RESUMO
As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 +/- 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.
Assuntos
Genoma de Planta , Mapeamento Físico do Cromossomo , Populus/genética , Cromossomos Artificiais Bacterianos , Haplótipos , Repetições Minissatélites , Polimorfismo Genético , Alinhamento de Sequência , Análise de Sequência de DNARESUMO
Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC clones spanning the human genome. The clone set provides coverage for at least 98% of the human fingerprint map, 99% of the current assembled sequence and has an effective resolving power of 79 kb. We have made the clone set publicly available, anticipating that it will generally facilitate FISH or array-CGH-based identification and characterization of chromosomal alterations relevant to disease.
Assuntos
Cromossomos Artificiais Bacterianos , Genoma Humano , Sequência de Bases , Clonagem Molecular , Humanos , Mapeamento Físico do CromossomoRESUMO
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.
Assuntos
Cromossomos Artificiais Bacterianos/genética , Cromossomos Artificiais de Levedura/genética , Genoma , Mapeamento Físico do Cromossomo/métodos , Animais , Automação , Cromossomos/genética , Clonagem Molecular/métodos , Biologia Computacional/métodos , Biologia Computacional/normas , Mapeamento de Sequências Contíguas/métodos , Mapeamento de Sequências Contíguas/normas , Impressões Digitais de DNA/métodos , Impressões Digitais de DNA/normas , Marcadores Genéticos/genética , Mapeamento Físico do Cromossomo/normas , Reação em Cadeia da Polimerase/métodos , Ratos , Análise de Sequência de DNA/métodos , Análise de Sequência de DNA/normasRESUMO
We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.
Assuntos
Genoma Viral , RNA Viral/genética , Coronavírus Relacionado à Síndrome Respiratória Aguda Grave/genética , Proteínas Virais/genética , Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Animais , Sequência de Bases , Sequência Conservada , Coronavirus/classificação , Coronavirus/genética , Proteínas M de Coronavírus , Proteínas do Nucleocapsídeo de Coronavírus , DNA Complementar , Mudança da Fase de Leitura do Gene Ribossômico , Humanos , Glicoproteínas de Membrana/química , Glicoproteínas de Membrana/genética , Proteínas do Nucleocapsídeo/química , Proteínas do Nucleocapsídeo/genética , Fases de Leitura Aberta , Filogenia , RNA Viral/isolamento & purificação , RNA Polimerase Dependente de RNA/química , RNA Polimerase Dependente de RNA/genética , Sequências Reguladoras de Ácido Nucleico , Coronavírus Relacionado à Síndrome Respiratória Aguda Grave/classificação , Coronavírus Relacionado à Síndrome Respiratória Aguda Grave/isolamento & purificação , Análise de Sequência de DNA , Síndrome Respiratória Aguda Grave/virologia , Glicoproteína da Espícula de Coronavírus , Proteínas do Envelope Viral/química , Proteínas do Envelope Viral/genética , Proteínas da Matriz Viral/química , Proteínas da Matriz Viral/genética , Proteínas Virais/químicaRESUMO
A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human-mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy.