Porphyra yezoensis Ueda is an intertidal marine red algae that has received increasing attention as a model organism owing to its important role in biological research and the agronomic industry. The two generations of Porphyra yezoensis, the sporophyte and the gametophyte, have the same genome but show great differences in many aspects, including structural features, habitat, and gene expression. To identify miRNAs and their probable roles in P. yezoensis development, we constructed and sequenced libraries of small RNA from P. yezoensis sporophytes and gametophytes. The sequencing data were analyzed, and 14 miRNAs were identified, with only one common to these two samples. Our results show that P. yezoensis has a complex small RNA processing system containing novel miRNAs that have no identifiable homolog in other organisms. These miRNAs might have important regulatory roles in development of the different generations of P. yezoensis. 1. Introduction Porphyra yezoensis Ueda is an intertidal marine red algae that has received increasing attention as a model organism owing to its important role in biological research and the agronomic industry [1]. P. yezoensis is one of the most valuable marine crops in the world and is cultivated widely in Asia, especially in Japan, China, and Republic of Korea [2]. As a red algae, whose relationship to other groups is by no means certain, P. yezoensis has many characteristics of lower eukaryotes, including the location of the small subunit of Rubisco in the chloroplast genome [3], the same accessory pigments as cyanobacteria [4], and the high degree of similarity between many of its genes and their homologs in bacteria. Owing to these features, red algae are believed to be original or degraded eukaryotic organisms [5]. P. yezoensis has a unique dimorphic life-cycle consisting of two generations, a microscopic diploid filamentous sporophyte and a macroscopic haploid foliate gametophyte, with completely different morphology [6]. The sporophyte and the gametophyte have the same genome but show great differences in many aspects, including structural features, habitat, and gene expression. The sporophyte is densely tufted with uniseriate filaments, whereas the gametophyte is monolayered. The sporophyte enters and germinates in shells, whereas the gametophyte lives on static substrates of the intertidal zone, experiencing stress caused by strong light, high temperature, and desiccation during low tide [7–9]. Analysis of expressed sequence tag (EST) groups generated from sporophytes and gametophytes of P. yezoensis found
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