Extensive DNA Sequence Variations in Two Lignin Genes, Cinnamate 4-Hydroxylase and Cinnamyl Alcohol Dehydrogenase from Acacia mangium and Acacia auriculiformis

Fariza, M.S. Nur; Pang, Shek Ling; Choong, Chee Yen; Wickneswari, R.

doi:10.3923/jbs.2008.687.690

Cited by 8 publications

(5 citation statements)

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“…The total number of isoforms detected in this study is generally lower than those found in A. thaliana [ 36 ] and P. trichocarpa [ 37 ]. The identified isoforms possessed 99% DNA sequence identity with previously characterized isoforms from A. auriculiformis × A. mangium hybrid for the five isoforms that we examined, namely PAL, C4H, COMT, CCoAOMT, and CAD [ 31 ]. The high sequence similarity between of A. auriculiformis , A. mangium and their hybrids will allow more efficient cross amplification in gene isolation and characterization efforts.…”

Section: Resultsmentioning

confidence: 88%

“…One SNP was estimated to occur in every 1,123 bp and 1,704 bp in the Aa and Am transcriptomes, respectively. Although these SNPs represent only a portion of the Acacia transcriptome, this study has provided a better SNPs estimation compared to a previous study [ 31 ] which was based on the SNPs variation in two lignin genes. Further investigations are being carried to validate these SNPs which are useful for the construction of Acacia hybrid linkage map.…”

Section: Resultsmentioning

confidence: 99%

“…However, no genomic resources is available for A. auriculiformis . Several important genes involved in monolignol biosynthesis and wood-related pathways including cinammate 4-hydroxylase (C4H), caffeoyl CoA 3-O-methyltransferase (CCoAOMT), cinnamyl alcohol dehydrogenase (CAD), phenylalanine ammonia lyase (PAL), caffeic acid O-methyltransferase (COMT) and cellulose synthase (CesA) have been successfully isolated and characterized from the Acacia hybrid [ 30 , 31 ].…”

Section: Introductionmentioning

confidence: 99%

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Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

2011

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BackgroundAcacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants.ResultsWe sequenced transcriptomes of A. auriculiformis and A. mangium from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. De novo assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for A. auriculiformis and A. mangium respectively. The assemblies of A. auriculiformis and A. mangium had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168) and one legume-specific family (miR2086). Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs) in the transcriptomes of A. auriculiformis and A. mangium, respectively, thus yielding useful markers for population genetics studies and marker-assisted selection.ConclusionWe have produced the first comprehensive transcriptome-wide analysis in A. auriculiformis and A. mangium using de novo assembly techniques. Our high quality and comprehensive assemblies allowed the identification of many genes in the lignin biosynthesis and secondary cell wall formation in Acacia hybrids. Our results demonstrated that Next Generation Sequencing is a cost-effective method for gene discovery, identification of regulatory sequences, and informative markers in a non-model plant.

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Section: Resultsmentioning

confidence: 88%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

2011

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“…In vitro SNPs were identified from cinammate 4 hydroxylase (C4H) and cinnamyl alcohol dehydrogenase (CAD) genes by sequencing 6 to 8 cDNA clones for each of the four parents [68]. These in vitro SNPs were validated using Illumina GoldenGate Assay in the natural germplasms [63].…”

Section: Methodsmentioning

confidence: 99%

Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data

2012

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BackgroundNext Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP) discovery in Acacia auriculiformis and Acacia mangium. Like other non-model species, SNP detection and genotyping in Acacia are challenging due to lack of genome sequences. The main objective of this study is to develop the first high-throughput SNP genotyping assay for linkage map construction of A. auriculiformis x A. mangium hybrids.ResultsWe identified a total of 37,786 putative SNPs by aligning short read transcriptome data from four parents of two Acacia hybrid mapping populations using Bowtie against 7,839 de novo transcriptome contigs. Given a set of 10 validated SNPs from two lignin genes, our in silico SNP detection approach is highly accurate (100%) compared to the traditional in vitro approach (44%). Further validation of 96 SNPs using Illumina GoldenGate Assay gave an overall assay success rate of 89.6% and conversion rate of 37.5%. We explored possible factors lowering assay success rate by predicting exon-intron boundaries and paralogous genes of Acacia contigs using Medicago truncatula genome as reference. This assessment revealed that presence of exon-intron boundary is the main cause (50%) of assay failure. Subsequent SNPs filtering and improved assay design resulted in assay success and conversion rate of 92.4% and 57.4%, respectively based on 768 SNPs genotyping. Analysis of clustering patterns revealed that 27.6% of the assays were not reproducible and flanking sequence might play a role in determining cluster compression. In addition, we identified a total of 258 and 319 polymorphic SNPs in A. auriculiformis and A. mangium natural germplasms, respectively.ConclusionWe have successfully discovered a large number of SNP markers in A. auriculiformis x A. mangium hybrids using next generation transcriptome sequencing. By using a reference genome from the most closely related species, we converted most SNPs to successful assays. We also demonstrated that Illumina GoldenGate genotyping together with manual clustering can provide high quality genotypes for a non-model species like Acacia. These SNPs markers are not only important for linkage map construction, but will be very useful for hybrid discrimination and genetic diversity assessment of natural germplasms in the future.

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“…Twenty-one single nucleotide polymorphisms (SNPs) were identified in the exons of CCR, of which nine were neutral mutations and 12 were missense mutations. DNA sequence variations in coding regions of two lignin genes, Cinnamate 4-hydroxylase (C4H) and Cinnamyl alcohol dehydrogenase (CAD) from Acacia mangium and Acacia auriculiformis have been demonstrated [60]. Twenty eight and thirty two SNPs were identified in the coding region of C4H and CAD region.…”

Section: Genetic Diversity and Biotechnological Studies In Sesamementioning

confidence: 99%

Sesame Crop: An Underexploited Oilseed Holds Tremendous Potential for Enhanced Food Value

Pathak¹,

Kumar²,

Kumari³

et al. 2014

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Sesame, an important oilseed crop, highly valued for its oil quality contains plethora of nutritive substances such as proteins, carbohydrates, polyunsaturated fatty acids (PUFA), lignans (sesamin and sesamolin), tocopherol, phytosterols, phytates and other micronutrients. The presence of these substances enhances the keeping quality of oil by preventing oxidative rancidity. Benefits of this underexploited crop include antioxidative, anticancer, antihypersensitive and tumor-suppressive properties. Despite of its high nutritional value, research on this valuable oilseed is meagre due to several biotic and abiotic stresses and absence of non-shattering cultivars. Thus, to explore the potential of sesame as an important oilseed possessing multifarious property, we have tried to provide a detailed overview of the crop and its genetic diversity available throughout the world. Sesame is a promising target oilseed crop for biotechnological applications and marker based studies. The genetic manipulation in the crop along with other strategies would enable development of varieties with high nutritional and functional value. Our aim is to explore the hidden heterogeneity in the crop and provide impetus for valuable oilseed research.

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Extensive DNA Sequence Variations in Two Lignin Genes, Cinnamate 4-Hydroxylase and Cinnamyl Alcohol Dehydrogenase from Acacia mangium and Acacia auriculiformis

Cited by 8 publications

References 18 publications

Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data

Sesame Crop: An Underexploited Oilseed Holds Tremendous Potential for Enhanced Food Value

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