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Novel and conserved miRNAs in the halophyte Suaeda maritima identified by deep sequencing and computational predictions using the ESTs of two mangrove plants.

Gharat SA, Shaw BP - BMC Plant Biol. (2015)

Bottom Line: In addition, 13 novel miRNAs were predicted using the ESTs of two mangrove plants, Rhizophora mangle and Heritiera littoralis, and the precursors of seven miRNAs were found in S. maritima.The distribution of conserved miRNAs among only 25 families indicated the possibility of identifying a greater number of miRNAs with increase in knowledge of the genomes of more halophytes.This study also indicated that the transcriptome of one species can be successfully used to computationally predict the miRNAs in other species, especially those that have similar metabolism, even if they are taxonomically separated.

View Article: PubMed Central - PubMed

Affiliation: Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India. sachingharat113@gmail.com.

ABSTRACT

Background: Although miRNAs are reportedly involved in the salt stress tolerance of plants, miRNA profiling in plants has largely remained restricted to glycophytes, including certain crop species that do not exhibit any tolerance to salinity. Hence, this manuscript describes the results from the miRNA profiling of the halophyte Suaeda maritima, which is used worldwide to study salt tolerance in plants.

Results: A total of 134 conserved miRNAs were identified from unique sRNA reads, with 126 identified using miRBase 21.0 and an additional eight identified using the Plant Non-coding RNA Database. The presence of the precursors of seven conserved miRNAs was validated in S. maritima. In addition, 13 novel miRNAs were predicted using the ESTs of two mangrove plants, Rhizophora mangle and Heritiera littoralis, and the precursors of seven miRNAs were found in S. maritima. Most of the miRNAs considered for characterization were responsive to NaCl application, indicating their importance in the regulation of metabolic activities in plants exposed to salinity. An expression study of the novel miRNAs in plants of diverse ecological and taxonomic groups revealed that two of the miRNAs, sma-miR6 and sma-miR7, were also expressed in Oryza sativa, whereas another two, sma-miR2 and sma-miR5, were only expressed in plants growing under the influence of seawater, similar to S. maritima.

Conclusion: The distribution of conserved miRNAs among only 25 families indicated the possibility of identifying a greater number of miRNAs with increase in knowledge of the genomes of more halophytes. The expression of two novel miRNAs, sma-miR2 and sma-miR5, only in plants growing under the influence of seawater suggested their metabolic regulatory roles specific to saline environments, and such behavior might be mediated by alterations in the expression of certain genes, modifications of proteins leading to changes in their activity and production of secondary metabolites as revealed by the miRNA target predictions. Moreover, the auxin responsive factor targeted by sma-miR7 could also be involved in salt tolerance because the target is conserved between species. This study also indicated that the transcriptome of one species can be successfully used to computationally predict the miRNAs in other species, especially those that have similar metabolism, even if they are taxonomically separated.

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Changes in the abundance of select conserved miRNAs in S. maritima in response to exposure to 340 mM NaCl, which is represented as a fold change relative to the control level. a The conserved miRNAs that showed twofold or more change. b The conserved miRNAs reported to be salt stress responsive. Negative and positive values represent decrease and increase, respectively, in abundance of a miRNA in response to NaCl treatment. RPM- Reads per million; the values are of the control or treated reads, whichever the maximum. The homologous miRNAs of sma-miR165a*, sma-miR165a**, sma-miR166e+, sma-miR166e++, sma-miR159a# and sma-miR159a## are ath-miR165a, aly-miR165a, bdi-miR166e, osa-miR166e, pta-miR159a and ath-miR159a respectively
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Fig2: Changes in the abundance of select conserved miRNAs in S. maritima in response to exposure to 340 mM NaCl, which is represented as a fold change relative to the control level. a The conserved miRNAs that showed twofold or more change. b The conserved miRNAs reported to be salt stress responsive. Negative and positive values represent decrease and increase, respectively, in abundance of a miRNA in response to NaCl treatment. RPM- Reads per million; the values are of the control or treated reads, whichever the maximum. The homologous miRNAs of sma-miR165a*, sma-miR165a**, sma-miR166e+, sma-miR166e++, sma-miR159a# and sma-miR159a## are ath-miR165a, aly-miR165a, bdi-miR166e, osa-miR166e, pta-miR159a and ath-miR159a respectively

Mentions: To determine the salt responsiveness of the identified miRNAs, their relative abundance in the control and NaCl-treated samples was calculated and represented as the fold change after NaCl treatment relative to the control level (Fig. 2). The results of only those miRNAs have been presented that either showed more than twofold change in abundance in response to NaCl exposure (Fig. 2a) or that showed less than twofold NaCl-induced changes in abundance, but reported to be stress responsive (Fig. 2b). The analysis showed great variation in the responses of miRNAs after exposure of the plants to NaCl, and the abundance of sma-miR166j decreased by more than sixfold while that of sma-miR399a increased by more than tenfold in response to the NaCl treatment (Fig. 2a). Among the miRNAs showing less than a twofold change in response to NaCl, the maximum upregulation was observed for sma-miR319a and the maximum downregulation was observed for sma-miR156b (Fig. 2b). In addition, most of the miRNAs that were present in high abundance with RPM (reads per million) of 50 or more showed less than a twofold change in response to salt treatment.Fig. 2


Novel and conserved miRNAs in the halophyte Suaeda maritima identified by deep sequencing and computational predictions using the ESTs of two mangrove plants.

Gharat SA, Shaw BP - BMC Plant Biol. (2015)

Changes in the abundance of select conserved miRNAs in S. maritima in response to exposure to 340 mM NaCl, which is represented as a fold change relative to the control level. a The conserved miRNAs that showed twofold or more change. b The conserved miRNAs reported to be salt stress responsive. Negative and positive values represent decrease and increase, respectively, in abundance of a miRNA in response to NaCl treatment. RPM- Reads per million; the values are of the control or treated reads, whichever the maximum. The homologous miRNAs of sma-miR165a*, sma-miR165a**, sma-miR166e+, sma-miR166e++, sma-miR159a# and sma-miR159a## are ath-miR165a, aly-miR165a, bdi-miR166e, osa-miR166e, pta-miR159a and ath-miR159a respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696257&req=5

Fig2: Changes in the abundance of select conserved miRNAs in S. maritima in response to exposure to 340 mM NaCl, which is represented as a fold change relative to the control level. a The conserved miRNAs that showed twofold or more change. b The conserved miRNAs reported to be salt stress responsive. Negative and positive values represent decrease and increase, respectively, in abundance of a miRNA in response to NaCl treatment. RPM- Reads per million; the values are of the control or treated reads, whichever the maximum. The homologous miRNAs of sma-miR165a*, sma-miR165a**, sma-miR166e+, sma-miR166e++, sma-miR159a# and sma-miR159a## are ath-miR165a, aly-miR165a, bdi-miR166e, osa-miR166e, pta-miR159a and ath-miR159a respectively
Mentions: To determine the salt responsiveness of the identified miRNAs, their relative abundance in the control and NaCl-treated samples was calculated and represented as the fold change after NaCl treatment relative to the control level (Fig. 2). The results of only those miRNAs have been presented that either showed more than twofold change in abundance in response to NaCl exposure (Fig. 2a) or that showed less than twofold NaCl-induced changes in abundance, but reported to be stress responsive (Fig. 2b). The analysis showed great variation in the responses of miRNAs after exposure of the plants to NaCl, and the abundance of sma-miR166j decreased by more than sixfold while that of sma-miR399a increased by more than tenfold in response to the NaCl treatment (Fig. 2a). Among the miRNAs showing less than a twofold change in response to NaCl, the maximum upregulation was observed for sma-miR319a and the maximum downregulation was observed for sma-miR156b (Fig. 2b). In addition, most of the miRNAs that were present in high abundance with RPM (reads per million) of 50 or more showed less than a twofold change in response to salt treatment.Fig. 2

Bottom Line: In addition, 13 novel miRNAs were predicted using the ESTs of two mangrove plants, Rhizophora mangle and Heritiera littoralis, and the precursors of seven miRNAs were found in S. maritima.The distribution of conserved miRNAs among only 25 families indicated the possibility of identifying a greater number of miRNAs with increase in knowledge of the genomes of more halophytes.This study also indicated that the transcriptome of one species can be successfully used to computationally predict the miRNAs in other species, especially those that have similar metabolism, even if they are taxonomically separated.

View Article: PubMed Central - PubMed

Affiliation: Environmental Biotechnology Laboratory, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India. sachingharat113@gmail.com.

ABSTRACT

Background: Although miRNAs are reportedly involved in the salt stress tolerance of plants, miRNA profiling in plants has largely remained restricted to glycophytes, including certain crop species that do not exhibit any tolerance to salinity. Hence, this manuscript describes the results from the miRNA profiling of the halophyte Suaeda maritima, which is used worldwide to study salt tolerance in plants.

Results: A total of 134 conserved miRNAs were identified from unique sRNA reads, with 126 identified using miRBase 21.0 and an additional eight identified using the Plant Non-coding RNA Database. The presence of the precursors of seven conserved miRNAs was validated in S. maritima. In addition, 13 novel miRNAs were predicted using the ESTs of two mangrove plants, Rhizophora mangle and Heritiera littoralis, and the precursors of seven miRNAs were found in S. maritima. Most of the miRNAs considered for characterization were responsive to NaCl application, indicating their importance in the regulation of metabolic activities in plants exposed to salinity. An expression study of the novel miRNAs in plants of diverse ecological and taxonomic groups revealed that two of the miRNAs, sma-miR6 and sma-miR7, were also expressed in Oryza sativa, whereas another two, sma-miR2 and sma-miR5, were only expressed in plants growing under the influence of seawater, similar to S. maritima.

Conclusion: The distribution of conserved miRNAs among only 25 families indicated the possibility of identifying a greater number of miRNAs with increase in knowledge of the genomes of more halophytes. The expression of two novel miRNAs, sma-miR2 and sma-miR5, only in plants growing under the influence of seawater suggested their metabolic regulatory roles specific to saline environments, and such behavior might be mediated by alterations in the expression of certain genes, modifications of proteins leading to changes in their activity and production of secondary metabolites as revealed by the miRNA target predictions. Moreover, the auxin responsive factor targeted by sma-miR7 could also be involved in salt tolerance because the target is conserved between species. This study also indicated that the transcriptome of one species can be successfully used to computationally predict the miRNAs in other species, especially those that have similar metabolism, even if they are taxonomically separated.

Show MeSH
Related in: MedlinePlus