Abstract
The area of plant and animal genomics covers the entire suite of issues in biology because it aims to determine the structure and function of genetic material. Although specific issues define research advances at an organism level, it is evident that many of the fundamental features of genome structure and the translation of encoded information to function share common ground. The Plant and Animal Genome (PAG) conference held in San Diego (California), in January each year provides an overview across all organisms at the genome level, and often it is evident that investments in the human area provide leadership, applications, and discoveries for researchers studying other organisms. This mini-review utilizes the plenary lectures as a basis for summarizing the trends in the genome-level studies of organisms, and the lectures include presentations by Ewan Birney (EBI, UK), Eric Green (NIH, USA), John Butler (NIST, USA), Elaine Mardis (Washington, USA), Caroline Dean (John Innes Centre, UK), Trudy Mackay (NC State University, USA), Sue Wessler (UC Riverside, USA), and Patrick Wincker (Genoscope, France). The work reviewed is based on published papers. Where unpublished information is cited, permission to include the information in this manuscript was obtained from the presenters.
Highlights
The analysis of genomes has been accelerated by advances in new technologies, such as the high-throughput sequencing of whole genomes, which provides an extensive view of the gene space of organisms
The need for long-range mapping of sequences in complex genomes arises because of the need to deal with the ambiguities generated by the presence of extensive tracts of retro-transposable elements
John Butler noted that the mini-satellite marker systems have stood the test of time and the high levels of polymorphisms continue to contribute to the DNA profile database that assays a set of 15 simple tandem repeats (STRs)
Summary
The analysis of genomes has been accelerated by advances in new technologies, such as the high-throughput sequencing of whole genomes, which provides an extensive view of the gene space of organisms. The high levels of recombination at these repetitive sequence loci lead to unequal crossing-over and to variation in repeat numbers and levels of polymorphisms that far exceed variation due to mutation alone In his plenary lecture, John Butler noted that the mini-satellite marker systems have stood the test of time and the high levels of polymorphisms continue to contribute to the DNA profile database that assays a set of 15 simple tandem repeats (STRs). The database allows genes of interest to be grouped with genes for which drugs have already been developed Another important output from proteome-level information is that it provides the capacity to identify unusual antigens that are unique to cells throughout the tumor and bind to MHC molecules. The sequences of these antigens can be used to design peptides for raising vaccines that target specific tumors (Waldmann 2003; Restifo et al 2012a, b)
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