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Table 1 Summary of small RNA sequencing from diverse tissues and organs of soybean

From: Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max

Tissue/Organa Stagea Lineb Library code GEO sample numberc Total reads (Millions) Number of uniquesd Number matching miRBasee Percent match to genomef
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
  1. 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.
  2. 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.
  3. cSample accession numbers for sequence samples entered into Gene Expression Ominbus (GEO) (http://www.ncbi.nlm.nih.gov/geo/). Accession numbers to be determined.
  4. 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.
  5. emiRBase (http://microrna.sanger.ac.uk/) the curated mature miRNA database maintained at the Sanger Institute.
  6. fPercent of unique matching the Glycine max genome at Phytozome [33].