Rapid Evolution of microRNA Loci in the Brown Algae.
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a single species, the filamentous brown alga Ectocarpus sp. Here, we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families. Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.
Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France.
J Mark
JM
Cock
Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
Fuli
F
Liu
Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.|Qingdao National Laboratory for Marine Science and Technology, Lab for Marine Biology and Biotechnology, Qingdao, China.
Delin
D
Duan
Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France.
Simon
S
Bourdareau
Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France.
Agnieszka P
AP
Lipinska
Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France.
Susana M
SM
Coelho
School of Earth Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom.
James E
JE
Tarver
D000460:Chlorophyta / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome / Q000235:genetics; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D000459:Phaeophyceae / Q000235:genetics*
D035683:MicroRNAs
Ectocarpus; Saccharina japonica; brown algae; heterokonts; microRNA; stramenopiles