Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family.
BACKGROUND
Genomic 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.


RESULTS
BAC 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.


CONCLUSIONS
The 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.
['Oren|Matan|M|', 'Barela Hudgell|Megan A|MA|', "D'Allura|Brian|B|", 'Agronin|Jacob|J|', 'Gross|Alexandra|A|', 'Podini|Daniele|D|', 'Smith|L Courtney|LC|0000-0001-7099-7852']
D000483:Alleles D000818:Animals D022202:Chromosomes, Artificial, Bacterial D017353:Gene Deletion D015723:Gene Library D023061:Gene Order D056726:Genetic Association Studies D056426:Genetic Loci D042822:Genomic Instability D007109:Immunity D018895:Microsatellite Repeats D005810:Multigene Family D056916:Segmental Duplications, Genomic D047270:Strongylocentrotus purpuratus
Strongylocentrotus purpuratus Gene diversification Allelic mispairing Genomic instability Sp185/333 Illumina vs. PacBio