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Novel miRNA and phasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4.

Xu M, Li Y, Zhang Q, Xu T, Qiu L, Fan Y, Wang L - PLoS ONE (2014)

Bottom Line: In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root.Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines.These findings suggest that miRNAs play an important role in the soybean response to SCN.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Research Institute, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.

ABSTRACT
The soybean cyst nematode (SCN), Heterodera glycines, is the most devastating pathogen of soybean worldwide. SiRNAs (small interfere RNAs) have been proven to induce the silencing of cyst nematode genes. However, whether small RNAs from soybean root have evolved a similar mechanism against SCN is unknown. Two genetically related soybean sister lines (ZP03-5373 and ZP03-5413), which are resistant and susceptible, respectively, to SCN race 4 infection were selected for small RNA deep sequencing to identify small RNAs targeted to SCN. We identified 71 less-conserved miRNAs-miRNAs* counterparts belonging to 32 families derived from 91 loci, and 88 novel soybean-specific miRNAs with distinct expression patterns. The identified miRNAs targeted 42 genes representing a wide range of enzymatic and regulatory activities. Roots of soybean conserved one TAS (Trans-acting siRNA) gene family with a similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profile. In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root. Multiple targets of these phasiRNAs were predicted and detected. Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines. Seven ZP03-5373-specific miRNAs were differentially expressed after SCN infection. Forty-four transcripts from SCN were predicted to be potential targets of ZP03-5373-specific differential miRNAs. These findings suggest that miRNAs play an important role in the soybean response to SCN.

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Related in: MedlinePlus

Five novel phasi-acting siRNA biogenesis pathways in soybean root.The abundance of each secondary siRNAs is plotted (left). The phasing secondary siRNAs corresponding to the miRNA cleavage sites are highlighted in red. The miRNA complementary sites are shown with red arrows. The length distribution is plotted on the right (middle). The phasing radial graph is represented next to this (right). Each spoke of the radial graph represents 1 of the 21 phasing registers, with the total number of sRNAs mapping to that register plotted as distance from the center. A, sense transcript; AS, antisense transcript.
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pone-0110051-g003: Five novel phasi-acting siRNA biogenesis pathways in soybean root.The abundance of each secondary siRNAs is plotted (left). The phasing secondary siRNAs corresponding to the miRNA cleavage sites are highlighted in red. The miRNA complementary sites are shown with red arrows. The length distribution is plotted on the right (middle). The phasing radial graph is represented next to this (right). Each spoke of the radial graph represents 1 of the 21 phasing registers, with the total number of sRNAs mapping to that register plotted as distance from the center. A, sense transcript; AS, antisense transcript.

Mentions: The secondary small RNAs derived from all identified miRNA targets by PsRobot [16] in soybean were searched, and four transcripts (Glyma01g33270.1, Glyma04g29220.3, Glyma09g02920.2, Glyma05g33260.1), targeted respectively by gma-miR171, gma-miR1507, gma-miR1515, and gma-miR2118, were identified to produce secondary siRNAs (Figure 3).


Novel miRNA and phasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4.

Xu M, Li Y, Zhang Q, Xu T, Qiu L, Fan Y, Wang L - PLoS ONE (2014)

Five novel phasi-acting siRNA biogenesis pathways in soybean root.The abundance of each secondary siRNAs is plotted (left). The phasing secondary siRNAs corresponding to the miRNA cleavage sites are highlighted in red. The miRNA complementary sites are shown with red arrows. The length distribution is plotted on the right (middle). The phasing radial graph is represented next to this (right). Each spoke of the radial graph represents 1 of the 21 phasing registers, with the total number of sRNAs mapping to that register plotted as distance from the center. A, sense transcript; AS, antisense transcript.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4214822&req=5

pone-0110051-g003: Five novel phasi-acting siRNA biogenesis pathways in soybean root.The abundance of each secondary siRNAs is plotted (left). The phasing secondary siRNAs corresponding to the miRNA cleavage sites are highlighted in red. The miRNA complementary sites are shown with red arrows. The length distribution is plotted on the right (middle). The phasing radial graph is represented next to this (right). Each spoke of the radial graph represents 1 of the 21 phasing registers, with the total number of sRNAs mapping to that register plotted as distance from the center. A, sense transcript; AS, antisense transcript.
Mentions: The secondary small RNAs derived from all identified miRNA targets by PsRobot [16] in soybean were searched, and four transcripts (Glyma01g33270.1, Glyma04g29220.3, Glyma09g02920.2, Glyma05g33260.1), targeted respectively by gma-miR171, gma-miR1507, gma-miR1515, and gma-miR2118, were identified to produce secondary siRNAs (Figure 3).

Bottom Line: In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root.Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines.These findings suggest that miRNAs play an important role in the soybean response to SCN.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Research Institute, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.

ABSTRACT
The soybean cyst nematode (SCN), Heterodera glycines, is the most devastating pathogen of soybean worldwide. SiRNAs (small interfere RNAs) have been proven to induce the silencing of cyst nematode genes. However, whether small RNAs from soybean root have evolved a similar mechanism against SCN is unknown. Two genetically related soybean sister lines (ZP03-5373 and ZP03-5413), which are resistant and susceptible, respectively, to SCN race 4 infection were selected for small RNA deep sequencing to identify small RNAs targeted to SCN. We identified 71 less-conserved miRNAs-miRNAs* counterparts belonging to 32 families derived from 91 loci, and 88 novel soybean-specific miRNAs with distinct expression patterns. The identified miRNAs targeted 42 genes representing a wide range of enzymatic and regulatory activities. Roots of soybean conserved one TAS (Trans-acting siRNA) gene family with a similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profile. In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root. Multiple targets of these phasiRNAs were predicted and detected. Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines. Seven ZP03-5373-specific miRNAs were differentially expressed after SCN infection. Forty-four transcripts from SCN were predicted to be potential targets of ZP03-5373-specific differential miRNAs. These findings suggest that miRNAs play an important role in the soybean response to SCN.

Show MeSH
Related in: MedlinePlus