Genomic Instability and Shared Mechanisms for Gene Diversification in Two Distant Immune Gene Families: The Plant NBS-LRR Genes and the Echinoid 185/333 Genes

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

“…We have proposed here and in previous communications [7, 21, 31] a range of possible mechanisms that could result in sequence diversification of the Sp185/333 genes in addition to variations in the size of the family among individuals. To date, diversification mechanisms that may result from regional instability in the genome have not been tested experimentally for the Sp185/333 gene family (or in any other gene system that diversifies based on genomic instability) and our speculations are based on computational analyses of the sequences within and surrounding the genes.…”

“…Similar to STRs, each one of these types of repeats may cause chromosomal misalignment during meiosis that may lead to variations in gene copy number plus sequence changes to individual genes resulting from homologous DNA repair processes. However, because these types of repeats appear within genes and include coding sequences (in contrast to the STRs), they may also lead to gene conversion, as has been suggested previously [7, 21]. The general lack of pseudogenes in the Sp185/333 gene family (only a single pseudogene has been identified, although it was one of two intronless genes that may be retroposons [20]), is very unexpected for such tightly linked genes that share sequences and are surrounded by STRs (see [19]).…”

“…The genes in the three Sp185/333 clusters are organized in the same general order, orientation, and spacing, which leads to the notion that these clusters may have originated from a single ancestral gene or cluster that was significantly expanded by processes that include duplications and deletions of genes, segments and clusters into tandem or ectopic locations [7]. The proposed genomic instabilities may result, in part, from the presence of both GA and GAT STRs in the clusters.…”

“…As has been suggested previously [21], the GAT STRs may be involved in the diversification process based on their unique positioning at the edges of the D1 segmental duplications and some of the E2 segmental duplications. Although the mechanisms by which this may occur is not understood, one possibility is that the duplications are the outcome of DNA breakage followed by repair that is based on misalignments to similar but non-identical sequences on the homologous chromosome [7]. During this process, chromosomal misalignment or meiotic mispairing, may lead to the deletion and duplication of genes by unequal crossing over between homologous chromosomes resulting in changes to the gene family size and composition in the subsequent generation.…”

“…In contrast, some genomic regions are regarded as unstable (also called “fragile” [2]) and show more rapid changes particularly when they appear in association with tandem sequence repeats [3–6]. These regions show a higher frequency of breakage and are subject to increased errors and mutation rates during homologous repair processes (reviewed in [7]). Genomic regions that contain repeats can show swift changes in sequence, of which some are subject to selection, leading to rapid genome evolution.…”