N per Million fragments mapped) was obtained by the CummeRbund R package, and tissue specificity

N per Million fragments mapped) was obtained by the CummeRbund R package, and tissue specificity score (JS score) was calculated for each transcript using the csSpecificity() function in this package.Filtering strategy used to identify lncRNAsfiltering Nutlin-3a chiralMedChemExpress Nutlin-3a chiral following the same pipeline described above. In addition, they were mapped to the F. vesca genome by BLAT with at least 95 sequence identity in the matched region (-minIdentity) and 50 matched in length.Conservation of lncRNAsTo determine conservation of lncRNAs, fve-lncRNAs were blasted against a few plant genomes and lncRNAs from other species using standalone blastn program (blast-2.2.28+, E-value < 0.001). The genomes of Arabidopsis (Arabidopsis_thaliana.TAIR10), maize (Zea_mays.AGPv3), and rice (Oryza_sativa.IRGSP-1.0) were downloaded from the release 28 of the ensemble website (http://plants.ensembl.org/index.html). The genomes of apple (Malus_x_domestica.v3.0.a1) and peach (Prunus_persica_v2.0.a1) were downloaded from GDR. The data resources of lncRNAs used in this study are shown in Table 2. The fifth version of unigenes from the genera of Malus and Prunus were downloaded from GDR. To discover lncRNAs from Malus and Prunus, their respective unigenes were similarly filtered (length > 200 bp; CPC < -1). House-keeping RNAs and conserved miRNAs were removed as well.Removal of transcripts that can yield small RNAs or contain repetitive sequenceAmong the assembled transcripts, the majority are partially (72,727, class_code "j") or completely (26,093, class_code "=") matched with the existing annotation. As the version 1.1 annotation includes only PC genes, these two categories (j and =) should represent PC genes and were thus excluded from further analysis. The transcripts with class_code "u" (unknown intergenic transcript), "o" (generic exonic overlap with a reference transcript), "x" (natural antisense transcript, NAT), and "i" (intronic transcript) were PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27488460 subjected to PC potential calculation [45]. Non-coding transcripts (coding potential score (CPC) < -1) larger than 200 bp were extracted for further analysis. Transcripts with unknown direction were kept only if both orientations possess no coding potential. Further, transcripts that encode any conserved protein domains were removed in the sense strand for multi-exonic transcripts or in either strand for singleexon transcripts. These transcripts were identified by searching against the Pfam database (E-value < 0.001) [62]. The remaining transcripts were blasted against the Rfam database (http://rfam.xfam.org/), tRNA database (http://gtrnadb.ucsc.edu/), and rRNA database (http:// ssu-rrna.org/) to remove any known transcripts (E-value < 0.001). To eliminate all possible pre-miRNAs, transcripts that perfectly match the 362 miRNAs found in the octoploid and diploid strawberries were filtered out [63?5]. To discover lncRNAs from ESTs (Expressed Sequence Tag), the fifth version of Fragaria unigene downloaded from GDR (www.rosaceae.org) was used forRaw small RNA-seq reads generated from nine tissue types in woodland strawberry YW5AF7 [48, 59] were previously deposited at the Gene Expression Omnibus (GEO) at NCBI under accession numbers GSE44930 and GSE61798. We re-analyzed the raw reads by quality-filtration (quality score = 28, percent of bases = 80 ), then combined all reads and clipped off the adaptors. The processed reads were collapsed into a single FASTA file by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The nu.