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Table 2 Conserved Brachypodium miRNAs and their sequence similarity to known miRNAs from other plant species.

From: Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

Name

Sequence (5'-3')

L

(nt)

Arm

/nt

Location

Plant species

     

Ara

Pop

Ric

Whe

bdi-miR156a

UGACAGAAGAGAGUGAGCAC

20

5'/123

super_2:28299658-28299677

++++

++++

++++

++++

bdi-miR156b

  

5'/123

super_2:28299895-28299914

    

bdi-miR156c

  

5'/152

super_2:28300123-28300142

    

bdi-miR156d

  

5'/112

super_5:10043111-10043130

    

bdi-miR156e

  

5'/112

super_6:14734765-14734784

    

bdi-miR156f

  

5'/186

super_8:656857-656876

    

bdi-miR156g

  

5'/124

super_10:7252868-7252887

    

bdi-miR160a

UGCCUGGCUCCCUGUAUGCCA

21

5'/116

super_0:10869231-10869251

++++

++++

++++

++++

bdi-miR160b

  

5'/126

super_0:34912728-34912748

    

bdi-miR160c

  

5'/129

super_3:8233739-8233759

    

bdi-miR160d

  

5'/121

super_6:15675857-15675877

    

bdi-miR162

UCGAUAAACCUCUGCAUCCGG

21

3'/133

super_5:10427165-10427185

+++

+++

+++

 

bdi-miR164a

UGGAGAAGCAGGGCACGUGCA

21

5'/186

super_0:24670885-24670905

++++

++++

++++

+++

bdi-miR164b

  

5'/127

super_2:4986204-4986224

    

bdi-miR164c

  

5'/161

super_2:12019567-12019587

    

bdi-miR164d

UGGAGAAGAAGGGCACAUGCA

21

5'/165

super_2:12019673-12019693

+

++

+

 

bdi-miR166a

UCGGACCAGGCUUCAUUCCCC

21

3'/222

super_0:8156180-8156200

++++

++++

++++

 

bdi-miR166b

  

3'/119

super_0:32809584-32809604

    

bdi-miR166c

  

3'/108

super_1:32626519-32626539

    

bdi-miR166d

  

3'/121

super_5:8578628-8578648

    

bdi-miR166e

  

3'/148

super_8:6993194-6993214

    

bdi-miR166f

  

3'/137

super_8:12758179-12758199

    

bdi-miR166g

UCGGACCAGGCUUCAUUCCUC

21

3'/115

super_12:6251912-6251932

+++

+++

++++

++

bdi-miR167a

UGAAGCUGCCAGCAUGAUCUA

21

5'/127

super_0:33041618-33041638

++++

++++

++++

++++

bdi-miR167b

  

5'/165

super_0:35725085-35725105

    

bdi-miR167c

  

5'/122

super_12:1692366-1692386

    

bdi-miR168

UCGCUUGGUGCAGAUCGGGAC

21

5'/101

super_6:17349865-17349885

++

++

++++

++++

bdi-miR169a

AGCCAAGGAUGACUUGCCGG

20

5'/138

super_0:11730514-11730533

+++

++

+++

+++

bdi-miR169b

  

5'/117

super_5:1266552-1266571

    

bdi-miR169c

UAGCCAAGGAUGACUUGCCUG

21

5'/129

super_5:16644104-16644124

++++

++

++++

 

bdi-miR169d

  

5'/138

super_5:16647089-16647109

    

bdi-miR169e

CAGCCAAGAAUGGCUUGCCUA

21

5'/112

super_7:4154045-4154066

+

+

+

+

bdi-miR169f

CAGCCAAGGAUGACUUGCCGG

21

5'/125

super_9:4769323-4769343

++++

+++

++++

++++

bdi-miR171a

UGAUUGAGCCGUGCCAAUAUC

21

3'/102

super_0:7984997-7985017

+

+

++++

+

bdi-miR171b

  

3'/132

super_0:32458278-32458298

    

bdi-miR171c

  

3'/130

super_1:34018204-34018224

    

bdi-miR171d

  

3'/125

super_9:5726634-5726654

    

bdi-miR172a

AGAAUCUUGAUGAUGCUGCAU

21

3'/123

super_5:4196588-4196608

+++

+++

+++

+++

bdi-miR172b

GAAUCUUGAUGAUGCUGCAU

20

3'/226

super_13:3713167-3713186

++++

++++

++++

++++

bdi-miR319

UUGGACUGAAGGGUGCUCCCU

21

3'/190

super_4:17219328-17219348

+++

++

+++

+++

bdi-miR390

AAGCUCAGGAGGGAUAGCGCC

21

5'/186

super_0:36774796-36774816

++++

++++

++++

++++

bdi-miR393

UCCAAAGGGAUCGCAUUGAUC

21

5'/125

super_9:7153943-7153963

+++

++++

++++

++++

bdi-miR394

UUGGCAUUCUGUCCACCUCC

20

5'/172

super_5:7680773-7680792

++++

++++

++++

 

bdi-miR395a

UGAAGUGUUUGGGGGAACUC

20

3'/90

super_1:16273497-16273476

+++

+

++

 

bdi-miR395b

  

3'/89

super_1:16273342-16273323

    

bdi-miR395c

  

3'/95

super_1:16272920-16272901

    

bdi-miR395d

  

3'/143

super_6:4370549-4370568

    

bdi-miR395e

  

3'/150

super_9:6484473-6484492

    

bdi-miR395f

  

3'/96

super_9:6484650-6484669

    

bdi-miR395g

  

3'/89

super_9:6484944-6484963

    

bdi-miR395h

  

3'/76

super_9:6485096-6485115

    

bdi-miR395i

  

3'/86

super_9:6485234-6485253

    

bdi-miR395j

  

3'/88

super_9:6485371-6485390

    

bdi-miR395k

  

3'/86

super_9:6485509-6485528

    

bdi-miR395l

  

3'/96

super_9:6485786-6485805

    

bdi-miR395m

  

3'/96

super_9:6486060-6486079

    

bdi-miR395n

  

3'/90

super_9:6486197-6486216

    

bdi-miR396a

UCCACAGGCUUUCUUGAACUG

21

5'/161

super_0:1364119-1364139

++

+

++++

 

bdi-miR396b

  

5'/176

super_5:545413-545433

    

bdi-miR397a

AUUGAGUGCAGCGUUGAUGAA

21

5'/115

super_6:15909808-15909828

+

+

+

+++

bdi-miR397b

  

5'/112

super_6:15937103-15937123

    

bdi-miR398

UGUGUUCUCAGGUCGCCCCUG

21

3'/131

super_4:6919237-6919257

+++

++++

++++

 

bdi-miR528

UGGAAGGGGCAUGCAGAGGAG

21

5'/119

super_1:34315939-34315959

  

++++

 

bdi-miR529

AGAAGAGAGAGAGUACAGCCU

21

5'/107

super_5:15162755-15162775

 

+++

+++

 

bdi-miR827

UUAGAUGACCAUCAGCAAACA

21

3'/141

super_10:7087762-7087782

++

++

+

 
  1. Name, the name of conserved Brachypodium miRNAs and underlines denote miRNAs whose miRNA* have been detected in Solexa sequencing analysis; Sequence, miRNA sequence cloned in the NC library and; L, the length of miRNA; Arm/nt, the miRNA location in the predicted hairpin structure (5' or 3' arm)/the length of the precursor; N, the number of loci in the genome for different miRNA families; Location, miRNA location in the genome; Ara, Arabidopsis; Pop, Populus; Ric, Rice; Whe, Wheat; For plus symbols in the table: ++++, miRNA sequences of Brachypodium were identical to those in other plant species; +++, miRNA sequences of Brachypodium were conserved in other plant species but have variations at 1 nucleotide positions; ++, miRNA sequences of Brachypodium were conserved in other plant species but have variations at 2 nucleotide positions; +, miRNA sequences of Brachypodium were conserved in other plant species but have variations at ≥ 3 nucleotide positions. For miRNAs whose homologs are not identified in rice, sequence comparison was only performed for the other four plant species.