Take our Survey

Reference: Fielman KT and Marsh AG (2005) Genome complexity and repetitive DNA in metazoans from extreme marine environments. Gene 362:98-108

Reference Help

Abstract


As genomics converges with ecology and evolution to identify the fundamental linkages between genome structure and function, genome and transcriptome complexity will need to be measured in organisms from more diverse habitats, most often in the absence of complete sequence data. Here, we describe the complexity of ten genomes measured by a novel, high-throughput fluorescence-based kinetic hybridization assay. We applied the Shannon information index, H, and a related, fluorescence-adjusted index, H(f), as unique metrics of the hybridization kinetics to complement the conventional rate constant, k. A strong, positive relationship was present between H(f), and the repetitive DNA content of five eukaryotic genomes previously determined by Cot kinetic analyses (Onchorynchus keta, Ilyanassa obsoleta, Bos taurus, Limulus polyphemus, Saccharyomyces cerevisiae). This relationship was used to characterize the complexity of previously unstudied genomic samples in five metazoan taxa from three marine environments, including deep-sea hydrothermal vents (Alvinella pompejana), the temperate subtidal (Streblospio benedicti), and Antarctic coastal bays (Sterechinus neumayeri, Odontaster validus, Tritonia antarctica). Contrary to the predictions of nucleotypic theory, Antarctic invertebrates consistently had the lowest quantities of repetitive DNA in conjunction with low metabolic rates and highly protracted rates of cell division and larval development. Conversely, hydrothermal vent species with rapid cell division and growth do not have significantly different genome sizes or particularly low amounts of repetitive DNA as compared to non-vent, deep-sea taxa. Furthermore, there appears to be a positive correlation between the temperature at which the most abundant repetitive sequence classes anneal and habitat thermal stability. Thus, our study reveals a potential shift in repetitive sequence representation between these extreme environments that may be related to genome function in species living at these different thermal regimes.

Reference Type
Journal Article | Research Support, Non-U.S. Gov't | Research Support, U.S. Gov't, Non-P.H.S.
Authors
Fielman KT, Marsh AG
Primary Lit For
Additional Lit For
Review For

Interaction Annotations


Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.

Interactor Interactor Type Assay Annotation Action Modification Phenotype Source Reference

Gene Ontology Annotations


Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

Gene Gene Ontology Term Qualifier Aspect Method Evidence Source Assigned On Annotation Extension Reference

Phenotype Annotations


Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details.

Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

Regulation Annotations


Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, SPELL, or YeastMine.

Regulator Target Experiment Assay Construct Conditions Strain Background Reference