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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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Correlations between the length and intron (A) or exon (B) count, between GC content and intron (C) or exon (D) count and between the nucleotide divergence and intron (E) or exon (F) count. The number (count) in the horizontal axis stands for the 1, 2-,..., 9 and 10-intron (or -exon) genes.
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Figure 5: Correlations between the length and intron (A) or exon (B) count, between GC content and intron (C) or exon (D) count and between the nucleotide divergence and intron (E) or exon (F) count. The number (count) in the horizontal axis stands for the 1, 2-,..., 9 and 10-intron (or -exon) genes.

Mentions: We further calculated the average exon (or intron) length, GC content and divergence as the increase of total exon numbers in a gene. Although the first few introns (particularly the 1st – 3rd introns) of the fewer-intron genes were shorter than the more-intron genes (e.g., 8091, 8397, 8888,..., 15017 bp for the first intron in the genes with 1, 2, 3,..., 10 introns in human, respectively), genes with fewer introns had relatively larger average intron length (Fig. 5A; e.g., 8091, 7200, 6567,..., 6369, bp for the genes with 1, 2, 3,..., 10 introns in human, respectively). Consistent results were also obtained for the decrease of exon length, when the last exon and UTR regions in each group of genes were excluded (Fig. 5B).


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)

Correlations between the length and intron (A) or exon (B) count, between GC content and intron (C) or exon (D) count and between the nucleotide divergence and intron (E) or exon (F) count. The number (count) in the horizontal axis stands for the 1, 2-,..., 9 and 10-intron (or -exon) genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Correlations between the length and intron (A) or exon (B) count, between GC content and intron (C) or exon (D) count and between the nucleotide divergence and intron (E) or exon (F) count. The number (count) in the horizontal axis stands for the 1, 2-,..., 9 and 10-intron (or -exon) genes.
Mentions: We further calculated the average exon (or intron) length, GC content and divergence as the increase of total exon numbers in a gene. Although the first few introns (particularly the 1st – 3rd introns) of the fewer-intron genes were shorter than the more-intron genes (e.g., 8091, 8397, 8888,..., 15017 bp for the first intron in the genes with 1, 2, 3,..., 10 introns in human, respectively), genes with fewer introns had relatively larger average intron length (Fig. 5A; e.g., 8091, 7200, 6567,..., 6369, bp for the genes with 1, 2, 3,..., 10 introns in human, respectively). Consistent results were also obtained for the decrease of exon length, when the last exon and UTR regions in each group of genes were excluded (Fig. 5B).

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