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. 2010:2010:128297.
doi: 10.1155/2010/128297. Epub 2010 Aug 2.

Computational Identification of Novel MicroRNAs and Their Targets in Vigna unguiculata

Yongzhong Lu  1 , Xiaoyun Yang
Affiliations

Computational Identification of Novel MicroRNAs and Their Targets in Vigna unguiculata

Yongzhong Lu et al. Comp Funct Genomics. 2010.

Abstract

MicroRNAs (miRNAs) are a class of endogenous, noncoding, short RNAs directly involved in regulating gene expression at the posttranscriptional level. High conservation of miRNAs in plant provides the foundation for identification of new miRNAs in other plant species through homology alignment. Here, previous known plant miRNAs were BLASTed against the Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS) databases of Vigna unguiculata, and according to a series of filtering criteria, a total of 47 miRNAs belonging to 13 miRNA families were identified, and 30 potential target genes of them were subsequently predicted, most of which seemed to encode transcription factors or enzymes participating in regulation of development, growth, metabolism, and other physiological processes. Overall, our findings lay the foundation for further researches of miRNAs function in Vigna unguiculata.

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Figures

Figure 1
Figure 1
Flowchart of Vigna unguiculata miRNA prediction.
Figure 2
Figure 2
Secondary structures of Vigna unguiculata new miRNA precursors. (a) vun-MIR156 precursor 1 (vun-MIR156a (2 to 21); vun-MIR156b (5 to 24); vun-MIR156c (1 to 21); vun-MIR156d (2 to 22)). (b) vun-MIR156 precursor 2 (vun-MIR156f (2 to 22); vun-MIR156g (1 to 21); vun-MIR156h (2 to 21)). (c) vun-MIR156 precursor 3 (vun-MIR156i (2 to 22); vun-MIR156j (1 to 21); vun-MIR156k (2 to 21)). (d) vun-MIR157 precursor (vun-MIR157a (1 to21); vun-MIR157b (2 to 21); vun-MIR157c (2 to 22)). (e) vun-MIR160 precursor (vun-MIR160a (1 to 21); vun-MIR160b (1 to 20)). (f) vun-MIR164 precursor (vun-MIR164 (1 to 21)). (g) vun-MIR169 precursor (vun-MIR169a (2 to 23); vun-MIR169b (2 to 22); vun-MIR169c (1 to 21)). (h) vun-MIR172 precursor 1 (vun-MIR172a (85 to 108); vun-MIR172c (85 to 105); vun-MIR172e (85 to 104)). (i) vun-MIR172 precursor 2 (vun-MIR172b (81 to 101); vun-MIR172d (81 to 100)). (j) vun-MIR319 precursor 1 (vun-MIR319a (152 to 172); vun-MIR319b (151 to 171); vun-MIR319c (152 to 171); vun-MIR319d (151 to 170); vun-MIR319e (152 to 170)). (k) vun-MIR319 precursor 2 (vun-MIR159 (167 to 187); vun-MIR319f (168 to 188); vun-MIR319g (167 to 186); vun-MIR319h (168 to 187); vun-MIR319i (168 to 186)). (l) vun-MIR395 precursor (vun-MIR395a (60 to 81); vun-MIR395b (60 to 80)). (m) vun-MIR399 precursor 1 (vun-MIR399a (57 to 77); vun-MIR399b (57 to 75)). (n) vun-MIR399 precursor 2 (vun-MIR399c (53 to 73); vun-MIR399d (53 to 71)). (o) vun-MIR1507 precursor 1 (vun-MIR1507a (67 to 88); vun-MIR1507b (67 to 87)). (p) vun-MIR1507 precursor 2 (vun-MIR1507c (67 to 88); vun-MIR1507d (67 to 87)). (q) vun-MIR2118 precursor (vun-MIR2118 (54 to 75)). (r) vun-MIR482 precursor (vun-MIR482 (57 to 80)). The position of each miRNA was shown in parentheses.
Figure 2
Figure 2
Secondary structures of Vigna unguiculata new miRNA precursors. (a) vun-MIR156 precursor 1 (vun-MIR156a (2 to 21); vun-MIR156b (5 to 24); vun-MIR156c (1 to 21); vun-MIR156d (2 to 22)). (b) vun-MIR156 precursor 2 (vun-MIR156f (2 to 22); vun-MIR156g (1 to 21); vun-MIR156h (2 to 21)). (c) vun-MIR156 precursor 3 (vun-MIR156i (2 to 22); vun-MIR156j (1 to 21); vun-MIR156k (2 to 21)). (d) vun-MIR157 precursor (vun-MIR157a (1 to21); vun-MIR157b (2 to 21); vun-MIR157c (2 to 22)). (e) vun-MIR160 precursor (vun-MIR160a (1 to 21); vun-MIR160b (1 to 20)). (f) vun-MIR164 precursor (vun-MIR164 (1 to 21)). (g) vun-MIR169 precursor (vun-MIR169a (2 to 23); vun-MIR169b (2 to 22); vun-MIR169c (1 to 21)). (h) vun-MIR172 precursor 1 (vun-MIR172a (85 to 108); vun-MIR172c (85 to 105); vun-MIR172e (85 to 104)). (i) vun-MIR172 precursor 2 (vun-MIR172b (81 to 101); vun-MIR172d (81 to 100)). (j) vun-MIR319 precursor 1 (vun-MIR319a (152 to 172); vun-MIR319b (151 to 171); vun-MIR319c (152 to 171); vun-MIR319d (151 to 170); vun-MIR319e (152 to 170)). (k) vun-MIR319 precursor 2 (vun-MIR159 (167 to 187); vun-MIR319f (168 to 188); vun-MIR319g (167 to 186); vun-MIR319h (168 to 187); vun-MIR319i (168 to 186)). (l) vun-MIR395 precursor (vun-MIR395a (60 to 81); vun-MIR395b (60 to 80)). (m) vun-MIR399 precursor 1 (vun-MIR399a (57 to 77); vun-MIR399b (57 to 75)). (n) vun-MIR399 precursor 2 (vun-MIR399c (53 to 73); vun-MIR399d (53 to 71)). (o) vun-MIR1507 precursor 1 (vun-MIR1507a (67 to 88); vun-MIR1507b (67 to 87)). (p) vun-MIR1507 precursor 2 (vun-MIR1507c (67 to 88); vun-MIR1507d (67 to 87)). (q) vun-MIR2118 precursor (vun-MIR2118 (54 to 75)). (r) vun-MIR482 precursor (vun-MIR482 (57 to 80)). The position of each miRNA was shown in parentheses.
Figure 2
Figure 2
Secondary structures of Vigna unguiculata new miRNA precursors. (a) vun-MIR156 precursor 1 (vun-MIR156a (2 to 21); vun-MIR156b (5 to 24); vun-MIR156c (1 to 21); vun-MIR156d (2 to 22)). (b) vun-MIR156 precursor 2 (vun-MIR156f (2 to 22); vun-MIR156g (1 to 21); vun-MIR156h (2 to 21)). (c) vun-MIR156 precursor 3 (vun-MIR156i (2 to 22); vun-MIR156j (1 to 21); vun-MIR156k (2 to 21)). (d) vun-MIR157 precursor (vun-MIR157a (1 to21); vun-MIR157b (2 to 21); vun-MIR157c (2 to 22)). (e) vun-MIR160 precursor (vun-MIR160a (1 to 21); vun-MIR160b (1 to 20)). (f) vun-MIR164 precursor (vun-MIR164 (1 to 21)). (g) vun-MIR169 precursor (vun-MIR169a (2 to 23); vun-MIR169b (2 to 22); vun-MIR169c (1 to 21)). (h) vun-MIR172 precursor 1 (vun-MIR172a (85 to 108); vun-MIR172c (85 to 105); vun-MIR172e (85 to 104)). (i) vun-MIR172 precursor 2 (vun-MIR172b (81 to 101); vun-MIR172d (81 to 100)). (j) vun-MIR319 precursor 1 (vun-MIR319a (152 to 172); vun-MIR319b (151 to 171); vun-MIR319c (152 to 171); vun-MIR319d (151 to 170); vun-MIR319e (152 to 170)). (k) vun-MIR319 precursor 2 (vun-MIR159 (167 to 187); vun-MIR319f (168 to 188); vun-MIR319g (167 to 186); vun-MIR319h (168 to 187); vun-MIR319i (168 to 186)). (l) vun-MIR395 precursor (vun-MIR395a (60 to 81); vun-MIR395b (60 to 80)). (m) vun-MIR399 precursor 1 (vun-MIR399a (57 to 77); vun-MIR399b (57 to 75)). (n) vun-MIR399 precursor 2 (vun-MIR399c (53 to 73); vun-MIR399d (53 to 71)). (o) vun-MIR1507 precursor 1 (vun-MIR1507a (67 to 88); vun-MIR1507b (67 to 87)). (p) vun-MIR1507 precursor 2 (vun-MIR1507c (67 to 88); vun-MIR1507d (67 to 87)). (q) vun-MIR2118 precursor (vun-MIR2118 (54 to 75)). (r) vun-MIR482 precursor (vun-MIR482 (57 to 80)). The position of each miRNA was shown in parentheses.
Figure 2
Figure 2
Secondary structures of Vigna unguiculata new miRNA precursors. (a) vun-MIR156 precursor 1 (vun-MIR156a (2 to 21); vun-MIR156b (5 to 24); vun-MIR156c (1 to 21); vun-MIR156d (2 to 22)). (b) vun-MIR156 precursor 2 (vun-MIR156f (2 to 22); vun-MIR156g (1 to 21); vun-MIR156h (2 to 21)). (c) vun-MIR156 precursor 3 (vun-MIR156i (2 to 22); vun-MIR156j (1 to 21); vun-MIR156k (2 to 21)). (d) vun-MIR157 precursor (vun-MIR157a (1 to21); vun-MIR157b (2 to 21); vun-MIR157c (2 to 22)). (e) vun-MIR160 precursor (vun-MIR160a (1 to 21); vun-MIR160b (1 to 20)). (f) vun-MIR164 precursor (vun-MIR164 (1 to 21)). (g) vun-MIR169 precursor (vun-MIR169a (2 to 23); vun-MIR169b (2 to 22); vun-MIR169c (1 to 21)). (h) vun-MIR172 precursor 1 (vun-MIR172a (85 to 108); vun-MIR172c (85 to 105); vun-MIR172e (85 to 104)). (i) vun-MIR172 precursor 2 (vun-MIR172b (81 to 101); vun-MIR172d (81 to 100)). (j) vun-MIR319 precursor 1 (vun-MIR319a (152 to 172); vun-MIR319b (151 to 171); vun-MIR319c (152 to 171); vun-MIR319d (151 to 170); vun-MIR319e (152 to 170)). (k) vun-MIR319 precursor 2 (vun-MIR159 (167 to 187); vun-MIR319f (168 to 188); vun-MIR319g (167 to 186); vun-MIR319h (168 to 187); vun-MIR319i (168 to 186)). (l) vun-MIR395 precursor (vun-MIR395a (60 to 81); vun-MIR395b (60 to 80)). (m) vun-MIR399 precursor 1 (vun-MIR399a (57 to 77); vun-MIR399b (57 to 75)). (n) vun-MIR399 precursor 2 (vun-MIR399c (53 to 73); vun-MIR399d (53 to 71)). (o) vun-MIR1507 precursor 1 (vun-MIR1507a (67 to 88); vun-MIR1507b (67 to 87)). (p) vun-MIR1507 precursor 2 (vun-MIR1507c (67 to 88); vun-MIR1507d (67 to 87)). (q) vun-MIR2118 precursor (vun-MIR2118 (54 to 75)). (r) vun-MIR482 precursor (vun-MIR482 (57 to 80)). The position of each miRNA was shown in parentheses.
Figure 2
Figure 2
Secondary structures of Vigna unguiculata new miRNA precursors. (a) vun-MIR156 precursor 1 (vun-MIR156a (2 to 21); vun-MIR156b (5 to 24); vun-MIR156c (1 to 21); vun-MIR156d (2 to 22)). (b) vun-MIR156 precursor 2 (vun-MIR156f (2 to 22); vun-MIR156g (1 to 21); vun-MIR156h (2 to 21)). (c) vun-MIR156 precursor 3 (vun-MIR156i (2 to 22); vun-MIR156j (1 to 21); vun-MIR156k (2 to 21)). (d) vun-MIR157 precursor (vun-MIR157a (1 to21); vun-MIR157b (2 to 21); vun-MIR157c (2 to 22)). (e) vun-MIR160 precursor (vun-MIR160a (1 to 21); vun-MIR160b (1 to 20)). (f) vun-MIR164 precursor (vun-MIR164 (1 to 21)). (g) vun-MIR169 precursor (vun-MIR169a (2 to 23); vun-MIR169b (2 to 22); vun-MIR169c (1 to 21)). (h) vun-MIR172 precursor 1 (vun-MIR172a (85 to 108); vun-MIR172c (85 to 105); vun-MIR172e (85 to 104)). (i) vun-MIR172 precursor 2 (vun-MIR172b (81 to 101); vun-MIR172d (81 to 100)). (j) vun-MIR319 precursor 1 (vun-MIR319a (152 to 172); vun-MIR319b (151 to 171); vun-MIR319c (152 to 171); vun-MIR319d (151 to 170); vun-MIR319e (152 to 170)). (k) vun-MIR319 precursor 2 (vun-MIR159 (167 to 187); vun-MIR319f (168 to 188); vun-MIR319g (167 to 186); vun-MIR319h (168 to 187); vun-MIR319i (168 to 186)). (l) vun-MIR395 precursor (vun-MIR395a (60 to 81); vun-MIR395b (60 to 80)). (m) vun-MIR399 precursor 1 (vun-MIR399a (57 to 77); vun-MIR399b (57 to 75)). (n) vun-MIR399 precursor 2 (vun-MIR399c (53 to 73); vun-MIR399d (53 to 71)). (o) vun-MIR1507 precursor 1 (vun-MIR1507a (67 to 88); vun-MIR1507b (67 to 87)). (p) vun-MIR1507 precursor 2 (vun-MIR1507c (67 to 88); vun-MIR1507d (67 to 87)). (q) vun-MIR2118 precursor (vun-MIR2118 (54 to 75)). (r) vun-MIR482 precursor (vun-MIR482 (57 to 80)). The position of each miRNA was shown in parentheses.
Figure 2
Figure 2
Secondary structures of Vigna unguiculata new miRNA precursors. (a) vun-MIR156 precursor 1 (vun-MIR156a (2 to 21); vun-MIR156b (5 to 24); vun-MIR156c (1 to 21); vun-MIR156d (2 to 22)). (b) vun-MIR156 precursor 2 (vun-MIR156f (2 to 22); vun-MIR156g (1 to 21); vun-MIR156h (2 to 21)). (c) vun-MIR156 precursor 3 (vun-MIR156i (2 to 22); vun-MIR156j (1 to 21); vun-MIR156k (2 to 21)). (d) vun-MIR157 precursor (vun-MIR157a (1 to21); vun-MIR157b (2 to 21); vun-MIR157c (2 to 22)). (e) vun-MIR160 precursor (vun-MIR160a (1 to 21); vun-MIR160b (1 to 20)). (f) vun-MIR164 precursor (vun-MIR164 (1 to 21)). (g) vun-MIR169 precursor (vun-MIR169a (2 to 23); vun-MIR169b (2 to 22); vun-MIR169c (1 to 21)). (h) vun-MIR172 precursor 1 (vun-MIR172a (85 to 108); vun-MIR172c (85 to 105); vun-MIR172e (85 to 104)). (i) vun-MIR172 precursor 2 (vun-MIR172b (81 to 101); vun-MIR172d (81 to 100)). (j) vun-MIR319 precursor 1 (vun-MIR319a (152 to 172); vun-MIR319b (151 to 171); vun-MIR319c (152 to 171); vun-MIR319d (151 to 170); vun-MIR319e (152 to 170)). (k) vun-MIR319 precursor 2 (vun-MIR159 (167 to 187); vun-MIR319f (168 to 188); vun-MIR319g (167 to 186); vun-MIR319h (168 to 187); vun-MIR319i (168 to 186)). (l) vun-MIR395 precursor (vun-MIR395a (60 to 81); vun-MIR395b (60 to 80)). (m) vun-MIR399 precursor 1 (vun-MIR399a (57 to 77); vun-MIR399b (57 to 75)). (n) vun-MIR399 precursor 2 (vun-MIR399c (53 to 73); vun-MIR399d (53 to 71)). (o) vun-MIR1507 precursor 1 (vun-MIR1507a (67 to 88); vun-MIR1507b (67 to 87)). (p) vun-MIR1507 precursor 2 (vun-MIR1507c (67 to 88); vun-MIR1507d (67 to 87)). (q) vun-MIR2118 precursor (vun-MIR2118 (54 to 75)). (r) vun-MIR482 precursor (vun-MIR482 (57 to 80)). The position of each miRNA was shown in parentheses.
Figure 3
Figure 3
The distribution of new miRNAs in different miRNA families.
Figure 4
Figure 4
Phylogenetic analysis of miRNAs in different families.
Figure 4
Figure 4
Phylogenetic analysis of miRNAs in different families.
Figure 4
Figure 4
Phylogenetic analysis of miRNAs in different families.
Figure 4
Figure 4
Phylogenetic analysis of miRNAs in different families.
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