Table 1.
List of snoRNA/scaRNA candidates
| IDa | Coordinatesb | Type | Putative target | Copies (TeloSII)c | cDNA/EST | RNA-Seq | Tissue | Homologyd | |
|---|---|---|---|---|---|---|---|---|---|
| Cluster1 △ | ncR1 | Chr1:14283553..14283663 | H/ACA | / | 9(1) | / | GSM893120 | flowers | A.ly |
| ncR2 | Chr1:14283835..14283886 | C/D | / | 4(1) | / | / | / | / | |
| ncR3 | Chr1:14283975..14284049 | C/D | 18S/Am1750 (D) | 5(1) | / | GSM442932 | roots | / | |
| ncR4 | Chr1:14284343..14284424 | C/D | 18S/Cm307 (D) | 2(1) | / | GSM575247 | flowers | A.ly | |
| Cluster2 | ncR5 | Chr2:1836965..1837036 | C/D | 25S/Cm2509 (D) | 1 | / | GSM893122 | flowers | A.ly |
| ncR6 | Chr2:1837308..1837401 | C/D | 18S/Gm275 (D) | 1 | / | GSM893120 | flowers | A.ly | |
| ncR7 | Chr2:1837461..1837557 | C/D | U2.4/Gm331 (D) | 12(1) | / | GSM893120 | flowers | A.ly | |
| Cluster3 | ncR9 | Chr2:5830603..5830668 | C/D | U5/Tm687 (D) | 2(1) | / | GSM893122 | flowers | Cru |
| ncR10 | Chr2:5831355..5831456 | C/D | U6.29/Cm590 (D) | 4(1) | / | GSM893123 | flowers | A.ly | |
| Cluster4 | ncR11 | Chr4:1480138..1480215 | C/D | 25S/Cm2616 (D) | 1 | / | GSM893120 | flowers | A.ly, C.ru |
| ncR12 | Chr4:1480326..1480415 | C/D | U4.1/Am223 (D) | 1 | / | GSM893121 | flowers | A.ly | |
| Cluster5 | ncR13 | Chr5:3642290..3642331 | C/D | U6.29/Am296 (D') | 1 | / | / | / | / |
| ncR14 | Chr5:3642496..3642628 | C/D | U6.26/Um774 (D) | 1 | / | SRR505744 | leaves | A.ly, C.ru, B.ra | |
| Cluster6 | ncR15 | Chr5:20313629..20313716 | C/D | / | 1 | / | GSM893122 | flowers | / |
| ncR16 | Chr5:20313841..20313928 | C/D | / | 1 | / | GSM893123 | flowers | A.ly | |
| ncR17 | Chr5:20314434..20314506 | C/D | U5/Am921 (D) | 1 | / | GSM893121 | flowers | A.ly | |
| Cluster7 | ncR20 | Chr2:9809815..9809713 | C/D | U6-29/Am21 (D) | 1 | EH971193 | SRR505743 | seedlings, roots | A.ly |
| ncR21 | Chr2:9809455..9809345 | C/D | U2.4/Cm143 (D) | 1 | / | SRR505745 | flowers | A.ly, C.ru | |
| Cluster8 | ncR22 | Chr4:5918068..5917991 | C/D | U2.3/Am345 (D) | 8(6) | / | GSM893121 | flowers | A.ly |
| ncR23 | Chr4:5917772..5917612 | C/D | U2.9/Tm207 (D) | 12(4) | / | GSM456944 | flowers | A.ly | |
| Cluster9 | ncR24 | Chr5:10673349..10673223 | H/ACA | / | 1 | / | GSM893122 | flowers | A.ly |
| ncR25 | Chr5:10672936..10672800 | H/ACA | / | 11(2) | / | GSM893121 | flowers | A.ly | |
| Cluster10 | ncR26 | Chr1:28889830..28889897 | C/D | U6.1/Cm740 (D) | 1 | / | GSM896913 | leaves | A.ly, Cru, B.ra |
| ncR27 △* | Chr1:28889966..28890048 | C/D | U6.1/Am177 (D) | 1 | / | GSM896913 | flowers | A.ly, Cru | |
| Single | ncR18 | Chr1:26010695..26010627 | C/D | 18S/Am1558 (D) | 1 | / | / | / | A.ly |
| Single | ncR28△ | Chr1:6140665..6140735 | C/D | 18S/Gm727 (D) | 1 | / | GSM893122 | flowers | / |
aID with triangle was also identified as long ncRNA by Liu et al. [38]. ID with asterisk was also identified as intermediate ncRNA by Wang et al. [39]. ID marked in bold was verified by RT-PCR in this study
bTermini were predicted by snoReport program, and fine-turned based on small RNA enrichments and RT-PCR validation
cNumbers within parentheses denote copies also containing TeloSII elements
dConservation analysis were performed in Arabidopsis lyrata (A.ly), Capsella rubella (C.ru), Brassica rapa (B.ra), Medicago truncatula (M.tr) and Oryza sativa (O.sa)