Lyzing two paralogous genes (e.g. gh1 and gh2) and doing
Lyzing two paralogous genes (e.g. gh1 and gh2) and doing so in two species (which have been separated for approximately 20 MY; ), identification of common conserved regions with presumed broad functional importance can be achieved. Further, regions which are found to be conserved only between species in one paralogue type may be important for differential regulatory control between the paralogues, while differences between species within a single paralogue type may help identify regions not important to PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26567541 regulation. Regions which are conserved between paralogues in only one species are candidates for regions which have undergone gene conversion subsequent to divergence between the two species. While gene conversion does not appear to haveoccurred at salmonid GH loci when examined at the gene level , an analysis of PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26268403 gene conversion has not been examined at larger scales now possible with genomic analyses. Understanding these sequence relationships has important practical ramifications since complete genomic resources are being developed for Atlantic salmon. It is important to determine the degree of conservation of this information with other important salmonid species such as Chinook salmon for extrapolation of emerging genomic information from one species to another. Bacterial artificial chromosomes (BACs) containing gh1 and gh2 from both Atlantic and Chinook salmon were assembled, annotated, and compared to each other in their coding, intronic, regulatory, and flanking regions. A core proximal promoter for transcription of both gh1 and gh2 is conserved between the two species of salmon. A 1600 bp insertion of a Tc1-like DNA transposon sequence was found within the promoter region of both gh2 genes, but not in the promoter of the gh1 genes. Furthermore, a Polinton-1 transposon is inserted in only the promoter for Chinook salmon GH1. Other differences within the promoters and intronic and 3'-flanking regions of the four genes provide evidence that supports the notion that they are regulated differently and thus may possess different functions. Intriguingly, Chinook salmon GH1 has undergone more than twice as many changes than any of the other GHs; changes not reflected in the surrounding noncoding DNA.ResultsConfirmation that the Atlantic salmon BACs we isolated were gh-containing BACs was performed by comparing HindIII-digested BAC fragment profiles to profiles on the internet Contig Explorer version 3.4 (iCE 3.4) database . The gene for the skeletal muscle sodium channel (scn) was also identified by PCR for each isolated BAC, suggesting that each BAC contained the 5'-region upstream of each gh gene. gh type (gh1 vs. gh2) was determined for BACs in both Atlantic and Chinook salmon by paralogue-specific PCR.BAC and GH comparisons Atlantic salmon (AS) and Chinook salmon (CS)gh loci were analyzed using DIGIT , which identified the presence, location, and direction of putative genes on each BAC. Each of these putative genes were assessed by BLASTX  to protein databases. BACs containing the gh genes also bore the genes for scn oriented in the same direction (Figure 1A). The sequences of the genes for interferon alpha-1 (ifna1), myosin alkali light chain (mlc) and microtubule associated protein Tau (mapt) were also identified, and found in opposite orientations relative to gh1 and gh2 (Figure 1A). The Chinook salmon gh1 and gh2containing BACs are PluriSIn 1 similarly organized.Page 2 of(page number not for citation purposes)BMC Genomics.
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