Yarrowia lipolytica consortium -- development of a physical
map as a framework for sequencing of the genome.
David Ogrydziak (1), Gerold Barth (2), Angel Dominguez (3),
Claude Gaillardin (4), Stefan Kerscher (5), Jeong-Yoon Kim (6), Richard
Rachubinski (7), Rod Wing (8)
(1) Food Science, University of California, One Shields Avenue, Davis,
CA 95616, USA (dmogrydziak@ucdavis.edu);
(2) Insitute of Microbiology, Dresden University of Technology,
Mommenstr. 13, D-01062 Dresden, Germany;
(3) Departmento de Microbiologia y and Genetica, IMB/CSIC, Plaza de los
Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca,
Spain;
(4) Laboratoire de Genetique Moleculaire et Cellulaire, INRA/CNRS/INA-PG, BP 01, F-78850 Thiverval-Grignon, France;
(5) Institut fur Biochemie I, Universitatsklinikum Frankfurt am Main,
Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany;
(6) Department of Microbiology, Chungnam National University, Daejon,
305-764, Korea;
(7) Department of Cell Biology, University of Alberta, Medical Sciences
Building 5-14, Edmonton, Alberta, T6G 2H7, Canada;
(8) Clemson University Genomics Institute (CUGI), 100 Jordan Hall,
Clemson, SC, 29634-5727 USA
To increase the attractiveness of Y. lipolytica for genome
sequencing, a consortium was organized in 2000 to fund end sequencing of
a BAC library. CUGI was chosen, and the director suggested also doing
HindIII fingerprinting and contigating of BAC clones by FPC to
develop a physical map. Over 2900 BAC-end sequence (BES) high quality
reads long enough (average of 470 bp) for screening for matches were
obtained. Inserts in the original library averaged 70 kb. Larger inserts
allow more accurate assignment of BACs to contigs, so CUGI constructed a
BAC library with 107 kb inserts. For the combined libraries, 4232 BACs
fell into 152 contigs covering 16.6 Mb. Four other types of information
useful for constructing the framework exist -- gene, rDNA, and
mitochondrial DNA sequences in the data bases; random sequence tags;
genes assigned to chromosomes by DNA hybridization; and genetic mapping
data. Contigs can be anchored to chromosomes by matches between BESs and
sequences of genes assigned to chromosomes. If BESs match sequenced
genes for which genetic map positions are known, then relative positions
of contigs on chromosomes can be determined. The consortium project was
a factor in Genoscope's decision to sequence the Y. lipolytica
genome, and Genoscope did BAC-end sequencing of the CUGI library. The
BES will be useful for ordering sequence contigs. Comparison of the
physical map and assembled sequence could confirm sequence assembly and
possibly reveal assembly errors.