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

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List of Tables 2.1 Association of rearrangement breakpoints with repeats . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2.2 Association of translocation and transposition breakpoints with particular repeats . 18 3.1 Comparison of the C. briggsae and C. elegans gene sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 3.2 Updating the C. elegans gene set using C. briggsae similarity . . . . . . . . . . . . . . . . . . . . . . 35 ix
Chapter 1 Overview The biology of the model nematode Caenorhabditis elegans is reviewed in detail in the book C. elegans II (Riddle et al., 1997). In this chapter I briefly introduce the Phylum Nematoda and nematode genomes. Each of the three topics researched for my Ph.D. is introduced in detail at the start of Chapters 2, 3 and 4. 1.1 THE PHYLUM NEMATODA If all the matter in the universe except the nematodes were swept away, our world would still be dimly recognisable, and if, as disembodied spirits, we could then investigate it, we should find its mountains, hills, vales, rivers, lakes, and oceans represented by a film of nematodes. . . (Cobb, 1915) Nematodes are non-segmented invertebrates that have a body cavity, a digestive tract, a nervous system, an excretory system, and a set of longitudinal muscles, but lack any appendages. Most nematodes are microscopic; the model organism Caenorhabditis elegans is just 1 mm long (Figure 1.1). In terms of the numbers of individuals, nematodes are the most abundant type of animal on earth (Chitwood and Chitwood, 1974; Andrássy and Zombori, 1976). So far 20,000 species have been classified, and there may be up to ten million species (Blaxter, 1998). This abundance results from their ability to adapt, and is due to a small size, a resistant cuticle, and a simple body plan. Small changes to their body plan have allowed invasion of many different habitats. Nematodes live in hot springs, polar ice, soil, fresh and salt water, and as parasites of plants, insects, vertebrates, and other nematodes (Andrássy and Zombori, 1976). This evolutionary plasticity has long fascinated biologists. However, a more urgent reason to study them is the damage they cause to human health and agriculture. Over 3.5 billion people are infected by nematodes, while each year plant parasitic nematodes cause about $100 billion of damage to crops (Lilley et al., 1999; Luong, 2003). 1
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 and 8: 4.2.3 Phases of Novel Introns . . .
Page 9: List of Figures 1.1 The model organ
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
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Fedorov, A., X. Cao, S. Saxonov, S.
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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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