Table 2

Identified miRNA targets found in both soybean seed coat and cotyledon
miRNA Tissue Target Target Annotation C.Site Location Category TP100M P-Value
gma-miR156 C100 Glyma02g13370.1 SBP domain containing protein 1219 CDS 0 92.52237 0.0477
C300 Glyma02g13370.1 SBP domain containing protein 1219 CDS 0 27.27151 0.0496
SC100 Glyma02g30670.1 SBP domain containing protein 768 CDS 0 335.5574 0.0445
C100 Glyma05g00200.1 SBP domain containing protein 1202 CDS 1 57.82648 0.015
gma-miR159* C25 Glyma04g15150.1 Myb family transcription factor 853 CDS 0 787.7315 0.0111
C300 Glyma04g15150.1 MYB family transcription factor 853 CDS 0 178.5044 0.0091
C25 Glyma06g47000.1 Myb family transcription factor 852 CDS 0 787.7315 0.0111
SC25 Glyma06g47000.1 Myb family transcription factor 852 CDS 0 18.44158 0.0123
C300 Glyma06g47000.1 MYB family transcription factor 852 CDS 0 178.5044 0.0091
SC100 Glyma13g34710.1 No functional annotation 1161 CDS 2 106.3962 0.0391
C300 Glyma13g34710.1 No Functional Annotation 1161 CDS 1 9.916913 0.0133
C25 Glyma19g40720.1 Anion Exchange protein 2162 CDS 1 28.27754 0.0157
gma-miR160# C100 Glyma10g35480.1 Auxin response factor 740 CDS 0 12166.69 0.0168
C100 Glyma11g20490.1 Auxin response factor 1510 CDS 0 12166.69 0.0071
C100 Glyma12g08110.1 Auxin response factor 1501 CDS 0 12166.69 0.0071
C100 Glyma12g29720.1 Auxin response factor 1626 CDS 0 1445.662 0.0168
C100 Glyma14g33730.1 Auxin response factor 1184 CDS 0 1144.964 0.027
SC25 Glyma04g43350.1 Auxin response factor 1337 CDS 0 1391.022 0.0379
C300 Glyma04g43350.1 Auxin response factor 1337 CDS 0 401.635 0.0281
SC25 Glyma10g06080.1 Auxin response factor 1355 CDS 0 821.9674 0.0379
gma-miR164* SC100 Glyma15g40510.1 No apical meristem protein 730 CDS 1 69.56677 0.0013
C100 Glyma04g33270.1 No apical meristem protein 634 CDS 0 150.3488 0.0026
SC100 Glyma04g33270.1 No apical meristem protein 634 CDS 0 425.585 0.0024
SC100 Glyma05g00930.1 No apical meristem protein 751 CDS 2 425.585 0.0433
gma-miR166 SC100 Glyma04g09000.1 START domain containing protein 93 CDS 3 16.36865 0.0478
SC100 Glyma05g30000.1 HD-ZIP transcription factor 1041 CDS 3 8.184326 0.0478
C25 Glyma05g30000.1 HD-ZIP transcription factor 1041 CDS 0 3389.265 0.0331
C300 Glyma05g30000.1 HD-ZIP transcription factor 1041 CDS 0 4321.295 0.0271
gma-miR167* C100 Glyma15g00770.1 Zinc finger family protein 1815 CDS 0 1480.358 0.0071
SC100 Glyma02g18250.3 Elongation Factor S-II 90 CDS 1 3592.919 0.0168
C100 Glyma02g40650.1 Auxin response factor 2924 CDS 0 855.8319 0.027
SC100 Glyma02g40650.1 Auxin response factor 2924 CDS 0 1239.925 0.0252
C25 Glyma02g40650.1 Auxin response factor 2924 CDS 0 2536.899 0.0343

Complete tables can be found in 1.

CDS: Coding Sequence; UTR: Untranslated Region; TP100M: Transcripts per 100 million; C.site (Cleavage site): Nucleotide number from 5’ end of cDNA; P-value ≤0.05 using Cleaveland pipeline.

Cot25 and SC25 are libraries from cotyledons and seed coats dissected from early-maturation green seed of 25–50 mg fresh wt.; Cot100 and SC100 are cotyledons and seed coats dissected from mid-maturation green seed of 100–200 mg fresh weight range; Cot300 are cotyledons dissected from late maturation yellow seeds of 300–400 mg weight range.

* and bold are miRNAs whose targets shown in the target plots (t-plots) (Figure 1).

# and bold are miRNAs whose RLM-5’RACE validated targets are shown in the target plots (t-plots) (Figure 2).

Shamimuzzaman and Vodkin

Shamimuzzaman and Vodkin BMC Genomics 2012 13:310   doi:10.1186/1471-2164-13-310

Open Data