Tissue/Organa | Stagea | Lineb | Library code | GEO sample numberc | Total reads (Millions) | Number of uniquesd | Number matching miRBasee | Percent match to genomef |
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Whole seed | 12-14 DAF | Williams | WS | GSM899820 | 3.0 | 38749 | 393 | 84 |
Seed coat | Immature | Richland | SCR | GSM543393 | 2.9 | 32846 | 475 | 85 |
Seed coat | Immature | Williams 55 | SCM | GSM543396 | 6.1 | 35413 | 263 | 92 |
Seed coat | Immature | Williams | SCW | GSM543394 | 2.9 | 27343 | 525 | 87 |
Cotyledon | Immature | Williams | Cot | GSM543395 | 3.0 | 27288 | 390 | 85 |
G. Cotyledon | 7 day seedling | Williams | GCot | GSM899821 | 12.5 | 38961 | 876 | 80 |
Stem | 2 week plants | PI194639 | ST | GSM899822 | 4.2 | 37539 | 486 | 59 |
Leaf | 1 month plants | PI462312 | LE | GSM899823 | 6.1 | 6855d | 273 | 70 |
- aWhole seed at 12-14 DAF (days after flowering); seed coat and cotyledon samples are dissected from immature, mid-maturation, green seed at fresh weight range of 50-75 mg per seed; G, germinating cotyledon from 7-day etiolated seedling; Stem, of 2-week-old plantlets, Leaf, first or second fully expanded trifoliates from 1-month-old plants.
- bThe standard Williams variety has the ii genotype that specifies pigment present in the hilum with an otherwise yellow, non-pigmented seed coat. Williams 55 is a pigmented seed coat mutant line in Williams that contains the homozygous recessive genotype (i/i) at the I locus and Richland has the dominant, fully yellow I/I genotype.
- cSample accession numbers for sequence samples entered into Gene Expression Ominbus (GEO) (http://www.ncbi.nlm.nih.gov/geo/). Accession numbers to be determined.
- dThe number of unique signatures after adapter trimming are adjusted to account for increased sequencing output. The unique signatures with less than 5 reads were eliminated from libraries with approximately 3 million reads; similarly uniques with less than 10 counts were eliminated in the seed coat (Williams 55) and leaf libraries and less than 16 reads were eliminated from the germinating cotyledon library. As will be discussed in the results, the leaf library (LE) was found to contain a single superabundant miRNA signature that composed 65% of the 6.1 million total reads, thus reducing the overall diversity of unique signatures.
- emiRBase (http://microrna.sanger.ac.uk/) the curated mature miRNA database maintained at the Sanger Institute.
- fPercent of unique matching the Glycine max genome at Phytozome [33].