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Table 2 List of computationally predicted Physcomitrella miRNAs using the micoHarvester program.

From: Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution

Name

Sequence 5'→3'

Length (nt)

Homologs

Precursor genomic

Precursor EST

Expression verified

miR156a

UGACAGAAGAGAGUGAGCAC

20

ath, gma, mtr, osa, ptc, ppt, sbi, sof, zma

1 (gnl|ti|850661024)

n.f.

n.e.

miR160-1*

UGCCUGGCUCCCUGUAUGCCA

21

ath, gma, mtr, osa, ptc, zma, sbi

1 (gnl|ti|1003375177)

n.f.

n.e.

miR160-2

CGCCUGGCUCCCUGUAUGCCA

21

ath, gma, mtr, osa, ptc, zma, sbi

1 (gnl|ti|893498247)

n.f.

n.e.

miR160-3

CGCCUGGCUCCCUGCAUGCCA

21

ath, gma, mtr, osa, ptc, zma, sbi

1 (gnl|ti|1023106236)

n.f.

n.e.

miR160-4

CGCCUGGCUCCCUGCAUGCCG

21

ath, gma, mtr, osa, ptc, zma, sbi

1 (gnl|ti|1003194173)

n.f.

n.e.

miR165

UCGGACCAGGCUUCAUUCCCCU

22

ath

1 (gnl|ti|1036028061)

n.f.

n.e.

miR166

UCGGACCAGGCUUCAUUCCCU

21

ath, gma, mtr, osa, ptc, zma, sbi

1 (gnl|ti|1006181867)

n.f.

n.e.

miR167

GGAAGCUGCCAGCAUGAUCCU

21

ath,gma,ptc,osa, sbi,sof,zma

1 (gnl|ti|1003199194)

n.f.

no

miR171-1*

AGAUUGAGCCGCGCCAAUAUC

21

ath, mtr, osa, ptc, sbi, zma

1 (gnl|ti|1024468070)

n.f.

n.e.

miR171-2

UUGAGCCGGGCCAAUAUCACA

21

ath, mtr, osa, ptc, sbi, zma

1 (gnl|ti|998754788)

n.f.

n.e.

miR172

AGAGAUUCUUGAUGAUGCUGAC

22

ath, gma, osa, ptc, sbi, zma

n.f.

1 (PR_miR172)

no

miR319-1

UUGGACUGAAGGGAGCUCCA

20

ath, gma, mtr, ptc, ppt

1 (gnl|ti|862775458)

n.f.

n.e.

miR319-2

CUCGGACUGAAGGGAGCUCCC

21

ath, gma, mtr, ptc, ppt

1 (gnl|ti|997238281)

n.f.

n.e.

miR390-1

GAGCUCAGGAGGGAUAGCGCC

21

ath, ptc, ppt, osa

n.f.

1 (PR_miR390-1)

n.e.

miR390-2a

AAGCUCAGGAGGGAUAGCGCC

21

ath, ptc, ppt, osa

2 (gnl|ti|866247913, gnl|ti|830400956)

n.f.

n.e.

miR395

CUGAAGCGUUUGGGGGAAAGG

21

ath,mtr,osa,ptc, sbi,zma

1 (gnl|ti|997006956)

n.f.

Yes (G)

miR408

CUGCACUGCAUCUUCCCUGUGC

22

ath, osa, ptc, sof, zma

n.f.

1 (PR_miR408)

Yes (G)

miR414

UCAUCCUCAUCAUCCUCGUCC

21

ath, osa

1 (gnl|ti|759459888)

n.f.

Yes (P)

miR418

ACAUGUGAUGAAGAACUGACA

21

ath, osa

n.f.

1 (PR_miR418)

no

miR419

UGAUGAAUGAUGACGAUGUAU

21

ath, osa

n.f.

1 (PR_miR419)

Yes (P/G)

miR473-1

CCUCUCCCUCAAAGGCUUCCA

21

ptc

n.f.

1 (PR_miR473-1)

n.e.

miR473-2

CCUCUCCCUCAAGGCUUCCA

20

ptc

1 (gnl|ti|1042068147)

n.f.

yes (P/G)

miR477

UUCUCCCUCAAAGGCUUCCAA

21

ptc

n.f.

2 (PR1_miR477, PR2_miR477)

yes (P/G)

miR533-1a

GAGCUGGCCAGGCUGUGAGGG

21

ppt

1 (gnl|ti|1006116182)

1 (PR_miR533-1)

n.e.

miR533-2

GAGCUGUCCAGGCUGUGAGGG

21

ppt

1 (gnl|ti|1017424894)

n.f.

n.e.

miR534-1a

UAUGUCCAUUGCAGUUGCAUAC

22

ppt

1 (gnl|ti|890445342)

1 (PR_miR534-1)

n.e.

miR534-2

UAUGUCCAUUACAGUUGCAUAC

22

ppt

1 (gnl|ti|1029229383)

n.f.

n.e.

miR535-1a

UGACAACGAGAGAGAGCACGC

21

osa, ppt

1 (gnl|ti|1020618162)

n.f.

n.e.

miR535-2

UGACAUCGAGAGAGAGCACGC

21

osa,ppt

1 (gnl|ti|1005915069)

n.f.

n.e.

  1. a Identified previously in Physcomitrella [17, 46]. * Identical to a miRNA in other plant species. ath: Arabidopsis thaliana, gma: Glycine max, mtr: Medicago truncatula, osa: Oryza stiva, ptc: Populus trichocarpa, ppt: Physcomitrella patens, sbi: Sorghum bicolor, sof: Saccharum officinarum, zma: Zea mays. Underlined accession numbers of genomic sequences indicate an identity greater than 95% to the EST sequence. n.e.: not examined, n.f.: not found. Different miRNA families are separated by lines. P: expressed in protonema tissue, G: expresses in gametophore tissue.
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BMC Plant Biology

ISSN: 1471-2229

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