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Supporting Information

Additional Supporting Information may be found in the online version of this article:

Figure S1: Length and nucleotide distributions of all qualified reads in nurse and forager samples. (a) Distribution of all qualified reads. (b, c) First nucleotide distributions.

Figure S2: Length and nucleotide distributions of all mappable reads in nurse and forager samples. (a) Distribution of all qualified reads. (b, c) First nucleotide distributions.

Table S1: All miRNAs identified in the honey bee head by RNA-seq. miR#(X) represents novel miRNA genes, which have not yet received a formal miRBase designation. Gene name, sequence, and conservation score are shown. Conservation score was calculated by adding one point for each species in which a gene is conserved, 0.5 points for each species in which a similar gene was found, and zero points for species in which the gene is not present. Genes are ordered from most- to lest-conserved genes as in Fig. 2.

Table S2: Distributions of the sequencing reads from small RNA libraries of forager and nurse. Shown in the table are the total number of raw sequencing reads, the number of qualified reads that can perfectly map to the corresponding honeybee genome, known and novel miRNA sequences, coding sequencing (CDS), 3′- and 5′-UTRs, intergenic regions, and intron and exon sequences. No mismatches were allowed for the mapping. The second number for each condition (column) is the percentage of reads relative to the total qualified reads.

Table S3: Previously annotated genes: raw and normalized (norm) transcript numbers for each miRNA in the nurse and forager library, along with total number of qualified and unqualified reads for each library.

Table S4: Novel miRNA genes: raw and normalized transcript numbers for each gene in the nurse and forager library, along with total number of qualified and unqualified reads for each library.

Table S5: List of 18 novel miRNA genomic loci and function annotation.

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