Balakirev ES et al. (2016), DNA polymorphism and selection at the bindin lo...

ECB-ART-44685

BMC Genet 2016 May 12;171:66. doi: 10.1186/s12863-016-0374-5.

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DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea).

Balakirev ES , Anisimova M , Pavlyuchkov VA , Ayala FJ .

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BACKGROUND: The sperm gene bindin encodes a gamete recognition protein, which plays an important role in conspecific fertilization and reproductive isolation of sea urchins. Molecular evolution of the gene has been extensively investigated with the attention focused on the protein coding regions. Intron evolution has been investigated to a much lesser extent. We have studied nucleotide variability in the complete bindin locus, including two exons and one intron, in the sea urchin Strongylocentrotus intermedius represented by two morphological forms. We have also analyzed all available bindin sequences for two other sea urchin species, S. pallidus and S. droebachiensis. RESULTS: The results show that the bindin sequences from the two forms of S. intermedius are intermingled with no evidence of genetic divergence; however, the forms exhibit slightly different patterns in bindin variability. The level of the bindin nucleotide diversity is close for S. intermedius and S. droebachiensis, but noticeably higher for S. pallidus. The distribution of variability is non-uniform along the gene; however there are striking similarities among the species, indicating similar evolutionary trends in this gene engaged in reproductive function. The patterns of nucleotide variability and divergence are radically different in the bindin coding and intron regions. Positive selection is detected in the bindin coding region. The neutrality tests as well as the maximum likelihood approaches suggest the action of diversifying selection in the bindin intron. CONCLUSIONS: Significant deviation from neutrality has been detected in the bindin coding region and suggested in the intron, indicating the possible functional importance of the bindin intron variability. To clarify the question concerning possible involvement of diversifying selection in the bindin intron evolution more data combining population genetic and functional approaches are necessary.

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Species referenced: Echinodermata
Genes referenced: bindin LOC100887844 LOC100893907

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	Fig. 1. DNA polymorphism in the bindin gene of the sea urchin Strongylocentrotus intermedius. The numbers above the top sequence represent the position of segregating sites and the start of a deletion or insertion. Nucleotides are numbered from the beginning of our sequence (position 877 in [59], starting the mature bindin protein). The coding nucleotides are in bold. Amino acid replacement polymorphisms are marked with asterisks. Dots indicate the same nucleotide as the reference sequence. The hyphens represent deleted nucleotides. ▲ denotes a deletion; † denotes the absence of a deletion; ▼ denotes an insertion; ‡ denotes the absence of an insertion. The recombinant sequence U-7 is in bold; the putative conversion tract is underlined. The exon - intron coordinates are: 1–237: exon I; 238–1191: intron; 1192–1518: exon II
	Fig. 2. Maximum likelihood tree of the strongylocentrotid sea urchins bindin sequences. The tree is based on Kimura 2-parameter (K2P) model as the best-fitting model of substitution under the maximum likelihood criterion [66] for constructing an ML tree of the bindin sequences. The numbers at the nodes are bootstrap percent probability values based on 1,000 replications. The bindin sequences of Hemicentrotus pulcherrimus (AF077318 and AF077319) are used as outgroups. The specimens of S. intermedius are marked with letters “G” and “U”. DRO = S. droebachiensis, PAL = S. pallidus; POL = S. polyacanthus; PUR = S. purpuratus; PUL = Hemicentrotus pulcherrimus
	Fig. 3. Sliding-window plots of polymorphism (π, thin line) and divergence (K, thick line) along the bindin gene of S. intermedius (INT), S. pallidus (PAL), and S. droebachiensis (DRO). The bindin sequence of S. polyacanthus (AF077317) was used for the K calculations. Window sizes are 100 nucleotides with 1-nucleotide increments. A schematic representation of the bindin gene is at the bottom. Vertical arrows indicate the locations of the regions with high within species polymorphism and low between species divergence
	Fig. 4. Sliding window plots of polymorphism-to-divergence ratio, and the average sliding G value along the bindin genes of S. intermedius, S. pallidus, and S. droebachiensis. The bindin sequence of S. polyacanthus (AF077317) was used as an outgroup. Window size is 10 variable substitutions for the polymorphism-to-divergence ratio and 12 variable substitutions for the average sliding G value. Other comments see Fig. 3
	Fig. 5. Sliding-window plots for the Wall’s (1999) B neutrality test statistic along the bindin gene region in S. intermedius (INT), S. pallidus (PAL), and S. droebachiensis (DRO). The total length of the sequence is 1398 bp with indels excluded. Window sizes are 50 nucleotides with five-nucleotide increments. Thin horizontal lines indicate expected values of the B neutrality test statistic with P = 0.01 (lower line) and P = 0.001 (upper line) obtained by coalescent simulations conditioned on the number of polymorphic sites without recombination. Other comments see Fig. 3

References [+] :

Addison, Multiple gene genealogies reveal asymmetrical hybridization and introgression among strongylocentrotid sea urchins. 2009, Pubmed, Echinobase