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Integrative analysis and expression profiling of secondary cell wall genes in C 4 biofuel model Setaria italica reveals targets for lignocellulose bioengineering

View Article: PubMed Central

ABSTRACT

Several underutilized grasses have excellent potential for use as bioenergy feedstock due to their lignocellulosic biomass. Genomic tools have enabled identification of lignocellulose biosynthesis genes in several sequenced plants. However, the non-availability of whole genome sequence of bioenergy grasses hinders the study on bioenergy genomics and their genomics-assisted crop improvement. Foxtail millet (Setaria italica L.; Si) is a model crop for studying systems biology of bioenergy grasses. In the present study, a systematic approach has been used for identification of gene families involved in cellulose (CesA/Csl), callose (Gsl) and monolignol biosynthesis (PAL, C4H, 4CL, HCT, C3H, CCoAOMT, F5H, COMT, CCR, CAD) and construction of physical map of foxtail millet. Sequence alignment and phylogenetic analysis of identified proteins showed that monolignol biosynthesis proteins were highly diverse, whereas CesA/Csl and Gsl proteins were homologous to rice and Arabidopsis. Comparative mapping of foxtail millet lignocellulose biosynthesis genes with other C4 panicoid genomes revealed maximum homology with switchgrass, followed by sorghum and maize. Expression profiling of candidate lignocellulose genes in response to different abiotic stresses and hormone treatments showed their differential expression pattern, with significant higher expression of SiGsl12, SiPAL2, SiHCT1, SiF5H2, and SiCAD6 genes. Further, due to the evolutionary conservation of grass genomes, the insights gained from the present study could be extrapolated for identifying genes involved in lignocellulose biosynthesis in other biofuel species for further characterization.

No MeSH data available.


Physical map showing the chromosomal locations of lignocellulose biosynthesis genes. Bars represent chromosomes and the numbers at the left corresponds to location (in Mb). Gene IDs are provided in the right. Tandemly duplicated gene pairs are highlighted with gray shade.
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Figure 4: Physical map showing the chromosomal locations of lignocellulose biosynthesis genes. Bars represent chromosomes and the numbers at the left corresponds to location (in Mb). Gene IDs are provided in the right. Tandemly duplicated gene pairs are highlighted with gray shade.

Mentions: The identified secondary cell wall biosynthesis genes were plotted onto the nine chromosomes of foxtail millet to generate the physical map (Figure 4), which showed that the majority of lignocellulose biosynthesis pathway genes (31; ~22%) were present in chromosome 2, followed by chromosome 9 (24 genes; ~17%) and chromosome 1 (21 genes; ~15%), and a minimum of 4 genes (~3%) were mapped on chromosome 8. Expansion of respective gene families within the genome were analyzed by investigating tandem and segmental duplication, which showed that 7 genes underwent tandem duplication, whereas segmental duplication did not occur among the lignocellulose pathway genes (Figure 4). SiCesA members were distributed on chromosomes 2 (4 genes), 4 (1), 5 (2), and 9 (3) and none of the genes were evidenced to undergo tandem or segmental duplication. SiCsl genes were found to be present in all the chromosomes except chromosome 8, and duplication analysis revealed that SiCslE3 and SiCslE4 were tandemly duplicated gene pairs on chromosome 2. SiGsl members were distributed on chromosomes 1 (2 genes), 2 (1), 4 (2), 5 (4), and 9 (3) and no duplication pattern in this gene family was observed.


Integrative analysis and expression profiling of secondary cell wall genes in C 4 biofuel model Setaria italica reveals targets for lignocellulose bioengineering
Physical map showing the chromosomal locations of lignocellulose biosynthesis genes. Bars represent chromosomes and the numbers at the left corresponds to location (in Mb). Gene IDs are provided in the right. Tandemly duplicated gene pairs are highlighted with gray shade.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4631826&req=5

Figure 4: Physical map showing the chromosomal locations of lignocellulose biosynthesis genes. Bars represent chromosomes and the numbers at the left corresponds to location (in Mb). Gene IDs are provided in the right. Tandemly duplicated gene pairs are highlighted with gray shade.
Mentions: The identified secondary cell wall biosynthesis genes were plotted onto the nine chromosomes of foxtail millet to generate the physical map (Figure 4), which showed that the majority of lignocellulose biosynthesis pathway genes (31; ~22%) were present in chromosome 2, followed by chromosome 9 (24 genes; ~17%) and chromosome 1 (21 genes; ~15%), and a minimum of 4 genes (~3%) were mapped on chromosome 8. Expansion of respective gene families within the genome were analyzed by investigating tandem and segmental duplication, which showed that 7 genes underwent tandem duplication, whereas segmental duplication did not occur among the lignocellulose pathway genes (Figure 4). SiCesA members were distributed on chromosomes 2 (4 genes), 4 (1), 5 (2), and 9 (3) and none of the genes were evidenced to undergo tandem or segmental duplication. SiCsl genes were found to be present in all the chromosomes except chromosome 8, and duplication analysis revealed that SiCslE3 and SiCslE4 were tandemly duplicated gene pairs on chromosome 2. SiGsl members were distributed on chromosomes 1 (2 genes), 2 (1), 4 (2), 5 (4), and 9 (3) and no duplication pattern in this gene family was observed.

View Article: PubMed Central

ABSTRACT

Several underutilized grasses have excellent potential for use as bioenergy feedstock due to their lignocellulosic biomass. Genomic tools have enabled identification of lignocellulose biosynthesis genes in several sequenced plants. However, the non-availability of whole genome sequence of bioenergy grasses hinders the study on bioenergy genomics and their genomics-assisted crop improvement. Foxtail millet (Setaria italica L.; Si) is a model crop for studying systems biology of bioenergy grasses. In the present study, a systematic approach has been used for identification of gene families involved in cellulose (CesA/Csl), callose (Gsl) and monolignol biosynthesis (PAL, C4H, 4CL, HCT, C3H, CCoAOMT, F5H, COMT, CCR, CAD) and construction of physical map of foxtail millet. Sequence alignment and phylogenetic analysis of identified proteins showed that monolignol biosynthesis proteins were highly diverse, whereas CesA/Csl and Gsl proteins were homologous to rice and Arabidopsis. Comparative mapping of foxtail millet lignocellulose biosynthesis genes with other C4 panicoid genomes revealed maximum homology with switchgrass, followed by sorghum and maize. Expression profiling of candidate lignocellulose genes in response to different abiotic stresses and hormone treatments showed their differential expression pattern, with significant higher expression of SiGsl12, SiPAL2, SiHCT1, SiF5H2, and SiCAD6 genes. Further, due to the evolutionary conservation of grass genomes, the insights gained from the present study could be extrapolated for identifying genes involved in lignocellulose biosynthesis in other biofuel species for further characterization.

No MeSH data available.