Genome Architecture (genome + architecture)

Distribution by Scientific Domains

Selected Abstracts

Book review: The Origins of Genome Architecture

Eugene E. Harris
No abstract is available for this article. [source]

Dynamics of genome evolution in facultative symbionts of aphids

Patrick H. Degnan
Summary Aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist Buchnera plus several bacteria that are not required for host survival. Among the latter, ,Candidatus Regiella insecticola' and ,Candidatus Hamiltonella defensa' are found in pea aphids and other hosts and have been shown to protect aphids from natural enemies. We have sequenced almost the entire genome of R. insecticola (2.07 Mbp) and compared it with the recently published genome of H. defensa (2.11 Mbp). Despite being sister species the two genomes are highly rearranged and the genomes only have ,55% of genes in common. The functions encoded by the shared genes imply that the bacteria have similar metabolic capabilities, including only two essential amino acid biosynthetic pathways and active uptake mechanisms for the remaining eight, and similar capacities for host cell toxicity and invasion (type 3 secretion systems and RTX toxins). These observations, combined with high sequence divergence of orthologues, strongly suggest an ancient divergence after establishment of a symbiotic lifestyle. The divergence in gene sets and in genome architecture implies a history of rampant recombination and gene inactivation and the ongoing integration of mobile DNA (insertion sequence elements, prophage and plasmids). [source]

A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei

Z.-Q. Du
Summary Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r2), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r2 increased with decreasing inter-marker distance from ,80 cm, and increased more rapidly from ,30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits. [source]

BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon

S. Lorenz
Summary A better understanding of the genotype,phenotype correlation of Atlantic salmon is of key importance for a whole range of production, life history and conservation biology issues attached to this species. High-density linkage maps integrated with physical maps and covering the complete genome are needed to identify economically important genes and to study the genome architecture. Linkage maps of moderate density and a physical bacterial artificial chromosome (BAC) fingerprint map for the Atlantic salmon have already been generated. Here, we describe a strategy to combine the linkage mapping with the physical integration of newly identified single nucleotide polymorphisms (SNPs). We resequenced 284 BAC-ends by PCR in 14 individuals and detected 180 putative SNPs. After successful validation of 152 sequence variations, genotyping and genetic mapping were performed in eight salmon families comprising 376 individuals. Among these, 110 SNPs were positioned on a previously constructed linkage map containing SNPs derived from expressed sequence tag (EST) sequences. Tracing the SNP markers back to the BACs enabled the integration of the genetic and physical maps by assigning 73 BAC contigs to Atlantic salmon linkage groups. [source]

Mitochondrial genomes of the sheep blowfly, Lucilia sericata, and the secondary blowfly, Chrysomya megacephala

Abstract This paper presents complete mitochondrial genomes for the sheep blowfly, Lucilia sericata (Meigen), and the secondary blowfly, Chrysomya megacephala (Fabricius). Both L. sericata and C. megacephala had standard dipteran-type mitochondrial genome architectures and lengths of 15 945 bp and 15 831 bp, respectively. Additionally, C. megacephala possessed a tRNA duplication either side of the D-loop, as previously reported in another Chrysomya species, C. putoria; this duplication appears to be synapomorphic for the genus Chrysomya. As in other insect mitochondrial genomes, base compositions had a high AT content, with both genomes more than 76% AT-rich. [source]