Abstract
BackgroundGenomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. A highly diverse immune gene family of the sea urchin (Strongylocentrotus purpuratus), called Sp185/333, is composed of clustered genes with similar sequence as well as several types of repeats ranging in size from short tandem repeats (STRs) to large segmental duplications. This repetitive structure may have been the basis for the incorrect assembly of this gene family in the sea urchin genome sequence. Consequently, we have resolved the structure of the family and profiled the members by sequencing selected BAC clones using Illumina and PacBio approaches.ResultsBAC insert assemblies identified 15 predicted genes that are organized into three clusters. Two of the gene clusters have almost identical flanking regions, suggesting that they may be non-matching allelic clusters residing at the same genomic locus. GA STRs surround all genes and appear in large stretches at locations of putatively deleted genes. GAT STRs are positioned at the edges of segmental duplications that include a subset of the genes. The unique locations of the STRs suggest their involvement in gene deletions and segmental duplications. Genomic profiling of the Sp185/333 gene diversity in 10 sea urchins shows that no gene repertoires are shared among individuals indicating a very high gene diversification rate for this family.ConclusionsThe repetitive genomic structure of the Sp185/333 family that includes STRs in strategic locations may serve as platform for a controlled mechanism which regulates the processes of gene recombination, gene conversion, duplication and deletion. The outcome is genomic instability and allelic mismatches, which may further drive the swift diversification of the Sp185/333 gene family that may improve the immune fitness of the species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3241-x) contains supplementary material, which is available to authorized users.
Highlights
Genomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes
Evaluation of the Sp185/333 gene content within genomes of 10 sea urchins using fragment length analysis shows exceptional diversity among individuals including unique gene sizes and repertoires. We propose that this genomic structure with shared sequences among tightly linked genes, Short tandem repeat (STR) associated with gene duplications, deletions and segmental duplications and allelic regions with mismatched genes, is highly unusual, is likely a basis for very swift changes to the gene family that is selected over generations through interactions with pathogens
Sp185/333-positive Bacterial artificial chromosome (BAC) clones were identified in the sea urchin large insert BAC library The Sp185/333 gene family in the S. purpuratus genome sequence (ver. 3.1; June 15th, 2011;) shows unexpectedly few members [21, 29]
Summary
Genomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. Clustered arrays of duplicated genes with similar sequence can be identified computationally as large tandem repeats, and relative to the practical problem of genome assembly, these regions are difficult to assemble from short sequencing reads [3, 8] This type of unstable genomic organization can be found in immune gene families in a wide range of organisms including human killer immunoglobulinlike receptor (KIR) gene family [9], genes encoding the fibrinogen related proteins (FREPs) in fresh water snails [10], allorecognition (alr) genes in a marine hydroid [11, 12], and disease resistance (R) genes in higher plants ([13, 14], reviewed in [15]). The beneficial outcome of genomic instability in regions that harbor immune gene clusters is the appearance of new genes within a family that increase its diversity (reviewed in [16]), which, when under positive selection from pathogen pressure, may result in improved immune function for detecting and responding to different pathogens or symbionts, and thereby improving the fitness and survival of the host
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