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Evidence for the expression of abundant microRNAs in the locust genome.

Wang Y, Jiang F, Wang H, Song T, Wei Y, Yang M, Zhang J, Kang L - Sci Rep (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China.

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.

No MeSH data available.


Number of miRNA precursors in the locust genome.(A) Summary of identified miRNA precursors in the present study and previous study. (B) Summary of identified miRNA precursors from miRBase in metazoan species. The vertebrate and insect miRNA precursors are the predominant representatives (~84%) of metazoan miRNA precursors in miRBase Release 21. The numbers of miRNA precursors at the top ranks are shown in insects and vertebrates.
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f1: Number of miRNA precursors in the locust genome.(A) Summary of identified miRNA precursors in the present study and previous study. (B) Summary of identified miRNA precursors from miRBase in metazoan species. The vertebrate and insect miRNA precursors are the predominant representatives (~84%) of metazoan miRNA precursors in miRBase Release 21. The numbers of miRNA precursors at the top ranks are shown in insects and vertebrates.

Mentions: Independent of the locust genome sequence, 50 conserved miRNA precursors and 185 lineage-specific miRNA precursors (The lineage-specific miRNAs represent the miRNAs showing no homology with insect miRNAs deposited in miRBase in this study) were identified using loop folding methods18. All the 50 conserved miRNAs and 136 of 185 lineage-specific miRNAs were detected in the present study (Fig. 1A). We manually checked the 49 lineage-specific miRNAs that were absent in the present study. A large number of these miRNAs (23 in 49) could not be aligned to the locust genome. Seventeen miRNAs that showed multiple genomic hits were related to the locust-specific repetitive elements, which were de novo identified by the RepeatModeler program. In addition, nine miRNAs failed to meet the minimum free energy (MFE) criterion of folding, which suggested their self-complementary hairpin origins from random genomic sequences.


Evidence for the expression of abundant microRNAs in the locust genome.

Wang Y, Jiang F, Wang H, Song T, Wei Y, Yang M, Zhang J, Kang L - Sci Rep (2015)

Number of miRNA precursors in the locust genome.(A) Summary of identified miRNA precursors in the present study and previous study. (B) Summary of identified miRNA precursors from miRBase in metazoan species. The vertebrate and insect miRNA precursors are the predominant representatives (~84%) of metazoan miRNA precursors in miRBase Release 21. The numbers of miRNA precursors at the top ranks are shown in insects and vertebrates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556993&req=5

f1: Number of miRNA precursors in the locust genome.(A) Summary of identified miRNA precursors in the present study and previous study. (B) Summary of identified miRNA precursors from miRBase in metazoan species. The vertebrate and insect miRNA precursors are the predominant representatives (~84%) of metazoan miRNA precursors in miRBase Release 21. The numbers of miRNA precursors at the top ranks are shown in insects and vertebrates.
Mentions: Independent of the locust genome sequence, 50 conserved miRNA precursors and 185 lineage-specific miRNA precursors (The lineage-specific miRNAs represent the miRNAs showing no homology with insect miRNAs deposited in miRBase in this study) were identified using loop folding methods18. All the 50 conserved miRNAs and 136 of 185 lineage-specific miRNAs were detected in the present study (Fig. 1A). We manually checked the 49 lineage-specific miRNAs that were absent in the present study. A large number of these miRNAs (23 in 49) could not be aligned to the locust genome. Seventeen miRNAs that showed multiple genomic hits were related to the locust-specific repetitive elements, which were de novo identified by the RepeatModeler program. In addition, nine miRNAs failed to meet the minimum free energy (MFE) criterion of folding, which suggested their self-complementary hairpin origins from random genomic sequences.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China.

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.

No MeSH data available.