Table 1.
Identification of Putative Arabidopsis miRNA Orthologs of Cloned Cucurbit Phloem miRNA Molecules
| miRNAa | Sequence (5′/3′) | Databases with FASTA Hits | Mismatchesb | Directionc | Arabidopsis Best Hit | Descriptiond | Target Gene Family |
|---|---|---|---|---|---|---|---|
| miR156e | TGACAGAAGAGAGTGAGCAC | Actinidia | 1 | R | At1g69170 | Squamosa-promoter binding protein–related, similar to squamosa-promoter binding protein 1 GI:1183865 from (Antirrhinum majus) | SQUAMOSA-PROMOTER BINDING PROTEIN (SBP-like proteins) |
| Arabidopsis | |||||||
| Populus | |||||||
| Actinidia | 1 | R | At2g42200 | Squamosa-promoter binding protein–related | SBP-like proteins | ||
| Arabidopsis | |||||||
| Eucalyptus | |||||||
| Glycine | |||||||
| Gossypium | |||||||
| Malus | |||||||
| Zea | |||||||
| Arabidopsis | 1 | R | At5g50670 | Expressed protein, contains similarity to squamosa promoter binding protein | SBP-like proteins | ||
| Eucalyptus | |||||||
| Populus | |||||||
| Arabidopsis | 1 to 2 | R | At5g43270 | Squamosa promoter binding protein–related 2 (emb/CAB56576.1) | SBP-like proteins | ||
| Eucalyptus | |||||||
| Pinus | |||||||
| Triticum | |||||||
| Vitis | |||||||
| Glycine | 1 to 3 | R | At1g53160 | Transcription factor–related, similar to GB:X92369 from (A. majus) | SBP-like proteins | ||
| Lolium | |||||||
| Medicago | |||||||
| Pinus | |||||||
| Zea | |||||||
| Actinidia | 2 to 3 | R | At3g15270 | Squamosa promoter binding protein–related 5, identical to GB:CAB56571 from (Arabidopsis) | SBP-like proteins | ||
| Eucalyptus | |||||||
| Lycopersicon | |||||||
| Populus | |||||||
| Vaccinium | |||||||
| miR159e | TTTGGATTGAAGGGAGCTCTA | Arabidopsis | 2 to 3 | R | At5g06100 | Myb family transcription factor, contains Pfam profile: PF00249 myb DNA binding domain | MYB transcription factors |
| Festuca | |||||||
| Populus | |||||||
| Triticum | |||||||
| Arabidopsis | 3 | R | At3g11440 | Myb family transcription factor, contains Pfam profile: PF00249 myb-like DNA binding domain | MYB transcription factors | ||
| Populus | |||||||
| Vitis | |||||||
| Similar to miR167e | TCAAGCTGCCAGCATGATCTGA | Actinidia | 3 | R | At1g30330 | ARF6 (ARF6) mRNA | Auxin response factors |
| Arabidopsis | |||||||
| Eucalyptus | |||||||
| Glycine | |||||||
| Lolium | |||||||
| Malus | |||||||
| Medicago | |||||||
| Pinus | |||||||
| Populus | |||||||
| Triticum | |||||||
| Vaccinium | |||||||
| Zea | |||||||
| Arabidopsis | 3 | R | At5g37020 | Auxin response factor 8 (ARF8) mRNA | Auxin response factors | ||
| Glycine | |||||||
| Medicago | |||||||
| miR171f | TGATTGAGCCGCGCCAATATC | Actinidia | 0 | R | At4g00150 | Scarecrow-like transcription factor 6 (SCL6) | GRAS domain transcription factors (SCARECROW-like) |
| Arabidopsis | |||||||
| Glycine | |||||||
| Lotus | |||||||
| Medicago | |||||||
| Pinus | |||||||
| Populus | |||||||
| Zea | |||||||
| Cucurbita | 0 to 3 | R | At4g36710 | Scarecrow transcription factor family | GRAS domain transcription factors (SCARECROW-like) | ||
| Eucalyptus | |||||||
| Glycine | |||||||
| Lotus | |||||||
| Lycopersicon | |||||||
| Populus |
Cloned and sequenced phloem sap small RNAs were interrogated by conducting FASTA analyses with the sense and complementary sequence directed against an EST-derived database. Sequences within each of these data sets were then mapped by TBLASTX against Arabidopsis genes. miR171 cloned from Arabidopsis apices was used as a control to validate our miRNA target identification process.
Bulges and G:U wobbles were included as mismatches in these analyses.
Direction: R represents the reverse, or complementary, reading frame.
Descriptions are from The Arabidopsis Information Resource ([TAIR]; http://www.arabidopsis.org/info/ontologies).
Phloem-mobile miRNA species.
Not detected in phloem sap.