TABLE CONTENTS

SESSION SIXTEEN – PLANT-PARASITIC NEMATODE GENOMES:
FROM EXPLORATION TO EXPLOITATION
CONVENORS: PIERRE ABAD & MAURICE MOENS
Sequencing and Analysis of the Meloidogyne hapla Genome: A Parasite
Shares its Secrets
Opperman, C.H. (1), D.M. Bird (1), V.W. Williamson (2), M. Burke (1), J. Cohn (1), S.
Graham (1), E. Scholl (1), E. Windham (1), D. Rohsar (3), K. Berrie (3) & T. Mitros (4)
(1) Center for the Biology of Nematode Parasitism, North Carolina State University, Raleigh, NC 27695. (2)
Department of Nematology, University of California-Davis, Davis, CA 95616. (3) Department of Energy Joint
Genome Institute, Walnut Creek, CA 94598. (4) Department of Molecular and Cell Biology, University of
California-Berkeley, Berkeley, CA 94700
Worldwide, Meloidogyne spp. are the most damaging and economically significant plantparasitic
nematodes. We selected M. hapla for complete genome sequencing based on its
small genome (54 Mbp) and established genetic system (sexually reproducing diploid). We
have completed the primary genome sequence of Meloidogyne hapla VW9 from multiple
libraries, including 3, 6, and 8 kb shotgun libraries and 40 kb fosmid ends. Our sequence
represents a 10.4X draft of the genome and covers >97% of the M. hapla genome in 1,523
scaffolds. We are merging a genetic (linkage) map with the genome sequence, using codominant
markers from a VW9 x VW8 (avirulent) cross. We placed 100% of the sequenced
markers on one or more scaffolds, and every marker examined has aligned with the sequence.
Extensive automatic and manual annotation has revealed that M. hapla has significantly
fewer genes than the free-living nematode C. elegans although they do share many genes in
common. This difference may reflect a diminished need for the parasite to carry as full a gene
complement as free-living species, due to dependence on the host to provide essential
resources. We are interested in what functions M. hapla may have dispensed with (and, of
course, what new functions this obligate parasite might have). Analysis further reveals areas
of microsynteny between M. hapla and C. elegans, although substantial rearrangements have
occurred. Analysis of the genome to date reveals suites of putative parasitism genes clustered
in several areas, numerous horizontal gene transfer candidates, and strong coverage of the
dauer pathway. The broader implications are substantial for developmental biology, evolution
and phylogenetics. The completion of the M. incognita (a more recently evolved RKN)
genome by Abad, et. al., coupled with other animal-parasitic and free-living nematode
genomes, provides a unique platform for comparative genomics among the Animalia.
5 th International Congress of Nematology, 2008 60