Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - Potential regulatory sequences in monolignol biosynthetic pathway

Seong Siang Ong, R Wickneswari V Ratnam

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Citations (Scopus)

Abstract

Background: Lignin, after cellulose, is the second most abundant biopolymer accounting for approximately 15- 35% of the dry weight of wood. As an important component during wood formation, lignin is indispensable for plant structure and defense. However, it is an undesirable component in the pulp and paper industry. Removal of lignin from cellulose is costly and environmentally hazardous process. Tremendous efforts have been devoted to understand the role of enzymes and genes in controlling the amount and composition of lignin to be deposited in the cell wall. However, studies on the impact of downregulation and overexpression of monolignol biosynthesis genes in model species on lignin content, plant fitness and viability have been inconsistent. Recently, non-coding RNAs have been discovered to play an important role in regulating the entire monolignol biosynthesis pathway. As small RNAs have critical functions in various biological process during wood formation, small RNA profiling is an important tool for the identification of complete set of differentially expressed small RNAs between low lignin and high lignin secondary xylem. Results: In line with this, we have generated two small RNAs libraries from samples with contrasting lignin content using Illumina GAII sequencer. About 10 million sequence reads were obtained in secondary xylem of Am48 with high lignin content (41%) and a corresponding 14 million sequence reads were obtained in secondary xylem of Am54 with low lignin content (21%). Our results suggested that A. mangium small RNAs are composed of a set of 12 highly conserved miRNAs families found in plant miRNAs database, 82 novel miRNAs and a large proportion of non-conserved small RNAs with low expression levels. The predicted target genes of those differentially expressed conserved and non-conserved miRNAs include transcription factors associated with regulation of the lignin biosynthetic pathway genes. Some of these small RNAs play an important role in epigenetic silencing. Differential expression of the small RNAs between secondary xylem tissues with contrasting lignin content suggests that a cascade of miRNAs play an interconnected role in regulating the lignin biosynthetic pathway in Acacia species. Conclusions: Our study critically demonstrated the roles of small RNAs during secondary wall formation. Comparison of the expression pattern of small RNAs between secondary xylem tissues with contrasting lignin content strongly indicated that small RNAs play a key regulatory role during lignin biosynthesis. Our analyses.

Original languageEnglish
Title of host publication10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet)
Volume12
EditionSUPPL. 3
DOIs
Publication statusPublished - 2011
Event10th International Conference on Bioinformatics and 1st ISCB Asia Joint Conference 2011: Computational Biology, InCoB 2011/ISCB-Asia 2011 - Kuala Lumpur
Duration: 30 Nov 20112 Dec 2011

Other

Other10th International Conference on Bioinformatics and 1st ISCB Asia Joint Conference 2011: Computational Biology, InCoB 2011/ISCB-Asia 2011
CityKuala Lumpur
Period30/11/112/12/11

Fingerprint

Acacia
Xylem
Acacia mangium
secondary xylem
regulatory sequences
Lignin
Biosynthetic Pathways
RNA
biochemical pathways
lignin
Tissue
MicroRNAs
Biosynthesis
Genes
Wood
tissues
biosynthesis
Cellulose
cellulose
genes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences (miscellaneous)
  • Artificial Intelligence
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Software
  • Biotechnology
  • Genetics

Cite this

Ong, S. S., & V Ratnam, R. W. (2011). Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - Potential regulatory sequences in monolignol biosynthetic pathway. In 10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet) (SUPPL. 3 ed., Vol. 12). [S13] https://doi.org/10.1186/1471-2164-12-S3-S13

Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - Potential regulatory sequences in monolignol biosynthetic pathway. / Ong, Seong Siang; V Ratnam, R Wickneswari.

10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). Vol. 12 SUPPL. 3. ed. 2011. S13.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ong, SS & V Ratnam, RW 2011, Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - Potential regulatory sequences in monolignol biosynthetic pathway. in 10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). SUPPL. 3 edn, vol. 12, S13, 10th International Conference on Bioinformatics and 1st ISCB Asia Joint Conference 2011: Computational Biology, InCoB 2011/ISCB-Asia 2011, Kuala Lumpur, 30/11/11. https://doi.org/10.1186/1471-2164-12-S3-S13
Ong SS, V Ratnam RW. Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - Potential regulatory sequences in monolignol biosynthetic pathway. In 10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). SUPPL. 3 ed. Vol. 12. 2011. S13 https://doi.org/10.1186/1471-2164-12-S3-S13
Ong, Seong Siang ; V Ratnam, R Wickneswari. / Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - Potential regulatory sequences in monolignol biosynthetic pathway. 10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). Vol. 12 SUPPL. 3. ed. 2011.
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abstract = "Background: Lignin, after cellulose, is the second most abundant biopolymer accounting for approximately 15- 35{\%} of the dry weight of wood. As an important component during wood formation, lignin is indispensable for plant structure and defense. However, it is an undesirable component in the pulp and paper industry. Removal of lignin from cellulose is costly and environmentally hazardous process. Tremendous efforts have been devoted to understand the role of enzymes and genes in controlling the amount and composition of lignin to be deposited in the cell wall. However, studies on the impact of downregulation and overexpression of monolignol biosynthesis genes in model species on lignin content, plant fitness and viability have been inconsistent. Recently, non-coding RNAs have been discovered to play an important role in regulating the entire monolignol biosynthesis pathway. As small RNAs have critical functions in various biological process during wood formation, small RNA profiling is an important tool for the identification of complete set of differentially expressed small RNAs between low lignin and high lignin secondary xylem. Results: In line with this, we have generated two small RNAs libraries from samples with contrasting lignin content using Illumina GAII sequencer. About 10 million sequence reads were obtained in secondary xylem of Am48 with high lignin content (41{\%}) and a corresponding 14 million sequence reads were obtained in secondary xylem of Am54 with low lignin content (21{\%}). Our results suggested that A. mangium small RNAs are composed of a set of 12 highly conserved miRNAs families found in plant miRNAs database, 82 novel miRNAs and a large proportion of non-conserved small RNAs with low expression levels. The predicted target genes of those differentially expressed conserved and non-conserved miRNAs include transcription factors associated with regulation of the lignin biosynthetic pathway genes. Some of these small RNAs play an important role in epigenetic silencing. Differential expression of the small RNAs between secondary xylem tissues with contrasting lignin content suggests that a cascade of miRNAs play an interconnected role in regulating the lignin biosynthetic pathway in Acacia species. Conclusions: Our study critically demonstrated the roles of small RNAs during secondary wall formation. Comparison of the expression pattern of small RNAs between secondary xylem tissues with contrasting lignin content strongly indicated that small RNAs play a key regulatory role during lignin biosynthesis. Our analyses.",
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N2 - Background: Lignin, after cellulose, is the second most abundant biopolymer accounting for approximately 15- 35% of the dry weight of wood. As an important component during wood formation, lignin is indispensable for plant structure and defense. However, it is an undesirable component in the pulp and paper industry. Removal of lignin from cellulose is costly and environmentally hazardous process. Tremendous efforts have been devoted to understand the role of enzymes and genes in controlling the amount and composition of lignin to be deposited in the cell wall. However, studies on the impact of downregulation and overexpression of monolignol biosynthesis genes in model species on lignin content, plant fitness and viability have been inconsistent. Recently, non-coding RNAs have been discovered to play an important role in regulating the entire monolignol biosynthesis pathway. As small RNAs have critical functions in various biological process during wood formation, small RNA profiling is an important tool for the identification of complete set of differentially expressed small RNAs between low lignin and high lignin secondary xylem. Results: In line with this, we have generated two small RNAs libraries from samples with contrasting lignin content using Illumina GAII sequencer. About 10 million sequence reads were obtained in secondary xylem of Am48 with high lignin content (41%) and a corresponding 14 million sequence reads were obtained in secondary xylem of Am54 with low lignin content (21%). Our results suggested that A. mangium small RNAs are composed of a set of 12 highly conserved miRNAs families found in plant miRNAs database, 82 novel miRNAs and a large proportion of non-conserved small RNAs with low expression levels. The predicted target genes of those differentially expressed conserved and non-conserved miRNAs include transcription factors associated with regulation of the lignin biosynthetic pathway genes. Some of these small RNAs play an important role in epigenetic silencing. Differential expression of the small RNAs between secondary xylem tissues with contrasting lignin content suggests that a cascade of miRNAs play an interconnected role in regulating the lignin biosynthetic pathway in Acacia species. Conclusions: Our study critically demonstrated the roles of small RNAs during secondary wall formation. Comparison of the expression pattern of small RNAs between secondary xylem tissues with contrasting lignin content strongly indicated that small RNAs play a key regulatory role during lignin biosynthesis. Our analyses.

AB - Background: Lignin, after cellulose, is the second most abundant biopolymer accounting for approximately 15- 35% of the dry weight of wood. As an important component during wood formation, lignin is indispensable for plant structure and defense. However, it is an undesirable component in the pulp and paper industry. Removal of lignin from cellulose is costly and environmentally hazardous process. Tremendous efforts have been devoted to understand the role of enzymes and genes in controlling the amount and composition of lignin to be deposited in the cell wall. However, studies on the impact of downregulation and overexpression of monolignol biosynthesis genes in model species on lignin content, plant fitness and viability have been inconsistent. Recently, non-coding RNAs have been discovered to play an important role in regulating the entire monolignol biosynthesis pathway. As small RNAs have critical functions in various biological process during wood formation, small RNA profiling is an important tool for the identification of complete set of differentially expressed small RNAs between low lignin and high lignin secondary xylem. Results: In line with this, we have generated two small RNAs libraries from samples with contrasting lignin content using Illumina GAII sequencer. About 10 million sequence reads were obtained in secondary xylem of Am48 with high lignin content (41%) and a corresponding 14 million sequence reads were obtained in secondary xylem of Am54 with low lignin content (21%). Our results suggested that A. mangium small RNAs are composed of a set of 12 highly conserved miRNAs families found in plant miRNAs database, 82 novel miRNAs and a large proportion of non-conserved small RNAs with low expression levels. The predicted target genes of those differentially expressed conserved and non-conserved miRNAs include transcription factors associated with regulation of the lignin biosynthetic pathway genes. Some of these small RNAs play an important role in epigenetic silencing. Differential expression of the small RNAs between secondary xylem tissues with contrasting lignin content suggests that a cascade of miRNAs play an interconnected role in regulating the lignin biosynthetic pathway in Acacia species. Conclusions: Our study critically demonstrated the roles of small RNAs during secondary wall formation. Comparison of the expression pattern of small RNAs between secondary xylem tissues with contrasting lignin content strongly indicated that small RNAs play a key regulatory role during lignin biosynthesis. Our analyses.

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