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Comp Funct Genomics
2011 Jan 01;2011:680673. doi: 10.1155/2011/680673.
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The roles and evolutionary patterns of intronless genes in deuterostomes.
Zou M
,
Guo B
,
He S
.
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Genes without introns are a characteristic feature of prokaryotes, but there are still a number of intronless genes in eukaryotes. To study these eukaryotic genes that have prokaryotic architecture could help to understand the evolutionary patterns of related genes and genomes. Our analyses revealed a number of intronless genes that reside in 6 deuterostomes (sea urchin, sea squirt, zebrafish, chicken, platypus, and human). We also determined the conservation for each intronless gene in archaea, bacteria, fungi, plants, metazoans, and other eukaryotes. Proportions of intronless genes that are inherited from the common ancestor of archaea, bacteria, and eukaryotes in these species were consistent with their phylogenetic positions, with more proportions of ancient intronless genes residing in more primitive species. In these species, intronless genes belong to different cellular roles and gene ontology (GO) categories, and some of these functions are very basic. Part of intronless genes is derived from other intronless genes or multiexon genes in each species. In conclusion, we showed that a varying number and proportion of intronless genes reside in these 6 deuterostomes, and some of them function importantly. These genes are good candidates for subsequent functional and evolutionary analyses specifically.
Figure 1. The numbers of intronless genes on each chromosome in human, chicken, and zebrafish. Both numbers and percentages are shown.
Figure 2. Distribution of intronless genes among different cellular roles in each species. Su: sea urchin; sq, sea squirt; z: zebrafish; c: chicken; p: platypus; h: human. AAB: amino acid biosynthesis; BOC: biosynthesis of cofactors; CE: cell envelope; CP: Cellular processes; CIM: Central intermediary metabolism; EM: energy metabolism; FAM: fatty acid metabolism; PAP: purines and pyrimidines; RF: regulatory functions; RAT: replication and transcription; T: translation; TAB: transport and binding.
Figure 3. Distribution of intronless genes among different kinds of gene ontology (GO) categories in each species. su: sea urchin; sq: sea squirt; z: zebrafish; c: chicken; p: platypus; h: human. ST: signal transducer; R: receptor; H: hormone; SP: structural protein; T: transporter; IC: ion channel; VGIC: voltage-gated ion channel; CC: cation channel; TR: transcription; TRR: transcription regulation; SR: stress response; IR: immune response; GF: growth factor; MIT: metal ions transport.
Figure 4. Distribution of intronless genes specific to different taxonomic group combinations for each species. su: sea urchin; sq: sea squirt; z: zebrafish; c: chicken; p: platypus; h: human. A: archaea; B: bacteria; E: eukaryote; AB: archaea and bacteria; AE: archaea and eukaryote; BE: bacteria and eukaryote; ABE: archaea, bacteria and eukaryote; ORFans: homologs not found in other organisms.
Figure 5. Distribution of eukaryote-specific intronless genes specific to different eukaryotic taxonomic group combinations for each species. su: sea urchin; sq: sea squirt; z: zebrafish; c: chicken; p: platypus; h: human. F: fungi; M: metazoans; O: other eukaryotes; P: plants; FM: fungi and metazoans; FO: fungi and other eukaryotes; FP: fungi and plants; MO: metazoans and other eukaryotes; MP: metazoans and plants; OP: other eukaryotes and plants; FMO: fungi, metazoans and other eukaryotes; FMP: fungi, metazoans and plants; FOP: fungi, other eukaryotes and plants; MOP: metazoan, other eukaryotes and plants FMOP: fungi, metazoans, other eukaryotes and plants.
Figure 6. Distribution of ORFans according to their functional categories in each species. The description of functional categories and species is the same as that given for Figure 2.
Figure 7. Functional distribution of conserved intronless genes in vertebrates. The description of functional categories is same as that given in Figure 2.
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