Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Sequencing Of Asparagus And Onion Revealed No Microsynteny With The Rice

JERNEJ JAKSE¹ , Foo Cheung² , Christopher D. Town² , Go Suzuki³ , Christian Jung⁴ , Michael J. Havey¹

¹  University of Wisconsin, Department of Horticulture, 1575 Linden Drive, Madison, WI, 53706, USA

²  The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, 20850, USA

³  Osaka Kyoiku University, Laboratory of Plant Molecular Genetics, Division of Natural Science, 4-698-1 Asahigaoka, Kashiwara, 582-8582 Osaka, Japan

⁴  Plantbreeding Institute, Am Botanischen Garten 1-9, 24098 Kiel, Germany

Asparagus and onion are members of a monophyletic group within the monocot order Asparagales and have relatively large nuclear genomes, 2.7 and 36 times larger than rice, respectively. We undertook the sequencing of a few asparagus and onion BACs to reveal the structure of these genomes and investigate possible synteny to rice as a representative of the grasses. Randomly chosen onion BACs were end sequenced to generate a total length of 300,771 bp from 463 distinct ends. Of these, only 16,144 (5%) showed hits to proteins in the databases and 74,627 bp (25%) to retroviral elements or transposons. The remaining 210,000 bp (70%) showed no significant protein similarities in any dataset. We sequenced one 60-kb asparagus BAC. This asparagus BAC carried coding regions with high similarities to Ca-dependent kinase (CDPK), sulfite reductase, and a hypothetical protein in Arabidopsis and rice, as well as retroviruses and transposons. We used translated searches to look for microsynteny between asparagus and rice. Sulfite reductase is a single-copy gene on rice chromosome 5. The asparagus CDPK-like gene had two good matches in rice, one on chromosome 3 and one on chromosome 7. The asparagus hypothetical protein also had two good matches to rice, one on chromosome 7 and the other on chromosome 12. The CDPK and hypothetical protein matches were located on opposite ends of rice chromosome 7. These sequencing results revealed relatively low gene density in onion and no evidence of microsynteny between asparagus and rice, as representatives of the Asparagales and grasses, respectively.