Abstract
Substantial accumulation of neutral sequences accounts for genome size expansion in animal genomes. Numerous novel microRNAs (miRNAs), which evolve in a birth and death manner, are considered evolutionary neutral sequences. The migratory locust is an ideal model to determine whether large genomes contain abundant neutral miRNAs because of its large genome size. A total of 833 miRNAs were discovered, and several miRNAs were randomly chosen for validation by Northern blot and RIP-qPCR. Three additional verification methods, namely, processing-dependent methods of miRNA biogenesis using RNAi, evolutionary comparison with closely related species, and evidence supported by tissue-specific expression, were applied to provide compelling results that support the authenticity of locust miRNAs. We observed that abundant local duplication events of miRNAs, which were unique in locusts compared with those in other insects with small genome sizes, may be responsible for the substantial acquisition of miRNAs in locusts. Together, multiple evidence showed that the locust genome experienced a burst of miRNA acquisition, suggesting that genome size expansion may have considerable influences of miRNA innovation. These results provide new insight into the genomic dynamics of miRNA repertoires under genome size evolution.
Highlights
Variations that disrupt the formation of miRNA hairpins; the decayed miRNAs cannot be recognized by miRNA processing endonucleases and are subsequently swept out from the genome[10]
These results suggested that genome size expansion had a profound effect on genomic dynamics of miRNA repertoires in locusts
The low quality reads, which represented ~1% of the raw sequencing reads, met the filtering criteria; they contained more than 3Ns, or consisted of simple repeat bases, or were not composed of bases with a minimum Phred score of Q20
Summary
Variations that disrupt the formation of miRNA hairpins; the decayed miRNAs cannot be recognized by miRNA processing endonucleases and are subsequently swept out from the genome[10]. MiRNA discovery in the locust genome can avoid the possible influence of whole genome duplication on genomic dynamics of miRNA repertoires This genome represents an ideal model to accurately study the effects of the increase in genome size on miRNA evolution. Comparative genomic searches across insect genomes indicated that the abundant local duplication events of miRNAs were unique in the locust genome, compared with other insect genomes with small genome sizes. These results suggested that genome size expansion had a profound effect on genomic dynamics of miRNA repertoires in locusts
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