Genomic tools development for Aquilegia: construction of a BAC-based physical map.
BACKGROUND
The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance.


RESULTS
BAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from A. formosa. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome) suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5%) across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs) from the minimal tiling path (MTP) allowed a preview of the Aquilegia genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in Aquilegia suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes indicated a higher similarity to grapevine (Vitis vinifera) than to rice and Arabidopsis in the transcriptomes.


CONCLUSIONS
The A. formosa BAC-based genomic resources provide valuable tools to study Aquilegia genome. Further integration of other existing genomics resources, such as ESTs, into the physical map should enable better understanding of the molecular mechanisms underlying adaptive radiation and elaboration of floral morphology.
Department of Genetics and Biochemistry, Clemson University, SC 29634, USA.
Guang-Chen
GC
Fang
Barbara P
BP
Blackmon
David C
DC
Henry
Margaret E
ME
Staton
Christopher A
CA
Saski
Scott A
SA
Hodges
Jeff P
JP
Tomkins
Hong
H
Luo
D031884:Aquilegia / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D020451:Contig Mapping; D016172:DNA Fingerprinting; D015723:Gene Library; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D009693:Nucleic Acid Hybridization; D020161:Physical Chromosome Mapping / Q000379:methods*; D016133:Polymerase Chain Reaction; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D026801:Synteny / Q000235:genetics; D027843:Vitis / Q000235:genetics
D005819:Genetic Markers