Difference between revisions of "GC content shift"
From CoGepedia
(→Comparison of Schizosaccharomyces fungi japonicus strain yFS275 and pombe 972h-) |
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− | GC content shift is an evolutionary genome-wide change in the GC content of an organism. The evolutionary consequences of such a | + | GC content shift is an evolutionary genome-wide change in the GC content of an organism. The evolutionary consequences of such a shift results in a chance in codon and amino acid usage. The selective pressures driving GC content shifts are unknown. They are detected by comparing the genomes of two related organisms that share a recent common ancestor, and determining if their have different: |
*AT/GC genomic composition | *AT/GC genomic composition | ||
*High rate of synonymous mutations for [[syntenic gene pairs]] | *High rate of synonymous mutations for [[syntenic gene pairs]] | ||
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! scope="row" | Codon Usage Table | ! scope="row" | Codon Usage Table | ||
| [[Image:Schizosaccharomyces japonicus strain yFS275 amino acid usage table.png|thumb|center|100px]] || [[Image:Schizosaccharomyces pombe 972h amino acid usage table.png|thumb|center|100px]] | | [[Image:Schizosaccharomyces japonicus strain yFS275 amino acid usage table.png|thumb|center|100px]] || [[Image:Schizosaccharomyces pombe 972h amino acid usage table.png|thumb|center|100px]] | ||
+ | |||
+ | |- | ||
+ | ! scope="row" | Histogram of [[CDS]] GC content | ||
+ | | [[Image:41589 min CDS gc.png|thumb|center|100px]] || [[Image:Schizosaccharomyces pombe 972h amino acid usage table.png|thumb|center|100px]] | ||
+ | |- | ||
+ | ! scope="row" | Histogram of [[CDS]] [[wobble position]] GC content | ||
+ | | [[Image:41589 wobble gc.pngthumb|center|100px]] || [[Image:Schizosaccharomyces pombe 972h amino acid usage table.png|thumb|center|100px]] | ||
+ | |- | ||
+ | ! scope="row" | Histogram of [[CDS]] GC content - [[wobble position]] GC content | ||
+ | | [[Image:41589 wobble gc diff.png|thumb|center|100px]] || [[Image:Schizosaccharomyces pombe 972h amino acid usage table.png|thumb|center|100px]] | ||
|} | |} | ||
Revision as of 18:31, 25 August 2010
GC content shift is an evolutionary genome-wide change in the GC content of an organism. The evolutionary consequences of such a shift results in a chance in codon and amino acid usage. The selective pressures driving GC content shifts are unknown. They are detected by comparing the genomes of two related organisms that share a recent common ancestor, and determining if their have different:
- AT/GC genomic composition
- High rate of synonymous mutations for syntenic gene pairs
- Amino acid usage frequencies
- Codon usage frequencies
Comparison of Schizosaccharomyces fungi japonicus strain yFS275 and pombe 972h-
japonicus | pombe | |
---|---|---|
Length | 11,300,431 | 10,082,004 |
GC% | 42.6 | 36 |
AT% | 54.9 | 64 |
CDS GC% | 45.5 | 39.5 |
CDS AT% | 54.5 | 60.5 |
Wobble GC% | 44.1 | 32.8 |
Wobble AT% | 55.9 | 67.2 |
Codon Usage Table | ||
Codon Usage Table | ||
Histogram of CDS GC content | ||
Histogram of CDS wobble position GC content | ||
Histogram of CDS GC content - wobble position GC content |