DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions

BACKGROUND: Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem. RESULTS: We have developed DNPTrapper, a shotgun sequence finishing tool, specifically designed to address the problems posed by the presence of repeated regions in the target sequence. The program detects and visualizes single base differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. The program is available under an Open Source license. CONCLUSION: With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes

Database of Trypanosoma cruzi repeated genes: 20 000 additional gene variants

<p>Abstract</p> <p>Background</p> <p>Repeats are present in all genomes, and often have important functions. However, in large genome sequencing projects, many repetitive regions remain uncharacterized. The genome of the protozoan parasite <it>Trypanosoma cruzi </it>consists of more than 50% repeats. These repeats include surface molecule genes, and several other gene families. In the <it>T. cruzi </it>genome sequencing project, it was clear that not all copies of repetitive genes were present in the assembly, due to collapse of nearly identical repeats. However, at the time of publication of the <it>T. cruzi </it>genome, it was not clear to what extent this had occurred.</p> <p>Results</p> <p>We have developed a pipeline to estimate the genomic repeat content, where shotgun reads are aligned to the genomic sequence and the gene copy number is estimated using the average shotgun coverage. This method was applied to the genome of <it>T. cruzi </it>and copy numbers of all protein coding sequences and pseudogenes were estimated. The 22 640 results were stored in a database available online. 18% of all protein coding sequences and pseudogenes were estimated to exist in 14 or more copies in the <it>T. cruzi </it>CL Brener genome. The average coverage of the annotated protein coding sequences and pseudogenes indicate a total gene copy number, including allelic gene variants, of over 40 000.</p> <p>Conclusion</p> <p>Our results indicate that the number of protein coding sequences and pseudogenes in the <it>T. cruzi </it>genome may be twice the previous estimate. We have constructed a database of the <it>T. cruzi </it>gene repeat data that is available as a resource to the community. The main purpose of the database is to enable biologists interested in repeated, unfinished regions to closely examine and resolve these regions themselves using all available shotgun data, instead of having to rely on annotated consensus sequences that often are erroneous and possibly misleading. Five repetitive genes were studied in more detail, in order to illustrate how the database can be used to analyze and extract information about gene repeats with different characteristics in <it>Trypanosoma cruzi</it>.</p

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

Medarbetarnas upplevelser av värdebaserat ledarskap : En studie om effekter av normativ styrning

Syfte: Vi har valt att, ur personalens perspektiv, studera effekterna av normativ styrning, i detta falli form av värdebaserat ledarskap och aspekter som kan påverka upplevelsen av det. Metod: Den här studien har ett konstruktionistiskt perspektiv som mynnar ut i en kvalitativundersökning med ett abduktivt angreppsätt. Materialet har vi fått genom semistruktureradeintervjuer som vi sedan har analyserat med hjälp av valda teoretiska begrepp. Teoretiska perspektiv: Till grund för den här studiens analys har vi studerat normativ styrning iform av värdebaserat ledarskap. Med valda teorier och utifrån vår insamlade empiri har vi sedanarbetat fram vår analys. Empiri: Studiens empiriska material bygger på intervjuer med fyra medarbetare och två chefer iden studerade organisationen samt en intervju med en fristående konsult som arbetat medimplementeringen av värdebaserat ledarskap i företaget. Totalt har sju intervjuer genomförts. Resultat: Vårt resultat visar att implementeringen av värdebaserat ledarskap inom den studeradeorganisationen inte har tagits väl emot bland medarbetarna. Vi fann att ledningen har en viktig rollvid implementering av värdebaserat ledarskap. Enligt våra slutsatser anser vi att värdebaseratledarskap kräver en stabil organisation. Det är också viktigt att ledningen är införstådda med detständiga arbete som krävs för att värdebaserat ledarskap ska få fäste bland personalen iorganisationen. Vi fann också att medarbetarna i den studerade organisationen kopplas ihopvärdebaserat ledarskap med nedskärning med ökade besparingskrav som gjorts inomorganisationen. Det kan dock vara för tidigt att dra några generella slutsatser då man inte har arbetatmed värdebaserat ledarskap mer än några år i vår studerade organisation.Purpose: We have chosen, from the employee's perspective, to studying the effects of normativecontrol, in this case in the form of value-based leadership and aspects that can affect the experienceof it. Method: This study is a constructionist perspective that culminates in a qualitative study with anabductive approach. The material we have received through semi-structured interviews, which wethen analyzed using the chosen theoretical concepts. Theoretical perspectives: The basis of this study, the analysis is that we studied the normativecontrol in the form of value-based leadership. We have developed our analysis based on theoriesand our accumulated empirical data that we obtained through our survey. Empiricism: The study's empirical data are based on interviews with four employees and twomanagers in the studied organization, as well as an interview with an independent consultant whohas worked with the implementation of value-based leadership in the company. A total of seveninterviews were conducted. Results: Our results show that the implementation of value-based leadership within the studiedorganization has not been well received among employees. We found that management has animportant role in the implementation of value-based leadership. According to our research, webelieve that value-based leadership requires a stable organization. It is also important that themanagement is aware of the constant effort required to get the value-based leadership successfulamong the staff of the organization. We also found that employees in the studied organization linkedvalue-based management to cut with increased savings requirements made in the organization.However, it may be too early to draw any general conclusions when they have not worked withvalue-based leadership more than a few years in our study organization

Correcting errors in shotgun sequences

Sequencing errors in combination with repeated regions cause major problems in shotgun sequencing, mainly due to the failure of assembly programs to distinguish single base differences between repeat copies from erroneous base calls. In this paper, a new strategy designed to correct errors in shotgun sequence data using defined nucleotide positions, DNPs, is presented. The method distinguishes single base differences from sequencing errors by analyzing multiple alignments consisting of a read and all its overlaps with other reads. The construction of multiple alignments is performed using a novel pattern matching algorithm, which takes advantage of the symmetry between indices that can be computed for similar words of the same length. This allows for rapid construction of multiple alignments, with no previous pair-wise matching of sequence reads required. Results from a C++ implementation of this method show that up to 99% of sequencing errors can be corrected, while up to 87% of the single base differences remain and up to 80% of the corrected reads contain at most one error. The results also show that the method outperforms the error correction method used in the EULER assembler. The prototype software, MisEd, is freely available from the authors for academic use

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease

Fil: El-Sayed, Najib M. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Myler, Peter J. Seattle Biomedical Research Institute; Estados Unidos.Fil: Bartholomeu, Daniella C. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Nilsson, Daniel. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Aggarwal, Gautam. Seattle Biomedical Research Institute; Estados Unidos.Fil: Tran, Anh-Nhi. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Ghedin, Elodie. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Worthey, Elizabeth A. Seattle Biomedical Research Institute; Estados Unidos.Fil: Delcher, Arthur L. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Blandin, Gaëlle. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Westenberger, Scott J. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Caler, Elisabet. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Cerqueira, Gustavo C. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Haas, Carole Branched Brian. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Anupama, Atashi. Seattle Biomedical Research Institute; Estados Unidos.Fil: Arner, Erik. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Åslund, Lena. Uppsala University. Department of Genetics and Pathology; Suecia.Fil: Attipoe, Philip. Seattle Biomedical Research Institute; Estados Unidos.Fil: Bontempi, Esteban. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Parasitología; Argentina.Fil: Bringaud, Frédéric. Université Victor Segalen Bordeaux II. Laboratoire de Génomique Fonctionnelle des Trypanosomatides; Francia.Fil: Burton, Peter. University of Glasgow. Wellcome Centre for Molecular Parasitology; Reino Unido.Fil: Cadag, Eithon. Seattle Biomedical Research Institute; Estados Unidos.Fil: Campbell, David A. University of California. Department of Microbiology; Estados Unidos.Fil: Carrington, Mark. University of Cambridge. Department of Biochemistry; Reino Unido.Fil: Crabtree, Jonathan. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Darban, Hamid. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Silveira, Jose Franco da. Universidade Federal de Sao Paulo. Departamento de Microbiologia; Brasil.Fil: Jong, Pieter de. Children’s Hospital Oakland Research Institute. BACPAC Resources; Estados Unidos.Fil: Edwards, Kimberly. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Englund, Paul T. Johns Hopkins University School of Medicine. Department of Biological Chemistry; Estados Unidos.Fil: Fazelina, Gholam. Seattle Biomedical Research Institute; Estados Unidos.Fil: Feldblyum, Tamara. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Ferella, Marcela. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Frasch, Alberto Carlos. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina.Fil: Gull, Keith. University of Oxford. Sir William Dunn School of Pathology; Reino Unido.Fil: Horn, David. London School of Hygiene and Tropical Medicine; Reino Unido.Fil: Hou, Lihua. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Huang, Yiting. Seattle Biomedical Research Institute; Estados Unidos.Fil: Kindlund, Ellen. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Klingbeil, Michele. University of Massachusetts. Department of Microbiology; Estados Unidos.Fil: Kluge, Sindy. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Koo, Hean. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Lacerda, Daniela. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Levin, Mariano J. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-CYTED project). Laboratorio de Biología Molecular de la Enfermedad de Chagas; Argentina.Fil: Lorenzi, Hernan. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-CYTED project). Laboratorio de Biología Molecular de la Enfermedad de Chagas; Argentina.Fil: Louie, Tin. Seattle Biomedical Research Institute; Estados Unidos.Fil: Machado, Carlos Renato. Universidade Federal de Minas Gerais. Departamento de Bioquímica e Imunologia; Brasil.Fil: McCulloch, Richard. University of Glasgow. Wellcome Centre for Molecular Parasitology; Reino Unido.Fil: McKenna, Alan. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Mizuno, Yumi. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Mottram, Jeremy C. University of Glasgow. Wellcome Centre for Molecular Parasitology; Reino Unido.Fil: Nelson, Siri. Seattle Biomedical Research Institute; Estados Unidos.Fil: Ochaya, Stephen. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Osoegawa, Kazutoyo. Children’s Hospital Oakland Research Institute. BACPAC Resources; Estados Unidos.Fil: Pai, Grace. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Parsons, Marilyn. Seattle Biomedical Research Institute; Estados Unidos.Fil: Pentony, Martin. Seattle Biomedical Research Institute; Estados Unidos.Fil: Pettersson, Ulf. Uppsala University. Department of Genetics and Pathology; Suecia.Fil: Pop, Mihai. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Ramirez, Jose Luis. Universidad Central de Venezuela. Instituto de Biología Experimental; Venezuela.Fil: Rinta, Joel. Seattle Biomedical Research Institute; Estados Unidos.Fil: Robertson, Laura. Seattle Biomedical Research Institute; Estados Unidos.Fil: Salzberg, Steven L. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Sanchez, Daniel O. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina.Fil: Seyler, Amber. Seattle Biomedical Research Institute; Estados Unidos.Fil: Sharma, Reuben. University of Cambridge. Department of Biochemistry; Reino Unido.Fil: Shetty, Jyoti. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Simpson, Anjana J. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Sisk, Ellen. Seattle Biomedical Research Institute; Estados Unidos.Fil: Tammi, Martti T. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Tarleton, Rick. University of Georgia. Center for Tropical and Emerging Global Diseases; Estados Unidos.Fil: Teixeira, Santuza. Universidade Federal de Minas Gerais. Departamento de Bioquímica e Imunologia; Brasil.Fil: Aken, Susan Van. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Vogt, Christy. Seattle Biomedical Research Institute; Estados Unidos.Fil: Ward, Pauline N. University of Glasgow. Wellcome Centre for Molecular Parasitology; Reino Unido.Fil: Wickstead, Bill. University of Oxford. Sir William Dunn School of Pathology; Reino Unido.Fil: Wortman, Jennifer. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: White, Owen. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Fraser, Claire M. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Stuart, Kenneth D. Seattle Biomedical Research Institute; Estados Unidos.Fil: Andersson, Björn. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease

Fil: El-Sayed, Najib M. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Myler, Peter J. Seattle Biomedical Research Institute; Estados Unidos.Fil: Bartholomeu, Daniella C. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Nilsson, Daniel. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Aggarwal, Gautam. Seattle Biomedical Research Institute; Estados Unidos.Fil: Tran, Anh-Nhi. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Ghedin, Elodie. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Worthey, Elizabeth A. Seattle Biomedical Research Institute; Estados Unidos.Fil: Delcher, Arthur L. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Blandin, Gaëlle. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Westenberger, Scott J. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Caler, Elisabet. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Cerqueira, Gustavo C. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Haas, Carole Branched Brian. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Anupama, Atashi. Seattle Biomedical Research Institute; Estados Unidos.Fil: Arner, Erik. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Åslund, Lena. Uppsala University. Department of Genetics and Pathology; Suecia.Fil: Attipoe, Philip. Seattle Biomedical Research Institute; Estados Unidos.Fil: Bontempi, Esteban. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Parasitología; Argentina.Fil: Bringaud, Frédéric. Université Victor Segalen Bordeaux II. Laboratoire de Génomique Fonctionnelle des Trypanosomatides; Francia.Fil: Burton, Peter. University of Glasgow. Wellcome Centre for Molecular Parasitology; Reino Unido.Fil: Cadag, Eithon. Seattle Biomedical Research Institute; Estados Unidos.Fil: Campbell, David A. University of California. Department of Microbiology; Estados Unidos.Fil: Carrington, Mark. University of Cambridge. Department of Biochemistry; Reino Unido.Fil: Crabtree, Jonathan. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Darban, Hamid. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Silveira, Jose Franco da. Universidade Federal de Sao Paulo. Departamento de Microbiologia; Brasil.Fil: Jong, Pieter de. Children’s Hospital Oakland Research Institute. BACPAC Resources; Estados Unidos.Fil: Edwards, Kimberly. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Englund, Paul T. Johns Hopkins University School of Medicine. Department of Biological Chemistry; Estados Unidos.Fil: Fazelina, Gholam. Seattle Biomedical Research Institute; Estados Unidos.Fil: Feldblyum, Tamara. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Ferella, Marcela. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Frasch, Alberto Carlos. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina.Fil: Gull, Keith. University of Oxford. Sir William Dunn School of Pathology; Reino Unido.Fil: Horn, David. London School of Hygiene and Tropical Medicine; Reino Unido.Fil: Hou, Lihua. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Huang, Yiting. Seattle Biomedical Research Institute; Estados Unidos.Fil: Kindlund, Ellen. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Klingbeil, Michele. University of Massachusetts. Department of Microbiology; Estados Unidos.Fil: Kluge, Sindy. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Koo, Hean. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Lacerda, Daniela. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Levin, Mariano J. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-CYTED project). Laboratorio de Biología Molecular de la Enfermedad de Chagas; Argentina.Fil: Lorenzi, Hernan. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-CYTED project). Laboratorio de Biología Molecular de la Enfermedad de Chagas; Argentina.Fil: Louie, Tin. Seattle Biomedical Research Institute; Estados Unidos.Fil: Machado, Carlos Renato. Universidade Federal de Minas Gerais. Departamento de Bioquímica e Imunologia; Brasil.Fil: McCulloch, Richard. University of Glasgow. Wellcome Centre for Molecular Parasitology; Reino Unido.Fil: McKenna, Alan. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Mizuno, Yumi. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Mottram, Jeremy C. University of Glasgow. Wellcome Centre for Molecular Parasitology; Reino Unido.Fil: Nelson, Siri. Seattle Biomedical Research Institute; Estados Unidos.Fil: Ochaya, Stephen. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Osoegawa, Kazutoyo. Children’s Hospital Oakland Research Institute. BACPAC Resources; Estados Unidos.Fil: Pai, Grace. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Parsons, Marilyn. Seattle Biomedical Research Institute; Estados Unidos.Fil: Pentony, Martin. Seattle Biomedical Research Institute; Estados Unidos.Fil: Pettersson, Ulf. Uppsala University. Department of Genetics and Pathology; Suecia.Fil: Pop, Mihai. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Ramirez, Jose Luis. Universidad Central de Venezuela. Instituto de Biología Experimental; Venezuela.Fil: Rinta, Joel. Seattle Biomedical Research Institute; Estados Unidos.Fil: Robertson, Laura. Seattle Biomedical Research Institute; Estados Unidos.Fil: Salzberg, Steven L. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Sanchez, Daniel O. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina.Fil: Seyler, Amber. Seattle Biomedical Research Institute; Estados Unidos.Fil: Sharma, Reuben. University of Cambridge. Department of Biochemistry; Reino Unido.Fil: Shetty, Jyoti. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Simpson, Anjana J. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Sisk, Ellen. Seattle Biomedical Research Institute; Estados Unidos.Fil: Tammi, Martti T. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Fil: Tarleton, Rick. University of Georgia. Center for Tropical and Emerging Global Diseases; Estados Unidos.Fil: Teixeira, Santuza. Universidade Federal de Minas Gerais. Departamento de Bioquímica e Imunologia; Brasil.Fil: Aken, Susan Van. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Vogt, Christy. Seattle Biomedical Research Institute; Estados Unidos.Fil: Ward, Pauline N. University of Glasgow. Wellcome Centre for Molecular Parasitology; Reino Unido.Fil: Wickstead, Bill. University of Oxford. Sir William Dunn School of Pathology; Reino Unido.Fil: Wortman, Jennifer. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: White, Owen. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Fraser, Claire M. The Institute for Genomic Research. Department of Parasite Genomics; Estados Unidos.Fil: Stuart, Kenneth D. Seattle Biomedical Research Institute; Estados Unidos.Fil: Andersson, Björn. Karolinska Institutet. Center for Genomics and Bioinformatics; Suecia.Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention

A Genetic Variation Map for Chicken with 2.8 Million Single-Nucleotide Polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines—in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.This article is from Nature 432 (2004): 717, doi:10.1038/nature03156.</p