Sequence analysis of bacterial artificial chromosome clones from the apospory-specific genomic region of Pennisetum and Cenchrus.
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.
Conner
Joann A
JA
Department of Horticulture, University of Georgia, Tifton, Georgia 31793-0748, USA.
Goel
Shailendra
S
Gunawan
Gunawati
G
Cordonnier-Pratt
Marie-Michele
MM
Johnson
Virgil Ed
VE
Liang
Chun
C
Wang
Haiming
H
Pratt
Lee H
LH
Mullet
John E
JE
DeBarry
Jeremy
J
Yang
Lixing
L
Bennetzen
Jeffrey L
JL
Klein
Patricia E
PE
Ozias-Akins
Peggy
P
D029681:Arabidopsis Proteins / Q000235:genetics; D031741:Cenchrus / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D003001:Cloning, Molecular; D004251:DNA Transposable Elements; D020440:Gene Duplication; D018745:Genome, Plant; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D031782:Pennisetum / Q000235:genetics*; D012100:Reproduction, Asexual; D017422:Sequence Analysis, DNA; D045868:Sorghum / Q000235:genetics; D026801:Synteny; D014157:Transcription Factors / Q000235:genetics
D029681:Arabidopsis Proteins; C518629:BABY BOOM protein, Arabidopsis; D004251:DNA Transposable Elements; D014157:Transcription Factors