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Abstract
Mapping expression Quantitative Trait Loci (eQTLs) represents a powerful and widely adopted approach to identifying putative regulatory variants and linking them to specific genes. Up to now eQTL studies have been conducted in a relatively narrow range of tissues or cell types. However, understanding the biology of organismal phenotypes will involve understanding regulation in multiple tissues, and ongoing studies are collecting eQTL data in dozens of cell types. Here we present a statistical framework for powerfully detecting eQTLs in multiple tissues ...
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Abstract
With the development of new sequencing techniques, the number of sequenced plant genomes is increasing. However, accurate annotation of these sequences remains a major challenge, in particular with regard to transposable elements (TEs). The aim of this chapter is to provide a roadmap for researchers involved in genome projects to address this issue. We list several widely used tools for each step of the TE annotation process, from the identification of TE families to the annotation of TE copies. We assess ...
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by Laure Ségurel, Emma E. Thompson, Timothée Flutre, et al.Jessica Lovstad, Aarti Venkat, Susan W. Margulis, Jill Moyse, Steve Ross, Kathryn Gamble, Guy Sella, Carole Ober, Molly Przeworski
posted to population_genetics primate
by timflutre
on 2012-10-25 23:42:36
Abstract
The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with ...
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Abstract
Current high-throughput techniques have made it feasible to sequence even the genomes of non-model organisms. However, the annotation process now represents a bottleneck to genome analysis, especially when dealing with transposable elements (TE). Combined approaches, using both de novo and knowledge-based methods to detect TEs, are likely to produce reasonably comprehensive and sensitive results. This chapter provides a roadmap for researchers involved in genome projects to address this issue. At each step of the TE annotation process, from the identification of ...
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by Philippe Leroy, Nicolas Guilhot, Hiroaki Sakai, et al.Aurélien Bernard, Frédéric Choulet, Sébastien Theil, Sébastien Reboux, Naoki Amano, Timothée Flutre, Céline Pelegrin, Hajime Ohyanagi, Michael Seidel, Franck Giacomoni, Mathieu Reichstadt, Michael Alaux, Emmanuelle Gicquello, Fabrice Legeai, Lorenzo Cerutti, Hisataka Numa, Tsuyushi Tanaka, Klaus Mayer, Takeshi Itoh, Hadi Quesneville, Catherine Feuillet
Abstract
In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is ...
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Abstract
Transposable elements (TEs) are DNA sequences that have the capacity to move and duplicate within genomes, and occasionally between them. They are present in almost all species and are especially prevalent in eukaryotes where they can account for most of the genomic content. As a result of their dynamics and their mere presence, TEs can profoundly shape genomes and gene expression. With the current pace of sequencing technology improvement, a rapidly increasing number of genomes, particularly from non-model species, are being ...
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Abstract
Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for ...
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(28 October 2010)
Abstract
Any living organism is the result of complex interactions bet- ween its genome and its environment, interactions characterized by transfers of matter and energy required for the survival of the organism and the transmission of its genome. Since the dis- covery in the years 1910 that the chromosome is the mechanical basis of the genetic information, the biologists study genomes in order to decipher the mecanisms and processes operating in the development of organisms and the evolution of populations. Thanks to the technological improvements of the last decades, several genomes ...
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by E. d'Alençon, H. Sezutsu, F. Legeai, et al.E. Permal, S. Bernard-Samain, S. Gimenez, C. Gagneur, F. Cousserans, M. Shimomura, A. Brun-Barale, T. Flutre, A. Couloux, P. East, K. Gordon, K. Mita, H. Quesneville, P. Fournier, R. Feyereisen
Abstract
The recent assembly of the silkworm Bombyx mori genome with 432 Mb on 28 holocentric chromosomes has become a reference in the genomic analysis of the very diverse Order of Lepidoptera. We sequenced BACs from two major pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, corresponding to 15 regions distributed on 11 B. mori chromosomes, each BAC/region being anchored by known orthologous gene(s) to analyze syntenic relationships and genome rearrangements among the three species. Nearly 300 genes and numerous transposable ...
Note (first note only)
- Syntenic genes were detected and annotated in the 15 genomic regions. In approximately half the cases, two genes in synteny over 50 kb in B. mori would be found within 34 kb of each other in the two noctuid species. This clearly indicates conservation of synteny at a macroscopic scale.
- We measured the number and length of synteny blocks, i.e., conserved segment corresponding to any region in which gene content and order are conserved.
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by P. Abad, J. Gouzy, J. M. Aury, et al.P. Castagnone-Sereno, E. Danchin, E. Deleury, L. Perfus-Barbeoch, V. Anthouard, F. Artiguenave, V. Blok, M. C. Caillaud, P. Coutinho, C. Dasilva, F. De Luca, F. Deau, M. Esquibet, T. Flutre, J. Goldstone, N. Hamamouch, T. Hewezi, O. Jaillon, C. Jubin, P. Leonetti, M. Magliano, T. Maier, G. Markov, P. McVeigh, G. Pesole, J. Poulain, M. Robinson-Rechavi, E. Sallet, B. Ségurens, D. Steinbach, T. Tytgat, E. Ugarte, C. van Ghelder, P. Veronico, T. Baum, M. Blaxter, T. Bleve-Zacheo, E. Davis, J. Ewbank, B. Favery, E. Grenier, B. Henrissat, J. Jones, V. Laudet, A. Maule, H. Quesneville, M. N. Rosso, T. Schiex, G. Smant, J. Weissenbach, P. Wincker
Abstract
Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number ...
Note (first note only)
- This is the first whole genome of a plant parasitic metazoan to be sequenced and analyzed. This genome is the first one sequenced and assembled for a strictly parthenogenetic species.
- Expected genome: 47-51 Mb. Assembled genome: 86 Mb. Most of the genome is composed of pairs of homologous segments that may denote former diverged alleles. This suggests that M. incognita is evolving without sex toward effective haploidy through the Meselson effect.
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