Tomato Functional Genomics Database (TFGD)

2024-05-13 03:46| 来源: 网络整理| 查看: 265

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.

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