The set of miRNA mature sequences with at least one matching EST have been classi fied on the basis of the species of origin. The binomial distribution was used to assess the statistical signifi cance for the represented plant species, this allowed identifying those species chosen from the initial dataset more or less frequently than random. Four different thresholds for selleck chem Brefeldin A the p values were applied. Matching ESTs have then been related to Unigene clus ters and the corresponding annotations were recorded. The GO slimmer tool available on the Gene Ontology website has been used to identify the GO slim terms more represented in the set of potential targets on the basis of the Unigene cluster annotations. For this analysis the Plant GO Slim subset has been used.

Identification of putative miRNA precursors True miRNA precursors should have both a mature sequence on one arm of the hairpin and a paired pas senger sequence on the opposite arm. To assess these features the precursor sequences were extracted from the consensus sequences, obtained by the Sequencer Software on Unigene clus ter assemblies, by cutting 13 nt before the 5 hit and 13 nt after the 3 hit, since this region was recently shown to have this average length in plants. In order to predict the secondary structure of the precursors, the software mfold 3. 2, free available at h rna form1. cgi, was used. The minimal fold ing free energy index and the GC content were calculated for each sequence. All the sequences with a MFEI greater than 0.

85 were considered potential miRNA precursors, besides, only 4 mismatches were allowed between the mature sequence and the passenger sequence, and only few and small asymmetric bulges were accepted. Identification of SNPs indels at miRNA target sites Polymorphisms in target genes have been searched through a comparison of the ESTs belonging to the same Unigene cluster. Each cluster has been assembled by Sequencer Software and polymorph isms have been searched on miRNA complementary sequence sites. AutoSNP database. au was also screened using target gene annotations as contig searching keywords. The large yellow croaker is an economically important marine fish in China, with an annual yield that exceeds any other single netcage farmed marine species. However, recent rapid develop ment of the large yellow croaker farming industry has led to increasingly severe outbreaks of infectious disease caused by marine bacteria such as Aeromonas hydro phila, resulting in great economic losses. However, little is known about the molecular mechanisms underlying the immune response to such pathogenic bacteria in this fish species, thereby hinder ing the establishment of effective Entinostat measures in disease control.