goode, Tobias J Sargeant, Mark D Robinson, Matthew J Wakefield, Shaun Mahony (+7 others)
2006 PLoS Biology  
We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution.  ...  The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds.  ...  The contig N50 length is 111 kb and the scaffold N50 length is 54 Mb (J. Chang, personal communication). MonDom2 is an interim assembly of unordered scaffolds.  ... 
doi:10.1371/journal.pbio.0040046 pmid:16435885 pmcid:PMC1351924 fatcat:jqlgm3k27zbddfsmk6rifxgy3m
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