Identification of the Conserved and Novel miRNAs in Mulberry by High-Throughput Sequencing

<div><p>miRNAs are a class of non-coding endogenous small RNAs. They play vital roles in plant growth, development, and response to biotic and abiotic stress by negatively regulating genes. Mulberry trees are economically important species with multiple uses. However, to date, little is known about mulberry miRNAs and their target genes. In the present study, three small mulberry RNA libraries were constructed and sequenced using high-throughput sequencing technology. Results showed 85 conserved miRNAs belonging to 31 miRNA families and 262 novel miRNAs at 371 loci. Quantitative real-time PCR (qRT-PCR) analysis confirmed the expression pattern of 9 conserved and 5 novel miRNAs in leaves, bark, and male flowers. A total of 332 potential target genes were predicted to be associated with these 113 novel miRNAs. These results provide a basis for further understanding of mulberry miRNAs and the biological processes in which they are involved.</p></div

Additional file 7: Figure S6. of Evolutionary and functional analysis of mulberry type III polyketide synthases

The subcellular localization of mulberry type III polyketide synthases. (A) The control vector pLGNL-EGFP, (B) pLGNL-MnPKS1-EGFP, (C) pLGNL-MnPKS2-EGFP, (D) pLGNL-MnCHS2-EGFP, (E) pLGNL-MnCHS6-EGFP, (G) pLGNL-MnSTS7-EGFP, and (F) pLGNL-MnSTS8-EGFP were transiently expressed in tobacco epidermal cells. Column (a), bright filed; column (b), EGFP fluorescence; and column (c), merged fluorescence. (PDF 3312 kb

The expression profile of 10 target genes belonging to 6 miRNAs in three mulberry tissues (leaf, bark, and male flower) using RT-PCR.

<p>Morus015493 and Morus018032 are the predicted target genes of miR156, so as Morus012124, Morus012122, and Morus012121 for miRn51, Morus008520 for miRn247, Morus019289 for miRn67, Morus011908 for miRn62, Morus002508 and Morus014466 for miRn157. The X axis represents different tissues. L indicates leaf tissue. B indicates bark tissue. MF indicates male flower tissue. The Y axis represents the relative expression level of target genes. MorusXXXXXX represented the target gene ID.</p

Reads per million of conserved miRNAs in mulberry leaves, bark, and male flowers.

<p>A) miRNAs with >1000 reads; B) miRNAs with 30–1000 reads; C) miRNAs with <30 reads. The X axis represents different conserved miRNAs. The Y axis represents the reads per million for different miRNAs. RPM means reads per million.</p

Relative expression of 14 miRNAs in three mulberry tissues (leaf, bark, and male flower) using stem-loop RT-PCR.

<p>The X axis represents different tissues. L indicates leaf tissue. B indicates bark tissue. MF indicates male flower tissue. The Y axis represents the relative expression level of miRNAs.</p

Classification of small RNAs in the mulberry leaves, bark, and male flowers.

<p>Classification of small RNAs in the mulberry leaves, bark, and male flowers.</p

Additional file 3: Figure S2. of Evolutionary and functional analysis of mulberry type III polyketide synthases

Comparison of mulberry type III polyketide synthase amino acid sequences. Conserved sites are shaded. The asterisk indicates the site contains a conserved Thr197 in CHS, but a Gly in PKS1 and PKS2. Purple arrow: positive selection and type II divergence sites; red arrow: positive selection sites; green arrow: type I divergence sites; yellow arrow: type II divergence sites. Red box: catalytic triad; blue box: co-enzyme A binding sites; yellow box: important residues for functional diversity. (PDF 2015 kb

[Adenophora sp.]

原著和名: [記載なし]科名: キキョウ科 = Campanulaceae採集地: 北海道 磯谷郡 蘭越町 港町 (北海道 後志 蘭越町 港町)採集日: 1974/7/21採集者: 萩庭丈壽整理番号: JH023564国立科学博物館整理番号: TNS-VS-973564備考: DB作成協力会による補足あ

Alangium premnifolium Ohwi

原著和名: シマウリノキ科名: ウリノキ科 = Alangiaceae採集地: 鹿児島県 種子島 中種子町 浜津脇 (大隅 種子島 中種子町 浜津脇)採集日: 1970/8/4採集者: 萩庭丈壽整理番号: JH024376国立科学博物館整理番号: TNS-VS-97437