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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Sequence Analysis of Bacterial Artificial Chromosome Clones from the Apospory-Specific Genomic Region of Pennisetum and Cenchrus^1,[W],[OA]

Department of Horticulture, University of Georgia, Tifton, Georgia 31793–0748 (J.A.C., S.G., G.G., P.O.-A.); Department of Plant Biology (M.-M.C.-P., C.L., H.W., L.H.P.), Department of Genetics (J.D., L.Y., J.L.B.), and Office of Research Services (V.E.J.) University of Georgia, Athens, Georgia 30602; and Department of Plant Biology Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843 (J.E.M., P.E.K.)

Apomixis, asexual reproduction through seed, is widespread among angiosperm families. Gametophytic apomixis in Pennisetum squamulatum and Cenchrus ciliaris is controlled by the apospory-specific genomic region (ASGR), which is highly conserved and macrosyntenic between these species. Thirty-two ASGR bacterial artificial chromosomes (BACs) isolated from both species and one ASGR-recombining BAC from P. squamulatum, which together cover approximately 2.7 Mb of DNA, were used to investigate the genomic structure of this region. Phrap assembly of 4,521 high-quality reads generated 1,341 contiguous sequences (contigs; 730 from the ASGR and 30 from the ASGR-recombining BAC in P. squamulatum, plus 580 from the C. ciliaris ASGR). Contigs containing putative protein-coding regions unrelated to transposable elements were identified based on protein similarity after Basic Local Alignment Search Tool X analysis. These putative coding regions were further analyzed in silico with reference to the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes using the resources at Gramene (www.gramene.org) and Phytozome (www.phytozome.net) and by hybridization against sorghum BAC filters. The ASGR sequences reveal that the ASGR (1) contains both gene-rich and gene-poor segments, (2) contains several genes that may play a role in apomictic development, (3) has many classes of transposable elements, and (4) does not exhibit large-scale synteny with either rice or sorghum genomes but does contain multiple regions of microsynteny with these species.

² Present address: Department of Botany, University of Delhi, Delhi, India 110007.

³ Present address: Department of Botany, Miami University, Oxford, OH 45056.

⁴ Present address: Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Peggy Ozias-Akins (pozias{at}uga.edu).

^[W] The online version of this article contains Web-only data.

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.108.119081

^* Corresponding author; e-mail pozias{at}uga.edu.

Received March 17, 2008; accepted May 25, 2008; published May 28, 2008.