ARS | Publication request: Large homogeneous genome regions (Isochores) in soybean (Glycine max (L.) Merr.)

Submitted to: Frontiers in Plant Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 14, 2012
Publication Date: May 5, 2012
Citation: Woody, J.L., Beavis, W., Shoemaker, R.C. 2012. Large homogeneous genome regions (Isochores) in soybean (Glycine max (L.) Merr.). Frontiers in Plant Genetics and Genomics. 3:98 DOI:10.3389/fgene.2012.00098.

Interpretive Summary: The cost of decoding genomes of living organisms has dropped precipitously in recent years. This has resulted in a huge increase in the hereditary sequences of complete genomes and the genetic landscape of entire genomes is now available for study. Although the genetic terrain can now be mapped, the functional characterization of the landscape is mostly still a mystery. In this paper the authors identified and characterized regions of the soybean genome that consist of highly similar DNA composition called isochores. The authors identified four distinct classes of these isochores and characterized the genetic composition of each. During this process two surprises were found. First, most of the genes found in the isochores were not in the family in which they were expected which is different from most other species. Secondly, genes involved in cellular energy steps were over represented in the isochors and the reason for this is unknown. These findings are important to understanding the composition and evolution of plant genomes and may play an important role in targeting transgenes for crop improvement.

Technical Abstract: The landscape of plant genomes, while slowly being characterized and defined, is still composed primarily of regions of undefined function. Many eukaryotic genomes contain isochore regions, mosaics of homogeneous GC content that can abruptly change from one neighboring isochore to the next. Isochore are broken into families which are characterized by their GC levels. We identified 4,339 compositionally distinct domains and 331 of these were identified as Long Homogeneous Genome Regions (LHGRs). We then assigned these to four families based on finite mixture models of GC content and characterized each family with respect to exon length, gene content and transposable elements. The LHGR pattern of soybeans is unique in that while the majority of the genes within LHGRs are found within a single LHGR family with a narrow GC-range (Family B), that family is not the highest in GC content as seen in vertebrates and invertebrates. Instead Family B has a mean GC content of 35%. The range of GC content for all LHGRs is 16-59% GC which is a larger range than what is typical of vertebrates. This is the first study in which LHGRs have been identified in soybeans and the functions of the genes within the LHGRs have been analyzed.