Traced orthologous amplified sequence tags (TOASTs) and mammalian comparative maps |
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Authors: | Z Jiang C Priat F Galibert |
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Institution: | (1) Laboratoire de Biochimie et Biologie Moléculaire, UPR41 CNRS ``Recombinaisons Génétiques', Faculté de Médecine, 2 Av. du Professeur Léon Bernard, 35043 Rennes Cedex, France, FR |
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Abstract: | Progress on mammalian comparative maps could be significantly accelerated by developing reagents defining orthologous landmarks
in the genome of many mammalian species. Using the large databases of gene sequences, we designed 225 orthologous gene-specific
primer pairs corresponding to 146 functional genes. Of these 225 primer pairs, 155 (68.9%), 182 (80.9%), 126 (56.0%), and
82 (36.4%) produced a single PCR product when tested against human, pig, dog, and hamster genomic DNA, respectively. In addition
to the general rules of primer designing, particular factors must be taken into consideration when choosing gene-specific
universal primers—for instance, preference for single-exon regions or highly conserved segments among species, avoidance of
GC-rich regions. Sequencing all the canine PCR products traced by these primers demonstrated that of 123 traced canine fragments
with readable and reliable sequences, 121 (98.4%) were found to match the GenBank orthologous sequences used for designing
the primers, after a BLAST search. Comparative characterization of PCR fragments among human, pig, dog, and hamster revealed
that the length of a single exon was much conserved among species, with few exceptions. As the fragments were traced with
amplification by orthologous gene-specific primers, we suggest they be termed Traced Orthologous Amplified Sequence Tags (TOASTs).
Received: 22 December 1997 / Accepted: 16 March 1998 |
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