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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

Length distribution of redundant and unique sRNA sequences.The length distribution of redundant and unique sRNAs in ZP03-5373 (a) and ZP03-5413 (b). The 21-nt of redundant is the predominant sRNA species and the 24-nt of unique is the most abundant.
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pone-0110051-g001: Length distribution of redundant and unique sRNA sequences.The length distribution of redundant and unique sRNAs in ZP03-5373 (a) and ZP03-5413 (b). The 21-nt of redundant is the predominant sRNA species and the 24-nt of unique is the most abundant.

Mentions: To investigate the role of soybean miRNAs in response to SCN infection, two genetically related soybean sister lines (ZP03-5373 and ZP03-5413) were subjected to deep sequencing. The sister lines shared the same parents and displayed a different resistance to SCN race 4. Line ZP03-5373 exhibited high resistance to SCN race 4, whereas ZP03-5413 was susceptible to race 4. Two sRNA libraries from the roots of the sister lines were constructed and sequenced using Illumina GAIIx. A total of 15,101,204 sRNA raw reads were generated. After removing adaptor sequences, filtering out low quality reads and cleaning up sequences derived from adaptor–adaptor ligation, 7,903,242 and 5,931,837 reads, respectively, were obtained. These sRNAs consisted of 4,979,640 unique sequences (Table S1), which were matched to the public soybean genomic database (Soybean Genome V9.0, http://www.phytozome.net/index.php) using the SOAP program, leading to 3,409,866 genome-matched unique reads. These reads were subjected to further analysis (Table S1). The 20–24-nt sRNAs constituted over 80% of the identified soybean sRNAs, and the 21-nt class of sRNAs was the most abundant in both lines (Figure 1A). Notably, the expression of the unique 24-nt sRNAs was markedly higher than the 21-nt class in both lines (Figure 1B).


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)

Length distribution of redundant and unique sRNA sequences.The length distribution of redundant and unique sRNAs in ZP03-5373 (a) and ZP03-5413 (b). The 21-nt of redundant is the predominant sRNA species and the 24-nt of unique is the most abundant.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110051-g001: Length distribution of redundant and unique sRNA sequences.The length distribution of redundant and unique sRNAs in ZP03-5373 (a) and ZP03-5413 (b). The 21-nt of redundant is the predominant sRNA species and the 24-nt of unique is the most abundant.
Mentions: To investigate the role of soybean miRNAs in response to SCN infection, two genetically related soybean sister lines (ZP03-5373 and ZP03-5413) were subjected to deep sequencing. The sister lines shared the same parents and displayed a different resistance to SCN race 4. Line ZP03-5373 exhibited high resistance to SCN race 4, whereas ZP03-5413 was susceptible to race 4. Two sRNA libraries from the roots of the sister lines were constructed and sequenced using Illumina GAIIx. A total of 15,101,204 sRNA raw reads were generated. After removing adaptor sequences, filtering out low quality reads and cleaning up sequences derived from adaptor–adaptor ligation, 7,903,242 and 5,931,837 reads, respectively, were obtained. These sRNAs consisted of 4,979,640 unique sequences (Table S1), which were matched to the public soybean genomic database (Soybean Genome V9.0, http://www.phytozome.net/index.php) using the SOAP program, leading to 3,409,866 genome-matched unique reads. These reads were subjected to further analysis (Table S1). The 20–24-nt sRNAs constituted over 80% of the identified soybean sRNAs, and the 21-nt class of sRNAs was the most abundant in both lines (Figure 1A). Notably, the expression of the unique 24-nt sRNAs was markedly higher than the 21-nt class in both lines (Figure 1B).

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