Abstract
Genomic regions with repeated sequences are unstable and prone to rapid DNA diversification. However, the role of tandem repeats within the coding region is not fully characterized. Here, we have identified a new hypervariable C-type lectin gene family with different numbers of tandem repeats (Rlecs; R means repeat) in oriental river prawn (Macrobrachium nipponense). Two types of repeat units (33 or 30 bp) are identified in the second exon, and the number of repeat units vary from 1 to 9. Rlecs can be classified into 15 types through phylogenetic analysis. The amino acid sequences in the same type of Rlec are highly conservative outside the repeat regions. The main differences among the Rlec types are evident in exon 5. A variable number of tandem repeats in Rlecs may be produced by slip mispairing during gene replication. Alternative splicing contributes to the multiplicity of forms in this lectin gene family, and different types of Rlecs vary in terms of tissue distribution, expression quantity and response to bacterial challenge. These variations suggest that Rlecs have functional diversity. The results of experiments on sugar binding, microbial inhibition and clearance, regulation of antimicrobial peptide gene expression and prophenoloxidase activation indicate that the function of Rlecs with the motif of YRSKDD in innate immunity is enhanced when the number of tandem repeats increases. Our results suggest that Rlecs undergo gene expansion through gene duplication and alternative splicing, which ultimately leads to functional diversity.
Highlights
Repetitive DNA sequences are widespread and abundant in genomic DNAs because almost half of the human genome consists of repeats [1,2]
We found a lectin gene containing tandem repeats by analysing the transcriptome data of M. nipponense
More than one band was amplified using a pair of gene-specific primers
Summary
Repetitive DNA sequences are widespread and abundant in genomic DNAs because almost half of the human genome consists of repeats [1,2]. A subset of repeating DNA are DNA fragments consisting of tandem repeats with short sequence units (e.g. CAG) that are adjacent to each other. Tandem repeats can be mutation hotspots due to their repetitive features. Tandem repeats have higher mutation rates, which are 10–10 000 times the average rate, compared with other genomic loci [3]. Most tandem repeats lose direct biological functions due to instability and the lacking genetic information. Such tandem repeats are referred to as ‘junk’ DNA [4,5]. Repeats are present in the functional (coding and regulatory) regions of genomes [7] and can alter the function and/or expression of genes to enable organisms to adapt quickly to new environments [8]
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