The Characterization of Repetitive DNA Elements in the Genome of Atlantic Salmon (Salmo Salar)
| Author | : John L. Goodier |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 1994 |
| Genre | : Atlantic salmon |
| ISBN | : |
The Characterization Of Repetitive Dna Elements In The Genome Of Atlantic Salmon Salmo Salar
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Repetitive Landscape of the Atlantic Salmon Genome
| Author | : Siemon Hian Siem Ng |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2006 |
| Genre | : Atlantic salmon |
| ISBN | : |
The duplication of genes and genomes is considered a major force in evolution. Ohno, in 1970, theorized that with two copies of the genome, one copy would be under normal evolutionary constraints while the other copy could serve as raw material for evolution. Salmonids are a classical example of species containing duplicated genomes, and they offer an opportunity to investigate how such genomes undergo reorganization as they attain a stable diploid state. Repetitive elements play an important role in genome reorganization. Therefore, I investigated the repeat structure and organization of the Atlantic salmon genome. An analysis of the fingerprinted CHORI-214 BACs classified the singletons, or those that contained few restriction sites, into three categories of repetitive structures. The first group contains histone genes in a tandemly repeating cluster of H4 - H2B - H1 - H2A - H3. A second group contains the ribosomal DNA (rDNA) cistron. Intriguingly, fluorescent in situ hybridization (FISH) analysis indicated that one of each of the duplicated histone and rDNA clusters was lost or rearranged in the genome. The remaining group of BACs contains novel repetitive sequences and tRNA clusters. The Atlantic salmon EST libraries and BAC-end sequences were data-mined for simple sequence repeats (SSRs) and 2,497 SSRs were recovered. 154 SSR loci gave clean PCR amplicons and 94 produced polymorphic banding patterns with eleven of the EST-SSRs indicating duplicated loci. These loci were mapped on the Atlantic salmon linkage map. Novel repetitive elements were detected in the sequences of Atlantic salmon BACs and ESTs. Using computational tools for data-mining, repetitive elements were identified and classified based on sequence similarity to other known repetitive elements such as SINES, LINEs and retrotransposons. A repeat database that can be used to mask repetitive elements, is now available for the Atlantic salmon genome. A website was developed to host the Atlantic salmon linkage and physical maps, correlating them based on marker hybridization. A BAC annotation pipeline analyzes the BAC sequences for ORFs, transcript similarity and repetitive elements. Information generated from sequence annotation, microsatellite development and repetitive element identification provides essential resources for investigating salmonid genomes.
The Fate of Duplicated Regions of the Atlantic Salmon (Salmo Salar) Genome [microform]
| Author | : Leslie Mitchell |
| Publisher | : Library and Archives Canada = Bibliothèque et Archives Canada |
| Total Pages | : 264 |
| Release | : 2004 |
| Genre | : Atlantic salmon |
| ISBN | : 9780494035382 |
Gene and genome duplications have played a major role in vertebrate evolution. Salmonids provide a useful resource for studying the consequences of these events as their common ancestor underwent a genome duplication between 25 and 120 miliion years ago. To understand how a genome reorganizes itself to cope with duplicated chromosomes and the importance of gene duplications for evolution and adaptation, homeologous regions of the Atlantic salmon genome were identified and studied within a large insert, genomic BAC library; these BACs contain the metallothionen event. A BAC from each region was subsequently shotgun subcloned and sequenced. Sequence analysis revealed the presence of 10 genes, retaining their collinearity between the BAcs, although pseudogenization events have occurred in one of the duplicate loci in two instances. Comparative genomic analysis revealed the existence of extraordinary conservation of syntney over time.
Some Aspects of Chromosome Structure and Function
| Author | : R.C. Sobti |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 239 |
| Release | : 2012-12-06 |
| Genre | : Science |
| ISBN | : 9401003343 |
It was at the end of the 19th century that a Swiss biologist, Karl Nageli first proposed the existence of hereditary organelles that carried information from parent to offspring. Ensuing decades experienced vigorous studies that led to the development of discovery that chromosomes are indeed the carriers of genetic information. Subsequent studies, especially by Morgan and Bridges, established unequivocally the chromosome theory of inheritance. Today, the structure of chromosome is well established. At the physical level, eukaryotic chromosomes are composed of a single, linear, double helix of DNA. The elementary helical structure involves nucleosomes, comprised of histones around which the DNA is wrapped. A hierarchy of higher order of chromosomal architecture may possibly be responsible for the regulation of gene helical structures expression. The localized condensations of DNA constitute chromomeres. Uncoiled structures sometimes extending from chromomeres, which form loops, is the result of discontinuities in the regular coiling of the DNA in the chromosome.
Evolutionary Genetics of Fishes
| Author | : Bruce Turner |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 651 |
| Release | : 2012-12-06 |
| Genre | : Science |
| ISBN | : 1468446525 |
It is my hope that this collection of reviews can be profitably read by all who are interested in evolutionary biology. However, I would like to specifically target it for two disparate groups of biologists seldom men tioned in the same sentence, classical ichthyologists and molecular biologists. Since classical times, and perhaps even before, ichthyologists have stood in awe at the tremendous diversity of fishes. The bulk of effort in the field has always been directed toward understanding this diversity, i. e. , extracting from it a coherent picture of evolutionary processes and lineages. This effort has, in turn, always been overwhelmingly based upon morphological comparisons. The practical advantages of such compari sons, especially the ease with which morphological data can be had from preserved museum specimens, are manifold. But considered objectively (outside its context of "tradition"), morphological analysis alone is a poor tool for probing evolutionary processes or elucidating relationships. The concepts of "relationship" and of "evolution" are inherently genetic ones, and the genetic bases of morphological traits are seldom known in detail and frequently unknown entirely. Earlier in this century, several workers, notably Gordon, Kosswig, Schmidt, and, in his salad years, Carl Hubbs, pioneered the application of genetic techniques and modes of reasoning to ichthyology. While certain that most contemporary ichth yologists are familiar with this body of work, I am almost equally certain that few of them regard it as pertinent to their own efforts.
Fish Cytogenetics
| Author | : E Pisano |
| Publisher | : CRC Press |
| Total Pages | : 534 |
| Release | : 2007-01-03 |
| Genre | : Science |
| ISBN | : 1000713407 |
In the past 20 years, fish cytogenetics has become an essential tool in fields as diverse as systematics and evolution, conservation, aquaculture and more recently, genomics. This book is organized in four sections (systematics and evolution; biodiversity conservation; stock assessment and aquaculture; genomics) covering the major fields of present
Isolation and Characterization of Atlantic Salmon, Salmo Salar, Olfactory Receptor Genes
| Author | : Jill Elizabeth Thorpe |
| Publisher | : |
| Total Pages | : 94 |
| Release | : 2000 |
| Genre | : Atlantic salmon |
| ISBN | : |
Studies in Viral Ecology, Volume 2
| Author | : Christon J. Hurst |
| Publisher | : John Wiley & Sons |
| Total Pages | : 444 |
| Release | : 2011-06-20 |
| Genre | : Science |
| ISBN | : 1118025695 |
This book explains the ecology of viruses by examining their interactive dynamics with their hosting species (in this volume, in animals), including the types of transmission cycles that viruses have evolved encompassing principal and alternate hosts, vehicles and vectoring species. Examining virology from an organismal biology approach and focusing on the concept that viral infections represent areas of overlap in the ecologies of the involved species, Viral Ecology is essential for students and professionals who either may be non-virologists or virologists whose previous familiarity has been very specialized.
Evolution and Characterization of the Fatty Acid-binding Proteins (fabps) in Atlantic Salmon (Salmo Salar)
| Author | : Yuk Yin Lai |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2012 |
| Genre | : Atlantic salmon |
| ISBN | : |
It is suggested that gene or genome duplication is the driving force in evolution that leads to speciation. Two models, the classical model and the duplication- degeneration-complementation (DDC) model, have been proposed on the fates of gene duplicates resulting from either a gene or a genome duplication event. The classical model suggests that one of the gene duplicates might result in loss of function (non- functionalization) or gain of a new function (neo-functionalization) depending on whether the accumulated mutations over the years are deleterious or beneficial to the organism. In the DDC model, it is proposed that each of the gene duplicates might accumulate different deleterious mutations in the regulatory region of the gene, such that these genes partition the ancestral gene function (sub-functionalization). Combinations of the phylogenetic analysis of many gene families support that salmonids have undergone two additional whole genome duplications compared to the mammals, one occurred in the common ancestors of teleosts and another happened in the common ancestor of salmonids approximately 25-120 million years ago. In this thesis, the evolution of the fatty acid-binding protein (fabp) family in fish and salmonids was examined. I have characterized eighteen unique fabp genes in Atlantic salmon. These include the seven fabp sub-families described previously in fish. Phylogenetic analyses and conservation of synteny support the two whole genome duplication events in the common ancestors of teleosts and salmonids and indicate when gene losses occurred. Genetic mapping of fabp gene duplicates to homeologous chromosomes in Atlantic salmon also support that they arose by the 4R genome duplication. I also searched for the signatures of neo-functionalization and sub-functionalization by calculating dN/dS ratios, examining the nature of amino acid substitutions and expression patterns, and suggested the fates of fabp gene duplicates in Atlantic salmon. Overall, the findings of this project provide insight into the evolutionary processes at play in salmonid genomes.
