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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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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].