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Title: COMPARATIVE-SEQUENCE AND GENETIC ANALYSES OF ASPARAGUS REVEAL NO MICROSYNTENY WITH RICE OR ONION

Author
item JAKSE, JERNEJ - UNIV OF LJUBLJANA, SLOVEN
item SUZUKI, GO - OSAKA KYOIKU UNIV, JAPAN
item CHEUNG, FOO - INST FOR GENOMIC RES, MD
item TOWN, CHRISTOPHER - INST FOR GENOMIC RES, MD
item MCCALLUM, JOHN - CROP & FOOD RES, NZ
item Havey, Michael

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/31/2006
Publication Date: 9/22/2006
Citation: Jakse, J., Suzuki, G., Cheung, F., Town, C.D., Mccallum, J., Havey, M.J. 2006. Comparative-sequence and genetic analyses of asparagus reveal no microsynteny with rice or onion. Journal of Theoretical and Applied Genetics. 114:31-39. Available: http://www.springerlink.com/content/h3617u2315348n08/?p=9d65c800a75a46d8ad2ce2053a432b43&pi=15.

Interpretive Summary: The grasses, onion and asparagus are among the most economically important monocots. Comparative genetic analyses have revealed that the major grasses have similar linear arrangements of genes on their chromosomes; however it is not known if these similarities are found in other major monocot plants such as onion and asparagus. We sequenced asparagus and onion DNA and observed long tracts of degenerated repetitive elements similar to the larger grass genomes. As expected, gene densities in asparagus and onion were less than in the grasses. Physically linked sequences in the asparagus DNA showed significant similarities to rice genes on different chromosomes, revealing no conservation of gene order between asparagus and rice across the sequenced regions. Physically linked asparagus sequences were used to select highly similar expressed regions from onion, which mapped to different onion chromosomes and no relationship was observed between physical linkages in asparagus and genetic linkages in onion. These results demonstrate that the smaller genomes of rice and asparagus are not appropriate models for the other monocots with larger amounts of DNA, like onion. This research is of interest to plant scientists and breeders interested in using the grasses as genetic models for other major monocots.

Technical Abstract: The Poales (includes the grasses) and Asparagales [includes onion (Allium cepa L.) and asparagus (Asparagus officinalis L.)] are the two most economically important monocot orders. Comparative genomic analyses among the grass genomes revealed a high degree of synteny; however it is not known if this synteny extends to other major monocot groups with enormous variation for genome sizes, such as the Asparagales. We sequenced asparagus and onion BACs and observed long tracts of degenerated retroviral elements and transposons similar to other larger plant genomes. As expected, gene densities in asparagus and onion were less than the smaller grass genomes. Physically linked sequences on the asparagus BACs showed significant similarities to rice genes on different chromosomes, revealing no microsynteny between asparagus and rice across the sequenced regions. Physically linked asparagus sequences were used to select highly similar (e<-20) expressed sequence tags of onion, which mapped to different onion chromosomes and no relationship was observed between physical linkages in asparagus and genetic linkages in onion. These results demonstrate that the smaller genomes of rice and asparagus are not appropriate models for the enormous nuclear genome of onion, and that genomic resources must be independently developed for the Alliums.