Codon usage has a profound effect at the intra and inter- proteome level and even at the organismal level. Heterobasidion annosum s.l. is one of the most destructive fungal pathogen of conifers in the Boreal hemisphere. Recently the whole genome sequence of the H. annosum was released at DOE Joint Genome Institute (DOE-JGI) with 8.23 X coverage (Olson et al. 2009) covering nuclear genome assembles in 39 scaffolds of total 33.7 Mbp estimated to cover 98.1% of the complete genome. We have carried out a genome wide codon usage analysis of this pathogenic fungus using mutivariate analysis and opular indices of codon usage. The results show that the G+C contents at three positions of codon are different GC1 (mean value of 58.37%±0.07); GC2 (mean value of 47.5%±0.09); GC3 (mean value of 60.9%±0.13) explain heterogeneity in the composition of the genes. For the identification of gene expression values we have systematically searched for the ribosomal proteins and have used them as a reference for calculating codon adaptation index (CAI). The heterogeneity in the genome was also relaeaved by plotting coordinates of H. annosum genes on axis 1 (COA/RSCU) which showed high negative correlation with GC3s and GC content (r = -0.965, P<0.01 and r = -0.858, P<0.01), and significant high positive correlation with Nc (r= 0.689, P<0.01) Furthermore, high significant negative correlation was observed between Nc and GC3s (r= -0.674, P<0.01) which also complements the observation that C-ending codons are preferred over G-ending codons in highly expressed genes. It was also observed that CAI value and GC3s also had a significant correlation (r = 0.789, P<0.01) which suggest that genes with higher expression level tend to use C or G at synonymous positions compared to genes with lower expression level. We further analyzed the correlation between the nucleotide bias and amino acid composition using the two other phylogentically closed fngal genomes
Sablok, G.; Nayak, K.C.; Potenza, E.; Emiliani, G.; La Porta, N. (2012). Multivariate analysis revealed translational selection and mutational bias in Heterobasidion annosum genome. In: Capretti, P.; Comparini, C.; Garbelotto, M.; La Porta, N.; Santini, A. (eds.). Proceeding of the XIII International Conference on Root and Butt Root of Forest Trees. Firenze (FI) – S. Martino di Castrozza (TN), Italy, 4th – 10th September 2012. University Press, Firenze, 2012. 280 pp. Firenze: Firenze University Press. (PROCEEDINGS E REPORT): 58-61. ISBN: 9788866553533. url: XIII Conference Root and Butt Rot of Forest Trees, IUFRO Working Party 7.02.01 handle: http://hdl.handle.net/10449/22120
Multivariate analysis revealed translational selection and mutational bias in Heterobasidion annosum genome
Sablok, Gaurav;Potenza, Emilio;La Porta, Nicola
2012-01-01
Abstract
Codon usage has a profound effect at the intra and inter- proteome level and even at the organismal level. Heterobasidion annosum s.l. is one of the most destructive fungal pathogen of conifers in the Boreal hemisphere. Recently the whole genome sequence of the H. annosum was released at DOE Joint Genome Institute (DOE-JGI) with 8.23 X coverage (Olson et al. 2009) covering nuclear genome assembles in 39 scaffolds of total 33.7 Mbp estimated to cover 98.1% of the complete genome. We have carried out a genome wide codon usage analysis of this pathogenic fungus using mutivariate analysis and opular indices of codon usage. The results show that the G+C contents at three positions of codon are different GC1 (mean value of 58.37%±0.07); GC2 (mean value of 47.5%±0.09); GC3 (mean value of 60.9%±0.13) explain heterogeneity in the composition of the genes. For the identification of gene expression values we have systematically searched for the ribosomal proteins and have used them as a reference for calculating codon adaptation index (CAI). The heterogeneity in the genome was also relaeaved by plotting coordinates of H. annosum genes on axis 1 (COA/RSCU) which showed high negative correlation with GC3s and GC content (r = -0.965, P<0.01 and r = -0.858, P<0.01), and significant high positive correlation with Nc (r= 0.689, P<0.01) Furthermore, high significant negative correlation was observed between Nc and GC3s (r= -0.674, P<0.01) which also complements the observation that C-ending codons are preferred over G-ending codons in highly expressed genes. It was also observed that CAI value and GC3s also had a significant correlation (r = 0.789, P<0.01) which suggest that genes with higher expression level tend to use C or G at synonymous positions compared to genes with lower expression level. We further analyzed the correlation between the nucleotide bias and amino acid composition using the two other phylogentically closed fngal genomes
| File | Dimensione | Formato | |
|---|---|---|---|
|
IUFRO 2011.pdf
accesso aperto
Licenza:
Tutti i diritti riservati (All rights reserved)
Dimensione
2.55 MB
Formato
Adobe PDF
|
2.55 MB | Adobe PDF | Visualizza/Apri |
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
