Tomato small RNAs (Updated on Sept. 2013)

The tomato small RNA database contains all tomato small RNAs collected from the following samples (Spet. 2013):

sample IDorganismcultivartissuelinkstudy
S0371Solanum lycopersicumHeinz 1706leafLink
S0372Solanum lycopersicumHeinz 1706flowerLink
S0373Solanum lycopersicumHeinz 1706fruitLink
S0707Solanum lycopersicumMicroTomclosed bud before flower bloomingGSM452712 Mohorianu et al. (2011) Plant J
S0708Solanum lycopersicumMicroTom flower, openGSM452713
S0709Solanum lycopersicumMicroTom fruit, 1mm to 3mm in diameterGSM452714
S0710Solanum lycopersicumMicroTom fruit, 5mm to 7mm in diameterGSM452715
S0711Solanum lycopersicumMicroTom fruit, 11mm to 14mm in diameterGSM452716
S0712Solanum lycopersicumMicroTom fruit, mature greenGSM452717
S0713Solanum lycopersicumMicroTom fruit, breaker stageGSM452718
S0714Solanum lycopersicumMicroTom fruit, 3 days post breakeGSM452719
S0715Solanum lycopersicumMicroTom fruit, 5 days post breakerGSM452720
S0716Solanum lycopersicumMicroTom fruit, 7 days post breakerGSM452721
S0717Solanum lycopersicumM82seedlings, two-week-old, replicate1GSM577998 Shivaprasad et al. (2012) EMBO J
S0718Solanum lycopersicumM82seedlings, two-week-old, replicate2GSM577999
S0719Solanum pennelliiLA716seedlings, two-week-old, replicate1GSM578000
S0720Solanum pennelliiLA716seedlings, two-week-old, replicate2GSM578001
S0721Solanum lycopersicum x S. pennelliiM82 x LA716 (F1)seedlings, two-week-old, replicate1GSM578002
S0722Solanum lycopersicum x S. pennelliiM82 x LA716 (F1)seedlings, two-week-old, replicate2GSM578003
S0723Solanum lycopersicum x S. pennelliiM82 x LA716 (F2)seedlings, two-week-old, replicate1GSM578004
S0724Solanum lycopersicum x S. pennelliiM82 x LA716 (F2)seedlings, two-week-old, replicate2GSM578005
S0725Solanum lycopersicum x S. pennelliiM82 x LA716 (F2)seedlings, two-week-old, replicate3GSM578006
S0726Solanum lycopersicumIL1-1seedlings, two-week-oldGSM578007
S0727Solanum lycopersicumIL2-5seedlings, two-week-old GSM578008
S0728Solanum lycopersicumIL8-1-1seedlings, two-week-old GSM578009
S0729Solanum lycopersicumIL8-1Dseedlings, two-week-oldGSM578010
S0730Solanum lycopersicumIL8-1-3seedlings, two-week-old GSM578011
S0731Solanum lycopersicumIL8-2seedlings, two-week-old GSM578012
S0732Solanum lycopersicumIL8-2-1seedlings, two-week-old GSM578013
S0733Solanum lycopersicumIL8-3seedlings, two-week-old GSM578014
S0734Solanum lycopersicumIL8-3-1seedlings, two-week-old GSM578015
S0735Solanum lycopersicumSunnyleaf, TSWV-infectedSRX328502
S0736Solanum lycopersicumAilsa Craigfruit, immature (17 days after anthesis)SRX099432 Zhong et al. (2013) Nature Biotech
S0737Solanum lycopersicumAilsa Craigfruit, mature green (39 days after anthesis)SRX099433
S0738Solanum lycopersicumAilsa Craigfruit, breaker (42 days after anthesis)SRX099433
S0739Solanum lycopersicumAilsa Craigfruit, red ripe (52 days after anthesis)SRX099432

The small RNA datasets were combined by removing redundancies (same sequences, same lengths, and same directions). Small RNAs derived from rRNA and tRNA were discarded. sRNAs with transcripts per million (TPM) >=50 in at least one sample and with length of 19-24 nt were included in the miRNA identification. These sRNAs were aligned to the tomato genome sequence and the flanking sequences (200bp to each side) of sRNAs with no more than 20 unique genome hits were extracted and folded with the RNAfold program. The structures were then checked with miRcheck to identify potential miRNA candidates. miRNA candidates were then compared to miRBase to identify conserved miRNA candidates (up to two mismatches). The miRNA targets (ITAG predicted cDNAs, v2.3) were identified using the target prediction tool developed and implemented in the database.