Evolution of the genomes of two nematodes in the ... - Ken Wolfe

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BLAST basic local alignment search tool BLOSUM blocks substitution matrix bp basepairs cDNA copy DNA DNA deoxy-ribonucleic acid EST expressed sequence tag HSP high-scoring segment pair kb kilobases Mb megabases mRNA messenger RNA Mya million years ago Myr million years RNA ribonucleic acid rRNA ribosomal RNA ORF open reading frame OST ORF sequence tag TIGR The Institute for Genomic Research TIR terminal inverted repeat Abbreviations vii
List of Figures 1.1 The model organism Caenorhabditis elegans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2 The relationships of the animal phyla . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.3 A phylogenetic tree of the phylum Nematoda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.1 Distribution of sizes of conserved segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 2.2 The Caenorhabditis elegans region surrounding the sex-1 locus . . . . . . . . . . . . . . . . . . . . 10 2.3 Location of conserved segments in the Caenorhabditis elegans genome . . . . . . . . . . . . . 13 2.4 Estimates of the C. briggsae-C. elegans speciation date . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 2.5 Sizes of inversions and transpositions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15 2.6 Method of detecting inversions and transpositions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 3.1 Joint refinement of C. elegans and C. briggsae gene models . . . . . . . . . . . . . . . . . . . . . . . . 31 3.2 A region on C. elegans chromosome III, and the syntenic C. briggsae region . . . . . . . 37 4.1 Identifying novel introns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 4.2 The exon splice site consensus of novel introns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 4.3 An example of a novel intron containing a repeat element . . . . . . . . . . . . . . . . . . . . . . . . . 48 viii
Page 1 and 2: Evolution of the genomes of two nem
Page 3 and 4: Acknowledgements Thankyou a billion
Page 5 and 6: Table of Contents List of Abbreviat
Page 7: 4.2.3 Phases of Novel Introns . . .
Page 11 and 12: Chapter 1 Overview The biology of t
Page 13 and 14: E Chordates Hemichordates Echinoder
Page 15 and 16: 1.4 TWO Caenorhabditis GENOMES In 2
Page 17 and 18: Chapter 2 Faster Rate of Genome Rea
Page 19 and 20: Nematode fossils are extremely scar
Page 21 and 22: ends) are distributed at random alo
Page 23 and 24: Figure 2.3: (A) Location of conserv
Page 25 and 26: Frequency Frequency 60 50 40 30 20
Page 27 and 28: Breakpoint type Number of Breakpoin
Page 29 and 30: transposon (Oosumi et al., 1996). C
Page 31 and 32: effects compared with the recombina
Page 33 and 34: smaller effective population size t
Page 35 and 36: genes whose chromosomal coordinates
Page 37 and 38: did not group together and/or the D
Page 39 and 40: Chapter 3 The Caenorhabditis briggs
Page 41 and 42: predictions, we chose the predictio
Page 43 and 44: C. briggsae C. elegans WS77 ∗ C.
Page 45 and 46: WS77 WS103 New genes 1275 985 New e
Page 47 and 48: C. elegans chrom. III, 9.8-9.9 Mb *
Page 49 and 50: 4. Each exon-cluster X consisted of
Page 51 and 52: 3.5.4 Estimating the C. briggsae-C.
Page 53 and 54: Chapter 4 Origins of Novel Introns
Page 55 and 56: http://wolfe.gen.tcd.ie/avril/intro
Page 57 and 58: Of the 78 genes that have gained in
Page 59 and 60:
novel introns that are either C. el
Page 61 and 62:
as supporting this hypothesis are b
Page 63 and 64:
4.4 METHODS 4.4.1 Sources of Sequen
Page 65 and 66:
1. the outgroup for the tree was a
Page 67 and 68:
Bibliography Aguinaldo, A. M., J. M
Page 69 and 70:
Fedorov, A., X. Cao, S. Saxonov, S.
Page 71 and 72:
Logsdon, J. M. J., M. G. Tyshenko,
Page 73 and 74:
Sankoff, D. (1999). Comparative map
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Evolution of the genomes of two nematodes in the ... - Ken Wolfe

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