Abstract
The draft sequences for a number of completely sequenced genomes (both prokaryotes and eukaryotes) are now available in the public domain. This allows the comparison of these genomes using parameters such as genome size, gene number, chromosomes (size and length), gene structures (single exon and multiple exon), junk (noncoding intergenic region) DNA, introns, and exons along with their content and arrangement. An understanding of genome content in different species organisms has to be established in the context of molecular evolution through genome comparison. The study and comparison of genomes to establish evolutionary relationship is computationally exhaustive and mathematically challenging. This chapter highlights some of the issues associated with the study of eukaryotic genes, genomes, function, design, and evolution. It should be noted that our current understanding of genomes in perspective of their known size to current design, organism level function, and evolution is limited.
Now this is not the end. It is not even the beginning of the end. But it is, perhaps, the end of the beginning.
Sir Winston Churchill
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References
Bagavathi S, Malathi R (1996) Introns and protein evolution – an analysis of the exon/intron organisation of actin genes. FEBS Lett 392:63–65
Boudet N, Aubourg S, Toffano-Nioche C et al (2001) Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila. Genome Res 11:2101–2114
Brett D, Hanke J, Lehmann G et al (2000) EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett 474:83–86
Brett D, Pospisil H, Valcarcel J et al (2002) Alternative splicing and genome complexity. Nature Genet 30:29–30
Brocke KS, Neu-Yilik G, Gehring NH et al (2002) The human intronless melanocortin 4-receptor gene is NMD insensitive. Hum Mol Genet 11:331–335
Brosius J (1999) Many G-protein coupled receptors are encoded by retro-genes. Trends Genet 15:304–305
Burset M, Seledtsov IA, Solovyev V (2001) SpliceDB: database of canonical and noncanonical mammalian splice sites. Nucleic Acids Res 29:255–259
Cavalier-Smith T (1985) Selfish DNA and the origin of introns. Nature 315:283–284
Christoffels A, van Gelder A, Greyling G et al (2001) STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res 29:234–238
Coghlan A, Wolfe KH (2004) Origins of recently gained introns in Caenorhabditis. Proc Natl Acad Sci 101:11362–11367
Croft L, Schandorff S, Clark F et al (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat Genet 24:340–341
Demchyshyn L, Sunahara RK, Miller K et al (1992) A human serotonin 1D receptor variant (5HT1D beta) encoded by an intronless gene on chromosome 6. Proc Natl Acad Sci 89:5522–5526
De Souza SJ (2003) The emergence of a synthetic theory of intron evolution. Genetica 118:117–121
Dibb NJ, Newman AJ (1989) Evidence that introns arose at proto-splice sites. EMBO J 8:2015–2021
Deutsch M, Long M (1999) Intron–exon structures of eukaryotic model organisms. Nucleic Acids Res 27:3219–3228
Doolittle WF (1978) Genes-in-pieces: were they ever together? Nature 272:581–582
Dorit RL, Schoenbach L, Gilbert W (1990) How big is the universe of exons? Science 250:1377–1382
Dralyuk I, Brudno M, Gelfand MS et al (2000) ASDB: database of alternatively spliced genes. Nucleic Acids Res 28:296–297
Fedorov A, Merican AF, Gilbert W (2002) Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc Natl Acad Sci 99:16128–16133
Fedorov A, Suboch G, Bujakov M et al (1992) Analysis of nonuniformity in intron phase distribution. Nucleic Acids Res 20:2553–2557
Fink GR (1987) Pseudogenes in yeast? Cell 49:5–6
Gentles AJ, Karlin S (1999) Why are human G-protein coupled receptors predominantly intronless? Trends Genet 15:47–49
Gilbert W (1978) Why genes in pieces? Nature 271:501–502
Grabowski PJ, Black DL (2001) Alternative RNA splicing in the nervous system. Prog Neurobiol 65:289–308
Hankeln T, Friedl H, Ebersberger I et al (1997) A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain. Gene 205:151–160
Hawkins JD (1988) A survey on intron and exon lengths. Nucleic Acids Res 16:9893–9908
Hill A, Sorscher E (2004) Common structural patterns in human genes. Bioinformatics 20:1632–1635
Huang YH, Chen YT, Lai JJ et al (2002) PALS db: Putative Alternative Splicing database. Nucleic Acids Res 30:186–190
Huang H, Horng J, Lee C et al (2003) ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data. Genome Biol 4:R29
Kan Z, Rouchka EC, Gish WR et al (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 11:889–900
Kobilka BKT, Frielle HG, Dohlman MA et al (1987) Delineation of the intronless nature of the genes for the human and hamster beta 2-adrenergic receptor and their putative promoter regions. J Biol Chem 262:7321–7327
Lander ES, Linton LM, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Lee C, Atanelov L, Modrek B et al (2003) ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res 31:101–105
Liang F, Holt I, Pertea G et al (2000) Gene index analysis of the human genome estimates approximately 120,000 genes. Nat Genet 25:239–240
Makalowski W (2003) Not junk after all. Science 300:1246–1247
Modrek B, Lee C (2002) A genomic view of alternative splicing. Nat Genet 30:13–19
Modrek B, Resch A, Grasso C et al (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res 29:2850–2859
Mount SM, Burks C, Hertz G et al (1992) Splicing signals in Drosophila: intron size, information content and consensus sequences. Nucleic Acids Res 20:4255–4262
Orgel LE, Crick FH (1980) Selfish DNA: the ultimate parasite. Nature 284:604–607
Palmer JD, Logsdon JM (1991) The recent origins of introns. Curr Opin Genet Dev 1:470–477
Pennacchio LA (2003) Insights from human/mouse genome comparisons. Mamm Genome 14:429–436
Perler F, Efstratiadis A, Lomedico P et al (1980) The evolution of genes: the chicken preproinsulin gene. Cell 20:555–566
Perumal BS, Sakharkar KR, Chow VTK et al (2005) Intron position conservation across eukaryotic lineages in tubulin genes. Front Biosci 10:2412–2419
Philips AV, Cooper TA (2000) RNA processing and human disease. Cell Mol Life Sci 57:235–249
Pospisil H, Herrmann A, Bortfeldt RH et al (2004) EASED: Extended Alternatively Spliced EST Database. Nucleic Acids Res 32:D70–D74
Rampazzo AF, Pivotto G, Occhi N et al (2000) Characterization of C14orf4, a novel intronless human gene containing a polyglutamine repeat, mapped to Human single exon genes 1395 the ARVD1 critical region. Biochem Biophys Res Commun 278:766–774
Roy SW, Fedorov A, Gilbert W (2003) Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci 100:7158–7162
Sakharkar KR, Chaturvedi I, Chow VTK et al (2005a) U-Genome: a database on genome design in unicellular genomes. In Silico Biol 5:611–615
Sakharkar MK, Chow VTK, Chaturvedi I et al (2004a) A report on single exon genes (SEG) in eukaryotes. Front Biosci 9:3262–3267
Sakharkar MK, Chow VTK, Ghosh K et al (2005b) Computational prediction of SEG (Single Exon Gene) function in humans. Front Biosci 10:1382–1395
Sakharkar MK, Chow VT, Kangueane P (2004b) Distributions of exons and introns in the human genome. In Silico Biol 4:387–393
Sakharkar MK, Kangueane P, Perumal BS et al (2005c) Human genome – from pieces to patterns. Front Biosci 10:2576–2584
Sakharkar MK, Kangueane P (2004) Genome SEGE: a database for “intronless” genes in eukaryotic genomes. BMC Bioinformatics 5:67
Sakharkar MK, Kangueane P, Long M et al (2005d) ExInt – An Exon Intron database. In: Fuchs J, Podda M (eds) Encyclopedia of medical genomics and proteomics (EMGP). Marcel Dekker, USA
Sakharkar MK, Kangueane P, Petrov DA et al (2002) SEGE: a database on “intron less/single exonic” genes from eukaryotes. Bioinformatics 18:1266–1267
Sakharkar MK, Perumal BS, Sakharkar KR et al (2005e) An analysis on gene architecture in human and mouse genomes. In Silico Biol 5:347–365
Smith CWJ, Valcarcel J (2000) Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem Sci 25:381–388
Sterner DA, Carlo T, Berget SM (1996) Architectural limits on split genes. Proc Natl Acad Sci 93:15081–15085
Sunahara RK, Niznik HB, Weiner DM et al (1990) Human dopamine D1 receptor encoded by an intronless gene on chromosome 5. Nature 347:80–83
Tabuchi M, Tanaka N, Nishida-Kitayama J et al (2002) Alternative splicing regulates the subcellular localization of divalent metal transporter 1 isoforms. Mol Biol Cell 13:4371–4387
Thanaraj TA, Stamm S, Clark F et al (2004) ASD: the Alternative Splicing Database. Nucleic Acids Res 32:D64–D69
Venter CJ, Adams MD, Myers EW et al (2001) The sequence of the human genome. Science 291:1304–1351
Wasserman WW, Palumbo M, Thompson W et al (2000) Human-mouse genome comparisons to locate regulatory sites. Nat Genet 26:225–228
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Kangueane, P. (2009). Eukaryotic Genes, Functions, Genomes, Design, and Evolution. In: Bioinformation Discovery. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-0519-2_10
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DOI: https://doi.org/10.1007/978-1-4419-0519-2_10
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