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

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it seems very possible that once again these tiny animals will be first in revealing some of nature’s deepest secrets. 6
Chapter 2 Faster Rate of Genome Rearrangement in Nematodes than Drosophila The research described in this chapter was published in Genome Res. (Coghlan and Wolfe, 2002). Our results were based on the 13% of the C. briggsae genome that had been sequenced by 2001. In this chapter I extend the discussion of the paper, to comment whether our results agree with later analysis of the whole C. briggsae genome (Stein et al., 2003). I have also added a section on future work. ABSTRACT We compared the genome of the nematode Caenorhabditis elegans to 13% of that of C. briggsae, identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio of translocations to inversions to transpositions being ∼1:1:2. We estimate that the species diverged 50–120 million years ago, and that since then there have been 4030 rearrangements between their whole genomes. Our estimate of the rearrangement rate, 0.4–1.0 chromosomal breakages/Mb per Myr, is at least four times that of Drosophila, which was previously reported to be the fastest rate among eukaryotes. The breakpoints of translocations are strongly associated with dispersed repeats and gene family members in the C. elegans genome. 2.1 INTRODUCTION The genes of Caenorhabditis elegans appear to have an unusually rapid rate of evolution. The substitution rates of many C. elegans genes are twice those of their orthologues in non-nematode metazoans (Aguinaldo et al., 1997; see Figure 3 in Mushegian et al., 1998). Even among nematodes, the C. elegans small subunit 7
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 and 10: List of Figures 1.1 The model organ
Page 11 and 12: Chapter 1 Overview The biology of t
Page 13 and 14: E Chordates Hemichordates Echinoder
Page 15: 1.4 TWO Caenorhabditis GENOMES In 2
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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