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Patterns of exon-intron architecture variation of genes in eukaryotic genomes.

Zhu L, Zhang Y, Zhang W, Yang S, Chen JQ, Tian D - BMC Genomics (2009)

Bottom Line: Our analyses revealed that three basic patterns of exon-intron variation were present in nearly all analyzed genomes (P < 0.001 in most cases): an ordinal reduction of length and divergence in both exon and intron, a co-variation between exon and its flanking introns in their length, GC content and divergence, and a decrease of average exon (or intron) length, GC content and divergence as the total exon numbers of a gene increased.Although the factors contributing to these patterns have not been identified, our results provide three important clues: common factor(s) exist and may shape both exons and introns; the ordinal reduction patterns may reflect a time-orderly evolution; and the larger first and last exons may be splicing-required.These clues provide a framework for elucidating mechanisms involved in the organization of eukaryotic genomes and particularly in building exon-intron structures.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, PR China. zhuliucun@gmail.com

ABSTRACT

Background: The origin and importance of exon-intron architecture comprises one of the remaining mysteries of gene evolution. Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. However, there is little study about the structural variation of exons and introns.

Results: We investigated the length, GC content, ordinal position and divergence in both exons and introns of 13 eukaryotic genomes, representing plant and animal. Our analyses revealed that three basic patterns of exon-intron variation were present in nearly all analyzed genomes (P < 0.001 in most cases): an ordinal reduction of length and divergence in both exon and intron, a co-variation between exon and its flanking introns in their length, GC content and divergence, and a decrease of average exon (or intron) length, GC content and divergence as the total exon numbers of a gene increased. In addition, we observed that the shorter introns had either low or high GC content, and the GC content of long introns was intermediate.

Conclusion: Although the factors contributing to these patterns have not been identified, our results provide three important clues: common factor(s) exist and may shape both exons and introns; the ordinal reduction patterns may reflect a time-orderly evolution; and the larger first and last exons may be splicing-required. These clues provide a framework for elucidating mechanisms involved in the organization of eukaryotic genomes and particularly in building exon-intron structures.

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Variation patterns of intron (A) or exon length (B), as a function of its ordinal number. Only introns or exons with ordinal numbers ≤ 40 were shown in the figures; each dot contains > 1000 samples.
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Figure 2: Variation patterns of intron (A) or exon length (B), as a function of its ordinal number. Only introns or exons with ordinal numbers ≤ 40 were shown in the figures; each dot contains > 1000 samples.

Mentions: In addition, intron length is negatively correlated with ordinal position in a gene across all genomes analyzed (P < 0.001, Additional file 2, Table S1). Fig. 2A depicts a decay curve formed between intron order and length for all these genomes, however, some of the correlations between intron order and GC content are more complicated (Additional file 1, Fig. S2A). A significant negative correlation (P < 0.001) is present in the rice genome as well as in chicken and fly genomes. In mammalian genomes, the GC content of the first intron is significantly higher than the others, and thereafter no perceptible difference was seen. In the other genomes, e.g., worm and zebrafish, no clear variation was found. The results of the systematic investigation on many genomes suggested the intron length was not randomly distributed in the ordinal positions. However, while this supposition may be partly true for the distribution of intron GC content in the ordinal positions, no clear pattern was obtained for the genomes analyzed.


Patterns of exon-intron architecture variation of genes in eukaryotic genomes.

Zhu L, Zhang Y, Zhang W, Yang S, Chen JQ, Tian D - BMC Genomics (2009)

Variation patterns of intron (A) or exon length (B), as a function of its ordinal number. Only introns or exons with ordinal numbers ≤ 40 were shown in the figures; each dot contains > 1000 samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2636830&req=5

Figure 2: Variation patterns of intron (A) or exon length (B), as a function of its ordinal number. Only introns or exons with ordinal numbers ≤ 40 were shown in the figures; each dot contains > 1000 samples.
Mentions: In addition, intron length is negatively correlated with ordinal position in a gene across all genomes analyzed (P < 0.001, Additional file 2, Table S1). Fig. 2A depicts a decay curve formed between intron order and length for all these genomes, however, some of the correlations between intron order and GC content are more complicated (Additional file 1, Fig. S2A). A significant negative correlation (P < 0.001) is present in the rice genome as well as in chicken and fly genomes. In mammalian genomes, the GC content of the first intron is significantly higher than the others, and thereafter no perceptible difference was seen. In the other genomes, e.g., worm and zebrafish, no clear variation was found. The results of the systematic investigation on many genomes suggested the intron length was not randomly distributed in the ordinal positions. However, while this supposition may be partly true for the distribution of intron GC content in the ordinal positions, no clear pattern was obtained for the genomes analyzed.

Bottom Line: Our analyses revealed that three basic patterns of exon-intron variation were present in nearly all analyzed genomes (P < 0.001 in most cases): an ordinal reduction of length and divergence in both exon and intron, a co-variation between exon and its flanking introns in their length, GC content and divergence, and a decrease of average exon (or intron) length, GC content and divergence as the total exon numbers of a gene increased.Although the factors contributing to these patterns have not been identified, our results provide three important clues: common factor(s) exist and may shape both exons and introns; the ordinal reduction patterns may reflect a time-orderly evolution; and the larger first and last exons may be splicing-required.These clues provide a framework for elucidating mechanisms involved in the organization of eukaryotic genomes and particularly in building exon-intron structures.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, PR China. zhuliucun@gmail.com

ABSTRACT

Background: The origin and importance of exon-intron architecture comprises one of the remaining mysteries of gene evolution. Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. However, there is little study about the structural variation of exons and introns.

Results: We investigated the length, GC content, ordinal position and divergence in both exons and introns of 13 eukaryotic genomes, representing plant and animal. Our analyses revealed that three basic patterns of exon-intron variation were present in nearly all analyzed genomes (P < 0.001 in most cases): an ordinal reduction of length and divergence in both exon and intron, a co-variation between exon and its flanking introns in their length, GC content and divergence, and a decrease of average exon (or intron) length, GC content and divergence as the total exon numbers of a gene increased. In addition, we observed that the shorter introns had either low or high GC content, and the GC content of long introns was intermediate.

Conclusion: Although the factors contributing to these patterns have not been identified, our results provide three important clues: common factor(s) exist and may shape both exons and introns; the ordinal reduction patterns may reflect a time-orderly evolution; and the larger first and last exons may be splicing-required. These clues provide a framework for elucidating mechanisms involved in the organization of eukaryotic genomes and particularly in building exon-intron structures.

Show MeSH