Abstract
Allozyme variation in Atlantic cod hemoglobins shows various signs of natural selection. We report a genomic exploration of globin genes in this non-model organism. Applying a PCR based strategy with a strict criterion of phylogenetically informative sites we estimate the number of linked β and α globin genes. We estimate PCR error rate by PCR of cloned DNA and recloning and by analysis of singleton variable sites among clones. Based on the error rate we exclude variable sites so that the remaining variation meets successively stricter criteria of doubleton and triplet variable site. Applying these criteria we find ten clusters of linked β/α globin genes in the genome of Atlantic cod. Six variable amino acid changes in both genes were found in linkage disequilibrium with silent nucleotide substitutions. A phylogenetic tree, based on our strictly phylogenetically informative sites among 57 clones from 19 individuals, is split into two major branches by an amino acid change in a β gene. This change is supported by extensive linkage disequilibrium between the amino acid change and numerous other phylogenetically informative silent nucleotide sites. The different gene sets in the genome may represent different loci encoding different globins and/or allelic variation at some loci.
| Original language | English |
|---|---|
| Pages (from-to) | 169-181 |
| Number of pages | 13 |
| Journal | Marine Genomics |
| Volume | 2 |
| Issue number | 3-4 |
| DOIs | |
| Publication status | Published - Sept 2009 |
Bibliographical note
Funding Information: We thank Professor Jarle Mork at NTNU in Trondheim for tissue samples of genotyped individuals. The work was supported by a grant from the Icelandic Research Fund . We thank Dr. Petur Henry Petersen and anonymous reviewers for critical comments on the manuscript.Other keywords
- Genomic exploration
- Hemoglobin
- Hemoglobin variability
- Linkage disequilibrium
- PCR errors
- β/α globin genes