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1. The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: a high frequency of deletions in tandem duplicates

Author

Brandstrom, Mikael and Ellegren, Hans

Subjects
Chickens -- Genetic aspects, Single nucleotide polymorphisms -- Evaluation, Phenotype -- Influence, Biological sciences
Abstract

It is increasingly recognized that insertions and deletions (indels) are an important source of genetic as well as phenotypic divergence and diversity. We analyzed length polymorphisms identified through partial (0.25X) shotgun sequencing of three breeds of domestic chicken made by the International Chicken Polymorphism Map Consortium. A data set of 140,484 short indel polymorphisms in unique DNA was identified after filtering for microsatellite structures. There was a significant excess of tandem duplicates at indel sites, with deletions of a duplicate motif outnumbering the generation of duplicates through insertion. Indel density was lower in microchromosomes than in macrochromosomes, in the Z chromosome than in autosomes, and in 100 bp of upstream sequence, 5'-UTR, and first introns than in intergenic DNA and in other introns. Indel density was highly correlated with single nucleotide polymorphism (SNP) density. The mean density of indels in pairwise sequence comparisons was 1.9 x [10.sup.-4] indel events/bp, ~5% the density of SNPs segregating in the chicken genome. The great majority of indels involved a limited number of nucleotides (median 1 bp), with A-rich motifs being overrepresented at indel sites. The overrepresentation of deletions at tandem duplicates indicates that replication slippage in duplicate sequences is a common mechanism behind indel mutation. The correlation between indel and SNP density indicates common effects of mutation and/or selection on the occurrence of indels and point mutations.

Published
2007

2. Genetic mapping in a natural population of collared flycatchers (ficedula albicollis): conserved synteny but gene order rearrangements on the avian Z chromosome

Author

Backstrom, Niclas, Brandstrom, Mikael, Gustafsson, Lars, Qvarnstrom, Anna, Cheng, Hans, and Ellegren, Hans

Subjects
Single nucleotide polymorphisms -- Genetic aspects, Genetic research, Biological sciences
Abstract

Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher--one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only ~50% that of chicken, challenging the widely held view that birds generally have high recombination rates.

Published
2006

3. Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias

Author

Brandstrom, Mikael and Ellegren, Hans

Subjects
Genetic polymorphisms -- Research, Nucleotide sequencing -- Analysis, Gene mutations -- Research, Health
Abstract

The whole-genome shotgun sequence data from three unrelated chicken individuals was used to get a clear idea about microsatellite variability in a vertebrate genome by circumventing the ascertainment bias related with inferring evolutionary process in microsatellite. It is suggested from the negative relationship between microsatellite abundance and single nucleotide polymorphism (SNP) density that a balance between rate of replication slippage and rate of point mutation regulates equilibrium microsatellite distributions.

Published
2008

4. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., International Chicken Genome Sequencing Consortium, ProdInra, Migration, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Zdobnov, Evgeny

Subjects
RNA, Untranslated, olfactory receptor, [SDV]Life Sciences [q-bio], mouse genome, QH75, Genome, 0302 clinical medicine, Gene Duplication, Coding region, ddc:576.5, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Short Interspersed Nucleotide Elements, Genetics, 0303 health sciences, Multidisciplinary, CHICKENS, recent segmental duplications, Untranslated, GENOME SEQUENCE, International Chicken Genome Sequencing Consortium, Genomics, Physical Chromosome Mapping, major histocompatibility complex, mammalian evolution, [SDV] Life Sciences [q-bio], Multigene Family, Vertebrates, SEQUENCE DU GENOME, Sequence Analysis, Pseudogenes, Biotechnology, brown-norway rat, animal structures, Evolution, General Science & Technology, Sequence analysis, Biology, Animal Breeding and Genomics, Synteny, Evolution, Molecular, Avian Proteins, 03 medical and health sciences, non-ltr retrotransposons, Animals, Humans, alcohol-dehydrogenase, Fokkerij en Genomica, SF, QP506, Gene, QH426, 030304 developmental biology, Whole genome sequencing, QL, phylogenetic analysis, QH, Human Genome, Molecular, Sequence Analysis, DNA, DNA, tissue-specific genes, EVOLUTION, Retroviridae, Long Interspersed Nucleotide Elements, Genes, Mutagenesis, Evolutionary biology, DNA Transposable Elements, Microchromosome, WIAS, RNA, Chickens, 030217 neurology & neurosurgery
Abstract

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Published
2004

5. Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians

Author

Malmstrom, Helena, Thomas P. Gilbert, M., G. Thomas, Mark, Brandstrom, Mikael, Stora, Jan, Molnar, Petra, KAndersen, Pernille K, Bendixen, Christian, Holmlund, Gunilla, Gotherstrom, Anders, Willerslev, Eske, Malmstrom, Helena, Thomas P. Gilbert, M., G. Thomas, Mark, Brandstrom, Mikael, Stora, Jan, Molnar, Petra, KAndersen, Pernille K, Bendixen, Christian, Holmlund, Gunilla, Gotherstrom, Anders, and Willerslev, Eske

Abstract

The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century[1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.

Published
2009
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6. Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears

Author

Valdiosera Morales, Cristina, García García, Nuria, Anderung, Cecilia, Dolén, Love, Cregut Bonnoure, Evelyne, Kahlke, Ralph Dietrich, Mathias, Stiller, Brandstrom, Mikael, Thomas, Mark G., Arsuaga Ferreras, Juan Luis, Götherström, Anders, Barnes, Ian, Valdiosera Morales, Cristina, García García, Nuria, Anderung, Cecilia, Dolén, Love, Cregut Bonnoure, Evelyne, Kahlke, Ralph Dietrich, Mathias, Stiller, Brandstrom, Mikael, Thomas, Mark G., Arsuaga Ferreras, Juan Luis, Götherström, Anders, and Barnes, Ian

Abstract

Models for the development of species distribution in Europe typically invoke restriction in three temperate Mediterranean refugia during glaciations, from where recolonization of central and northern Europe occurred. The brown bear, Ursus arctos, is one of the taxa from which this model is derived. Sequence data generated from brown bear fossils show a complex phylogeographical history for western European populations. Long-term isolation in separate refugia is not required to explain our data when considering the palaeontological distribution of brown bears. We propose continuous gene flow across southern Europe, from which brown bear populations expanded after the last glaciation., Depto. de Geodinámica, Estratigrafía y Paleontología, Fac. de Ciencias Geológicas, TRUE, pub

Published
2007

7. Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., and Wilson, Richard K.

Abstract

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature03154

Published
2005

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