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Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton.

Xie F, Wang Q, Sun R, Zhang B - J. Exp. Bot. (2014)

Bottom Line: CitationRank-based literature mining was employed to determinhe the importance of genes related to drought and salinity stress.The NAC, MYB, and MAPK families were ranked top under the context of drought and salinity, indicating their important roles for the plant to combat drought and salinity stress.These results will contribute to cotton stress-resistant breeding as well as understanding fibre development.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, East Carolina University, Greenville, NC 27858, USA.

No MeSH data available.


Related in: MedlinePlus

Size distribution of redundant and unique small RNA reads in cotton. (A and C) Size distribution of redundant small RNA reads from control, drought, and salt libraries. (B and D) Size distribution of unique small RNA reads from control, drought, and salt libraries. (C and D) Small RNA reads were fully mapped back to EST and GSS of upland cotton and the G. ramondii genome.
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Figure 1: Size distribution of redundant and unique small RNA reads in cotton. (A and C) Size distribution of redundant small RNA reads from control, drought, and salt libraries. (B and D) Size distribution of unique small RNA reads from control, drought, and salt libraries. (C and D) Small RNA reads were fully mapped back to EST and GSS of upland cotton and the G. ramondii genome.

Mentions: A total of 51 857 063 reads were generated from the three cotton small RNA libraries generated from salinity (18 808 997) and drought (16 938 676) treatment as well the control (16 109 390), representing a total of 16 126 755 unique sequences (Table 1). As the upland cotton genome is still not available, these sequence reads were first aligned against the GSS and EST databases of upland cotton. An average of 15.99% reads and 51.63% reads were fully (100%) matched back to the upland cotton data sets (EST and GSS) and the D genome of G. ramondii, respectively, resulting in a mean of 54.59% successful matches in upland cotton and G. ramondii (Table 1). Overall, the reads generated and the matched reads are similar in the three libraries. The Jaccard index was calculated for the 5000 most abundant small RNA reads in each library in order to evaluate the overall sequence similarity among the three libraries (Mohorianu et al., 2011). The similarity between salt- and drought-treated libraries was 97.39% (Table 2). Furthermore, the two libraries showed a similar sequence similarity with the control library (control versus drought, 42.27%; and control versus salt, 46.94%), respectively. This indicates that some common small RNAs relatively rich in abundance might be readily induced to cope with abiotic stress in cotton, such as drought and salinity stress. All three libraries displayed similar distributions to other RNA families including rRNA (~1.34% for the unique and ~6.57% for the redundant reads), snRNA (~0.02% for the unique and ~0.01% for the redundant reads), snoRNA (~0.01% for the unique and ~0.00% for the redundant reads), and tRNA (~0.13% for the unique and ~1. 03% for the redundant reads) (Table 1). A similar size distribution for redundant reads, unique reads, and matched unique reads was observed in the three libraries, in which the 24 nucleotide reads account for the majority (Fig. 1). However, the matched redundant reads have the most reads in the 21 nucleotide class following by 24 nucleotides. The small RNA abundance and size in cotton were largely consistent with the results reported in Arabidopsis (Rajagopalan et al., 2006) and rice (Wei et al., 2011).


Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton.

Xie F, Wang Q, Sun R, Zhang B - J. Exp. Bot. (2014)

Size distribution of redundant and unique small RNA reads in cotton. (A and C) Size distribution of redundant small RNA reads from control, drought, and salt libraries. (B and D) Size distribution of unique small RNA reads from control, drought, and salt libraries. (C and D) Small RNA reads were fully mapped back to EST and GSS of upland cotton and the G. ramondii genome.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4321542&req=5

Figure 1: Size distribution of redundant and unique small RNA reads in cotton. (A and C) Size distribution of redundant small RNA reads from control, drought, and salt libraries. (B and D) Size distribution of unique small RNA reads from control, drought, and salt libraries. (C and D) Small RNA reads were fully mapped back to EST and GSS of upland cotton and the G. ramondii genome.
Mentions: A total of 51 857 063 reads were generated from the three cotton small RNA libraries generated from salinity (18 808 997) and drought (16 938 676) treatment as well the control (16 109 390), representing a total of 16 126 755 unique sequences (Table 1). As the upland cotton genome is still not available, these sequence reads were first aligned against the GSS and EST databases of upland cotton. An average of 15.99% reads and 51.63% reads were fully (100%) matched back to the upland cotton data sets (EST and GSS) and the D genome of G. ramondii, respectively, resulting in a mean of 54.59% successful matches in upland cotton and G. ramondii (Table 1). Overall, the reads generated and the matched reads are similar in the three libraries. The Jaccard index was calculated for the 5000 most abundant small RNA reads in each library in order to evaluate the overall sequence similarity among the three libraries (Mohorianu et al., 2011). The similarity between salt- and drought-treated libraries was 97.39% (Table 2). Furthermore, the two libraries showed a similar sequence similarity with the control library (control versus drought, 42.27%; and control versus salt, 46.94%), respectively. This indicates that some common small RNAs relatively rich in abundance might be readily induced to cope with abiotic stress in cotton, such as drought and salinity stress. All three libraries displayed similar distributions to other RNA families including rRNA (~1.34% for the unique and ~6.57% for the redundant reads), snRNA (~0.02% for the unique and ~0.01% for the redundant reads), snoRNA (~0.01% for the unique and ~0.00% for the redundant reads), and tRNA (~0.13% for the unique and ~1. 03% for the redundant reads) (Table 1). A similar size distribution for redundant reads, unique reads, and matched unique reads was observed in the three libraries, in which the 24 nucleotide reads account for the majority (Fig. 1). However, the matched redundant reads have the most reads in the 21 nucleotide class following by 24 nucleotides. The small RNA abundance and size in cotton were largely consistent with the results reported in Arabidopsis (Rajagopalan et al., 2006) and rice (Wei et al., 2011).

Bottom Line: CitationRank-based literature mining was employed to determinhe the importance of genes related to drought and salinity stress.The NAC, MYB, and MAPK families were ranked top under the context of drought and salinity, indicating their important roles for the plant to combat drought and salinity stress.These results will contribute to cotton stress-resistant breeding as well as understanding fibre development.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, East Carolina University, Greenville, NC 27858, USA.

No MeSH data available.


Related in: MedlinePlus