Comparative Study of Genome Divergence in Salmonids with Various Rates of Genetic Isolation (original) (raw)
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A salmonid EST genomic study: genes, duplications, phylogeny and microarrays
BMC Genomics, 2008
Background: Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish.
Preliminary studies on evolutionary of genetic markers in the salmonid species
This study deals with evolutionary genetics of salmonids populations, with the special emphasis on the roles of migration, random genetic drift, mutation, and natural selection affecting the patterns of molecular variation across contemporary and historical time scales. Studies of nuclear DNA and mitochondrial genomic variation supported the hypothesis that salmonid populations differ from the geographical regions, indicating for genetic diversity between populations. This study were used some genes for nuclear DNA genomic and mitochondrial DNA genomic for evaluation of the rate diversity. We suggest that the region of geographically is important to rate of diversity between and within populations. Were used marker genetic techniques such as the microsatellites markers, SNPs, RFLP, and some genes from mitochondrial genomic that engaged on the rate of diversity in populations of salmonids. Between and within population of S. salar and S. trutta were found single mutation by SNPs technique. RFLP analysis by nuclear DNA genomic such as microsatellites and growth hormone gene and also mitochondrial DNA genomic as cytochrome b and 12S rRNA gene and markers also showed the low variation between and within salmonids populations
Gene, 2000
This study examines sequence divergence in three spacer regions of the ribosomal DNA (rDNA) cistron, to test the hypothesis of unequal mutation rates. Portions of two transcribed spacers (ITS-1 and 5∞ ETS) and the non-transcribed spacer (NTS ) or intergenic spacer (IGS ) formed the basis of comparative analyses. Sequence divergence was measured both within an individual lake trout (Salvelinus namaycush) and among several related salmonid species ( lake trout; brook trout, Salvelinus fontinalis; Arctic char, Salvelinus alpinus; Atlantic salmon, Salmo salar; and brown trout, Salmo trutta). Despite major differences in the length of the rDNA cistron within individual lake trout, minimal sequence difference was detected among cistrons. Interspecies comparisons found that molecular variation in the rDNA spacers did not conform to the predicted pattern of evolution (ITS spacers<ETS spacers<IGS). Specifically, the IGS contains a region that appears to be as highly, or more conserved than the ITS-1.
Genome, 1993
BENTZEN, P., AND WRIGHT, J. M. 1993. Nucleotide sequence and evolutionary conservation of a minisatellite variable number tandem repeat cloned from Atlantic salmon, Salmo salar. Genome, 36: 271-277. We describe the nucleotide sequence, extent of polymorphism, and evolutionary conservation of a minisatellite cloned from a fish, Atlantic salmon (Salmo salar). The Ssal minisatellite contains a 16-bp repeat exhibiting partial sequence identity to bird and mammal minisatellites but most closely resembling an insect minisatellite (81% sequence identity). The Ssal locus exhibits a minimum of three to seven alleles per population in three eastern North American salmon populations. A probe based on the nonrepetitive 5' flank of Ssal detected a polymorphic locus in a variety of salmoid species, suggesting that this locus has persisted in its polymorphic state for >25 million years. Multiple polymorphic bands detected by the same probe suggest the presence in salmonid genomes of additional minisatellite loci that are related to Ssal either through the tetraploidization of the salmonid genome or some other mechanism of gene duplication.
BMC Genetics, 2011
Background: Salmonids are regarded as 4R derivative species, having experienced 4 whole genome duplication events in their ancestry. Many duplicated chromosome regions still share extensive homology with one another which is maintained primarily through male-based homeologous chromosome pairings during meiosis. The formation of quadrivalents during meiosis leads to pseudolinkage. This phenomenon is more prevalent within 5 of the 12 ancestral teleost linkage groups in salmonids. Results: We constructed a genetic linkage map for brook charr and used this in combination with the genetic map from Arctic charr, to make comparisons with the genetic map of rainbow trout. Although not all chromosome arms are currently mapped, some homologous chromosome rearrangements were evident between Arctic charr and brook charr. Notably, 10 chromosome arms in brook charr representing 5 metacentric chromosomes in Arctic charr have undergone rearrangements. Three metacentrics have one arm translocated and fused with another chromosome arm in brook charr to a make a new metacentrics while two metacentrics are represented by 4 acrocentric pairs in brook charr. In two cases (i.e., BC-4 and BC-16), an apparent polymorphism was observed with the identification of both a putative metacentric structure (similar to metacentric AC-4 = BC-4 and a joining of acrocentric AC-16 + one arm of AC-28 = BC-16), as well as two separate acrocentric linkage groups evident in the mapping parents. Forty-six of the expected 50 karyotypic arms could be inter-generically assigned. SEX in brook charr (BC-4) was localized to the same homologous linkage group region as in Arctic charr (AC-4). The homeologous affinities detected in the two charr species facilitated the identification of 20 (expected number = 25) shared syntenic regions with rainbow trout, although it is likely that some of these regions were partial or overlapping arm regions. Conclusions: Inter-generic comparisons among 2 species of charr (genus Salvelinus) and a trout (genus Oncorhynchus) have identified that linkage group arm arrangements are largely retained among these species. Previous studies have revealed that up to 7 regions of high duplicate marker retention occur between Salmo species (i.e., Atlantic salmon and brown trout) and rainbow trout, with 5 of these regions exhibiting higher levels of pseudolinkage. Pseudolinkage was detected in the charr species (i.e., BC-1/21, AC-12/27, AC-6/23, = RT-2p/29q, RT-12p/16p, and RT-27p/31p, respectively) consistent with three of the five 'salmonid-specific' pseudolinkage regions. Chromosome arms with the highest number of duplicated markers in rainbow trout are the linkage group arms with the highest retention of duplicated markers in both charr species.
Journal of Molecular Evolution, 1996
Short interspersed repetitive elements (SINEs), known as the HpaI family, are present in the genomes of all salmonid species (Kido et al., Proc. Natl, Acad. Sci. USA 1991, 88: 2326-2330). Recently, we showed that the retropositional efficiency of the SINE family in the lineage of chum sahnon is extraordinarily high in comparison with that in other salmonid lineages (Takasaki et al., Proc. Natl. Acad. Sci. USA 1994, 91: 10153-10157). To investigate the reason for this high efficiency, we searched for members of the HpaI SINE family that have been amplified species-specifically in pink salmon. Since the efficiency of the species-specific amplification in pink salmon is not high and since other members of the same subfamily of SINEs were also amplified species-specifically in pink salmon, the actual sequence of this subfamily might not be the cause of the high retropositional efficiency of SINEs in chum salmon. Rather, it appears that a highly dominant source gene for the subfamily may have been newly created by retroposition, and some aspect of the local environment around the site of retroposition may have been responsible for the creation of this dominant source gene in chum salmon. Furthermore, a total of 11 sequences of HpaI SINEs that have been amplified species-specifically in Correspondence ~o: N. Okada three salmon lineages was compiled and characterized. Judging from the distribution of members of the samesequence subfamily of SINEs in different lineages and from the distribution of the different-sequence subfamilies in the same lineage, we have concluded that multiple dispersed loci are responsible for the amplification of SINEs. We also discuss the additional possibility of horizontal transmission of SINEs between species. The availability of the sets of primers used for the detection of the species-specific amplifications of the SINEs provides a convenient and reliable method for identification of these salmonid species.
Isolation and characterization of salmonid telomeric and centromeric satellite DNA sequences
Genetica, 2007
Satellite DNA clones with a 37 bp repeat unit were obtained from BglII-digested genomic DNA of masu salmon (Oncorhynchus masou) and chum salmon (O. keta). Fluorescence in situ hybridization (FISH) analysis with the isolated clones as a probe showed that these repetitive sequences were localized in the telomeric regions of chromosomes in both species. Southern and dot blot analyses suggested conservation of homologous sequences with similar repeat unit in other salmonids including the species of the genus Oncorhynchus and Salvelinus, but lack or scarcity of such sequences in the genus Hucho and Salmo. Similarly, polymerase chain reaction (PCR)-based cloning of satellite DNA referring to a reported Rainbow trout (O. mykiss) centromeric sequence was successful for the Oncorhynchus, Salvelinus and Hucho species. The obtained satellite DNA clones were localized with FISH in the centromeric regions of chromosomes of the species from these three genera. Although PCR cloning of the centromeric satellite DNA was failed in the Salmo species due to some base changes in the priming sites, dot blot hybridization analysis suggested conservation of homologous satellite DNA in the genus Salmo as in the other three genera. In the neighbor-joining tree of cloned centromeric satellite DNA sequences, the genus Oncorhynchus and Salvelinus formed adjacent clades, and the clade of the genus Hucho included the reported centromeric sequence of the genus Salmo. Conservation pattern and molecular phylogeny of the telomeric and centromeric satellite DNA sequences isolated herein support a close phylogenetic relationship between the genus Oncorhynchus and Salvelinus and between the Salmo and Hucho.
Journal of Fish Biology, 1989
The increasing exploitation of Atlantic salmon as a food source and sport fish demands a better understanding of salmon genetics and the dynamics of Atlantic salmon populations. Surveys of salmon populations for protein electrophoretic variation reveal that the average heterozygosity in Salmo sulur is low and that four gene loci account for more than 95% of the total electrophoretically detectable variation. Populations that have been studied by this means fall into one of three groups: Western Atlantic, Eastern Atlantic or Baltic. However, biochemical genetics involving starch gel electrophoresis cannot be used routinely to identify the continent of origin of an Atlantic salmon, let alone its native river. The mitochondrial genome can be used to identify North American or European salmon with the aid of restriction endonucleases that have six base pair recognition sites. Restriction endonucleases that recognize four base pairs appear to be able to identify salmon from a particular river system. There has been a move from protein variation to mitochondria1 DNA variation and this will inevitably lead to more extensive studies on the nuclear genome. Chromosomal studies suggest differences between salmon from Europe and North America but these have been hampered by lack of good banding procedures. Preliminary studies using cloned segments of salmonid genomes suggest that repeated sequences such as the genes for ribosomal RNA will be most useful for identifying specific stocks of Atlantic salmon. The need for continued genetic studies on the Atlantic salmon and the relevance and importance of the results of this research for stock identification, enhancement programmes, aquaculture and basic science are discussed.
THE 4R GENOME DUPLICATION IN SALMONINE FISHES: INSIGHTS FROM CONSERVED NON-CODING ELEMENTS
2008
Gene and genome duplications are important processes in evolution. Salmonids are ideal animal model systems in which to study these processes, as they originated from a tetraploid ancestor. Conserved non-coding elements (CNEs) are of interest because of their highly conserved DNA consensus motifs spanning lineages as diverse and divergent as humans and fish. The main goal of this study is to test CNEs as a tool to study genome duplications and to revisit the “4R” hypothesis and phylogeny of Salmonine fishes (Salmonidae) Salmo salar, Salvelinus alpinus and Oncorhynchus mykiss through the study of copy number and nucleotide variation in six pairs of CNEs. Allele numbers for most CNE sequence pairs are consistent with the 4R hypothesis, as is the symmetric phylogenetic topology shown by some CNE pairs; the estimated date of CNE duplication is consistent with the only reported range of 25-100Mya. However, the phylogenetic relationships within Salmoninae remain unresolved.