Molecular Biology and Biochemistry, Department of

Receive updates for this collection

Genomic Organization and Evolution of the Atlantic salmon Hemoglobin Repertoire

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploidstate. Given the genome duplication and extensive biological data available for salmonids, they are excellent modelorganisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the geneticand physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapodhemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleosthemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid speciesfor genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmentalconditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structureand organization of the Atlantic salmon a and b hemoglobin genes is of great interest.Results: We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clustersspanning the entire a and b hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomallocations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping,demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced andassembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-likegenes. This revealed that the tail-to-tail organization and alternating pattern of the a and b hemoglobin genes arewell conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobingenes, including non-Bohr b globin genes, than the genomes of other teleosts that have been sequenced.Conclusions: We suggest that the most parsimonious evolutionary path leading to the present organization of theAtlantic salmon hemoglobin genes involves the loss of a single hemoglobin gene cluster after the whole genomeduplication (WGD) at the base of the teleost radiation but prior to the salmonid-specific WGD, which thenproduced the duplicated copies seen today. We also propose that the relatively high number of hemoglobingenes as well as the presence of non-Bohr b hemoglobin genes may be due to the dynamic life history of salmonand the diverse environmental conditions that the species encounters.Data deposition: BACs S0155C07 and S0079J05 (fps135): GenBank GQ898924; BACs S0055H05 and S0014B03(fps1046): GenBank GQ898925

Document type: 
Article

Assignment of Atlantic salmon (Salmo salar) Linkage Groups to Specific Chromosomes: Conservation of Large Syntenic Blocks Corresponding to Whole Chromosome Arms in Rainbow Trout (Oncorhynchus mykiss)

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2009
Abstract: 

Background: Most teleost species, especially freshwater groups such as the Esocidae which are theclosest relatives of salmonids, have a karyotype comprising 25 pairs of acrocentric chromosomes and 48–52 chromosome arms. After the common ancestor of salmonids underwent a whole genome duplication,its karyotype would have 100 chromosome arms, and this is reflected in the modal range of 96–104 seenin extant salmonids (e.g., rainbow trout). The Atlantic salmon is an exception among the salmonids as ithas 72–74 chromosome arms and its karyotype includes 12 pairs of large acrocentric chromosomes, whichappear to be the result of tandem fusions. The purpose of this study was to integrate the Atlantic salmon'slinkage map and karyotype and to compare the chromosome map with that of rainbow trout.Results: The Atlantic salmon genetic linkage groups were assigned to specific chromosomes in theEuropean subspecies using fluorescence in situ hybridization with BAC probes containing genetic markersmapped to each linkage group. The genetic linkage groups were larger for metacentric chromosomescompared to acrocentric chromosomes of similar size. Comparison of the Atlantic salmon chromosomemap with that of rainbow trout provides strong evidence for conservation of large syntenic blocks in thesespecies, corresponding to entire chromosome arms in the rainbow trout.Conclusion: It had been suggested that some of the large acrocentric chromosomes in Atlantic salmonare the result of tandem fusions, and that the small blocks of repetitive DNA in the middle of the armsrepresent the sites of chromosome fusions. The finding that the chromosomal regions on either side ofthe blocks of repetitive DNA within the larger acrocentric chromosomes correspond to different rainbowtrout chromosome arms provides support for this hypothesis.

Document type: 
Article

Chlamydomonas fla Mutants Reveal a Link Between Deflagellation and Intraflagellar Transport

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2003
Abstract: 

Background: Cilia and flagella are often lost in anticipation of mitosis or in response to stress.There are two ways that a cell can lose its flagella: resorption or deflagellation. Deflagellationinvolves active severing of the axoneme at the base of the flagellum; this process is defective inChlamydomonas fa mutants. In contrast, resorption has been thought to occur as a consequence ofconstitutive disassembly at the tip in the absence of continued assembly, which requiresintraflagellar transport (IFT). Chlamydomonas fla mutants are unable to build and maintain flagelladue to defects in IFT.Results: fla10 cells, which are defective in kinesin-II, the anterograde IFT motor, resorb theirflagella at the restrictive temperature (33°C), as previously reported. We find that in standardmedia containing ~300 microM calcium, fla10 cells lose flagella by deflagellation at 33°C. Thistemperature-induced deflagellation of a fla mutant is not predicted by the IFT-based model forflagellar length control. Other fla mutants behave similarly, losing their flagella by deflagellationinstead of resorption, if adequate calcium is available. These data suggest a new model wherebyflagellar resorption involves active disassembly at the base of the flagellum via a mechanism withcomponents in common with the severing machinery of deflagellation. As predicted by this model,we discovered that deflagellation stimuli induce resorption if deflagellation is blocked either bymutation in a FA gene or by lack of calcium. Further support for this model comes from ourdiscovery that fla10-fa double mutants resorb their flagella more slowly than fla10 mutants.Conclusions: Deflagellation of the fla10 mutant at the restrictive temperature is indicative of anactive disassembly signal, which can manifest as either resorption or deflagellation. We proposethat when IFT is halted by either an inactivating mutation or a cellular signal, active flagellardisassembly is initiated. This active disassembly is distinct from the constitutive disassembly whichplays a role in flagellar length control.

Document type: 
Article

Characterization of the Astacin Family of Metalloproteases in C. elegans

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: Astacins are a large family of zinc metalloproteases found in bacteria and animals. They have diverseroles ranging from digestion of food to processing of extracellular matrix components. The C. elegans genomecontains an unusually large number of astacins, of which the majority have not been functionally characterized yet.Results: We analyzed the expression pattern of previously uncharacterized members of the astacin family to tryand obtain clues to potential functions. Prominent sites of expression for many members of this family are thehypodermis, the alimentary system and several specialized cells including sensory sheath and sockets cells, whichare located at openings in the body wall. We isolated mutants affecting representative members of the varioussubfamilies. Mutants in nas-5, nas-21 and nas-39 (the BMP-1/Tolloid homologue) are viable and have no apparentphenotypic defects. Mutants in nas-6 and nas-6; nas-7 double mutants are slow growing and have defects in thegrinder of the pharynx, a cuticular structure important for food processing.Conclusions: Expression data and phenotypic characterization of selected family members suggest a diversity offunctions for members of the astacin family in nematodes. In part this might be due to extracellular structuresunique to nematodes.

Document type: 
Article

Genomic Organisation Analysis of Novel Immunoglobulin-like Transcripts in Atlantic Salmon (Salmo salar) Reveals a Tightly Clustered and Multigene Family

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: Several novel immunoglobulin-like transcripts (NILTs) which have previously been identified in thesalmonid species rainbow trout (Oncorhynchus mykiss) contain either one or two extracellular Ig domains of theV-type. NILTs also possess either an immunoreceptor tyrosine-based activating motif (ITAM) or immunoreceptortyrosine-based inhibitory motifs (ITIMs) in the cytoplasmic region resulting in different signalling abilities. Here wereport for the first time the genomic organisation and structure of the multigene family of NILTs in Atlantic salmon(Salmo salar) using a BAC sequencing approach.Results: We have identified six novel Atlantic salmon NILT genes (Ssa-NILT1-6), two pseudogenes (Ssa-NILTp1 andSsa-NILTp2) and seven genes encoding putative transposable elements in one BAC covering more than 200 kbp.Ssa-NILT1, 2, 4, 5 and 6 contain one Ig domain, all having a CX3C motif, whereas Ssa-NILT3 contains two Igdomains, having a CX6C motif in Ig1 and a CX7C motif in Ig2. Atlantic salmon NILTs possess several ITIMs in thecytoplasmic region and the ITIM-bearing exons are in phase 0. A comparison of identity between the amino acidsequences of the CX3C Ig domains from NILTs varies from 77% to 96%. Ssa-NILT1, 2, 3 and 4 were all confirmed tobe expressed either by their presence in EST databases (Ssa-NILT1) or RT-PCR (Ssa-NILT2, 3, and 4) using cDNA astemplate. A survey of the repertoire of putative NILT genes in a single individual revealed three novel genes (Ssa-NILT7-9) represented by the Ig domain, which together with Ig domains from Ssa-NILT1-6 could be divided intodifferent groups based on specific motifs.Conclusions: This report reveals a tightly clustered, multigene NILT family in Atlantic salmon. By screening a highlyredundant Atlantic salmon BAC library we have identified and characterised the genomic organisation of six genesencoding NILT receptors. The genes show similar characteristics to NILTs previously identified in rainbow trout,having highly conserved cysteines in the Ig domain and several inhibitory signalling motifs in the cytoplasmicregion. In a single individual three unique NILT Ig domain sequences were discovered at the genomic DNA level,which were divided into two different groups based on a four residue motif after the third cysteine. Our resultsfrom the BAC screening and analysis on the repertoire of NILT genes in a single individual indicates that manygenes of this expanding Ig containing NILT family are still to be discovered in fish.

Document type: 
Article

Gene Structure Evolution of the Na+-Ca2+ Exchanger (NCX) Family

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2008
Abstract: 

Background: The Na+-Ca2+ exchanger (NCX) is an important regulator of cytosolic Ca2+ levels.Many of its structural features are highly conserved across a wide range of species. Invertebrateshave a single NCX gene, whereas vertebrate species have multiple NCX genes as a result of at leasttwo duplication events. To examine the molecular evolution of NCX genes and understand the roleof duplicated genes in the evolution of the vertebrate NCX gene family, we carried out phylogeneticanalyses of NCX genes and compared NCX gene structures from sequenced genomes and individualclones.Results: A single NCX in invertebrates and the protochordate Ciona, and the presence of at leastfour NCX genes in the genomes of teleosts, an amphibian, and a reptile suggest that a four membergene family arose in a basal vertebrate. Extensive examination of mammalian and avian genomesand synteny analysis argue that NCX4 may be lost in these lineages. Duplicates for NCX1, NCX2,and NCX4 were found in all sequenced teleost genomes. The presence of seven genes encodingNCX homologs may provide teleosts with the functional specialization analogous to the alternatesplicing strategy seen with the three NCX mammalian homologs.Conclusion: We have demonstrated that NCX4 is present in teleost, amphibian and reptilianspecies but has been secondarily and independently lost in mammals and birds. Comparative studieson conserved vertebrate homologs have provided a possible evolutionary route taken by geneduplicates subfunctionalization by minimizing homolog number.

Document type: 
Article

OrthoClusterDB: An Online Platform for Synteny Blocks

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2009
Abstract: 

Background: The recent availability of an expanding collection of genome sequences driven bytechnological advances has facilitated comparative genomics and in particular the identification ofsynteny among multiple genomes. However, the development of effective and easy-to-use methodsfor identifying such conserved gene clusters among multiple genomes–synteny blocks–as well asdatabases, which host synteny blocks from various groups of species (especially eukaryotes) andalso allow users to run synteny-identification programs, lags behind.Descriptions: OrthoClusterDB is a new online platform for the identification and visualization ofsynteny blocks. OrthoClusterDB consists of two key web pages: Run OrthoCluster and View Synteny.The Run OrthoCluster page serves as web front-end to OrthoCluster, a recently developed programfor synteny block detection. Run OrthoCluster offers full control over the functionalities ofOrthoCluster, such as specifying synteny block size, considering order and strandedness of geneswithin synteny blocks, including or excluding nested synteny blocks, handling one-to-manyorthologous relationships, and comparing multiple genomes. In contrast, the View Synteny page givesaccess to perfect and imperfect synteny blocks precomputed for a large number of genomes,without the need for users to retrieve and format input data. Additionally, genes are cross-linkedwith public databases for effective browsing. For both Run OrthoCluster and View Synteny, identifiedsynteny blocks can be browsed at the whole genome, chromosome, and individual gene level.OrthoClusterDB is freely accessible.Conclusion: We have developed an online system for the identification and visualization ofsynteny blocks among multiple genomes. The system is freely available at http://genome.sfu.ca/orthoclusterdb/.

Document type: 
Article

Identifying Novel Genes in C. elegans Using SAGE Tags

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

AbstractBackground: Despite extensive efforts devoted to predicting protein-coding genes in genome sequences, manybona fide genes have not been found and many existing gene models are not accurate in all sequenced eukaryotegenomes. This situation is partly explained by the fact that gene prediction programs have been developed basedon our incomplete understanding of gene feature information such as splicing and promoter characteristics.Additionally, full-length cDNAs of many genes and their isoforms are hard to obtain due to their low level or rareexpression. In order to obtain full-length sequences of all protein-coding genes, alternative approaches arerequired.Results: In this project, we have developed a method of reconstructing full-length cDNA sequences based onshort expressed sequence tags which is called sequence tag-based amplification of cDNA ends (STACE). Expressedtags are used as anchors for retrieving full-length transcripts in two rounds of PCR amplification. We havedemonstrated the application of STACE in reconstructing full-length cDNA sequences using expressed tags minedin an array of serial analysis of gene expression (SAGE) of C. elegans cDNA libraries. We have successfully appliedSTACE to recover sequence information for 12 genes, for two of which we found isoforms. STACE was used tosuccessfully recover full-length cDNA sequences for seven of these genes.Conclusions: The STACE method can be used to effectively reconstruct full-length cDNA sequences of genes thatare under-represented in cDNA sequencing projects and have been missed by existing gene prediction methods,but their existence has been suggested by short sequence tags such as SAGE tags.

Document type: 
Article

A Linkage Map of the Atlantic Salmon (Salmo salar) Based on EST-Derived SNP mMarkers

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2008
Abstract: 

Background: The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, thespecies displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with fullgenome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it isimportant to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundredsingle nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage mapscontaining SNP and microsatellite markers. We also investigated further the distribution of male and femalerecombination events across the genome, and estimated levels of LD between pairs of markers.Results: The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which weresuccessfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicatingthat there is little overlap between regions in which male and female crossovers occur. The female map is likely to haveclose to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regionswhere male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodalfashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence ofrecent admixture in the population, the population being a 'synthetic' breeding population with contributions fromseveral distinct rivers. Levels of r2 dropped to half its maximum value (above baseline) within 15 cM, and were higherthan 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM.Conclusion: The linkage map presented here is an important resource for genetic, comparative, and physical mappingof the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the malemap length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparentlysmall physical regions where male crossovers occur. 'Useful LD' was found at inter-marker distances less than 5 cM.

Document type: 
Article