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1.  A molecular recombination map of Antirrhinum majus 
BMC Plant Biology  2010;10:275.
Background
Genetic recombination maps provide important frameworks for comparative genomics, identifying gene functions, assembling genome sequences and for breeding. The molecular recombination map currently available for the model eudicot Antirrhinum majus is the result of a cross with Antirrhinum molle, limiting its usefulness within A. majus.
Results
We created a molecular linkage map of A. majus based on segregation of markers in the F2 population of two inbred lab strains of A. majus. The resulting map consisted of over 300 markers in eight linkage groups, which could be aligned with a classical recombination map and the A. majus karyotype. The distribution of recombination frequencies and distorted transmission of parental alleles differed from those of a previous inter-species hybrid. The differences varied in magnitude and direction between chromosomes, suggesting that they had multiple causes. The map, which covered an estimated of 95% of the genome with an average interval of 2 cM, was used to analyze the distribution of a newly discovered family of MITE transposons and tested for its utility in positioning seven mutations that affect aspects of plant size.
Conclusions
The current map has an estimated interval of 1.28 Mb between markers. It shows a lower level of transmission ratio distortion and a longer length than the previous inter-species map, making it potentially more useful. The molecular recombination map further indicates that the IDLE MITE transposons are distributed throughout the genome and are relatively stable. The map proved effective in mapping classical morphological mutations of A. majus.
doi:10.1186/1471-2229-10-275
PMCID: PMC3017841  PMID: 21159166
2.  Tracing the Evolution of the Floral Homeotic B- and C-Function Genes through Genome Synteny 
Molecular Biology and Evolution  2010;27(11):2651-2664.
The evolution of the floral homeotic genes has been characterized using phylogenetic and functional studies. It is possible to enhance these studies by comparing gene content and order between species to determine the evolutionary history of the regulatory genes. Here, we use a synteny-based approach to trace the evolution of the floral B- and C-function genes that are required for specification of the reproductive organs. Consistent with previous phylogenetic studies, we show that the euAP3–TM6 split occurred after the monocots and dicots diverged. The Arabidopsis TM6 and papaya euAP3 genes are absent from the respective genomes, and we have detected loci from which these genes were lost. These data indicate that either the TM6 or the euAP3 lineage genes can be lost without detriment to flower development. In contrast, PI is essential for male reproductive organ development; yet, contrary to predictions, complex genomic rearrangements have resulted in almost complete breakdown of synteny at the PI locus. In addition to showing the evolution of B-function genes through the prediction of ancestral loci, similar reconstructions reveal the origins of the C-function AG and PLE lineages in dicots, and show the shared ancestry with the monocot C-function genes. During our studies, we found that transposable elements (TEs) present in sequenced Antirrhinum genomic clones limited comparative studies. A pilot survey of the Antirrhinum data revealed that gene-rich regions contain an unusually high degree of TEs of very varied types, which will be an important consideration for future genome sequencing efforts.
doi:10.1093/molbev/msq156
PMCID: PMC2955736  PMID: 20566474
synteny; B-function; C-function; comparative genomics; evolution
3.  Enhanced AGAMOUS expression in the centre of the Arabidopsis flower causes ectopic expression over its outer expression boundaries 
Planta  2009;230(4):857-862.
Spatial regulation of C-function genes controlling reproductive organ identity in the centre of the flower can be achieved by adjusting the level of their expression within the genuine central expression domain in Antirrhinum and Petunia. Loss of this control in mutants is revealed by enhanced C-gene expression in the centre and by lateral expansion of the C-domain. In order to test whether the level of central C-gene expression and hence the principle of ‘regulation by tuning’ also applies to spatial regulation of the C-function gene AGAMOUS (AG) in Arabidopsis, we generated transgenic plants with enhanced central AG expression by using stem cell-specific CLAVATA3 (CLV3) regulatory sequences to drive transcription of the AG cDNA. The youngest terminal flowers on inflorescences of CLV3::AG plants displayed homeotic features in their outer whorls indicating ectopic AG expression. Dependence of the homeotic feature on the age of the plant is attributed to the known overall weakening of repressive mechanisms controlling AG. Monitoring AG with an AG-I::GUS reporter construct suggests ectopic AG expression in CLV3::AG flowers when AG in the inflorescence is still repressed, although in terminating inflorescence meristems, AG expression expands to all tissues. Supported by genetic tests, we conclude that upon enhanced central AG expression, the C-domain laterally expands necessitating tuning of the expression level of C-function genes in the wild type. The tuning mechanism in C-gene regulation in Arabidopsis is discussed as a late security switch that ensures wild-type C-domain control when other repressive mechanism starts to fade and fail.
doi:10.1007/s00425-009-0966-7
PMCID: PMC2729976  PMID: 19554348
Arabidopsis; Boundary; C-function; Tuning
4.  The mechanics of cell fate determination in petals. 
The epidermal cells of petals of many species are specialized, having a pronounced conical shape. A transcription factor, MIXTA, is required for the formation of conical cells in Antirrhinum majus; in shoot epidermal cells of several species, expression of this gene is necessary and sufficient to promote conical cell formation. Ectopic expression has also shown MIXTA to be able to promote the formation of multicellular trichomes, indicating that conical cells and multicellular trichomes share elements of a common developmental pathway. Formation of conical cells or trichomes is also mutually exclusive with stomatal formation. In Antirrhinum, MIXTA normally only promotes conical cell formation on the inner epidermal layer of the petals. Its restricted action in cell fate determination results from its specific expression pattern. Expression of MIXTA, in turn, requires the activity of B-function genes, and biochemical evidence suggests that the products of DEFICIENS, GLOBOSA and SEPALLATA-related genes directly activate MIXTA expression late in petal development, after the completion of cell division in the petal epidermis. A MIXTA-like gene, AmMYBML1, is also expressed in petals. AmMYBML1 expression is high early in petal development. This gene may direct the formation of trichomes in petals. In specifying the fates of different cell types in petals, regulatory genes like MIXTA may have been duplicated. Changes in the timing and spatial localization of expression then provides similar regulatory genes which specify different cell fates.
doi:10.1098/rstb.2002.1089
PMCID: PMC1692987  PMID: 12079676
5.  Comparison of ESTs from juvenile and adult phases of the giant unicellular green alga Acetabularia acetabulum 
BMC Plant Biology  2004;4:3.
Background
Acetabularia acetabulum is a giant unicellular green alga whose size and complex life cycle make it an attractive model for understanding morphogenesis and subcellular compartmentalization. The life cycle of this marine unicell is composed of several developmental phases. Juvenile and adult phases are temporally sequential but physiologically and morphologically distinct. To identify genes specific to juvenile and adult phases, we created two subtracted cDNA libraries, one adult-specific and one juvenile-specific, and analyzed 941 randomly chosen ESTs from them.
Results
Clustering analysis suggests virtually no overlap between the two libraries. Preliminary expression data also suggests that we were successful at isolating transcripts differentially expressed between the two developmental phases and that many transcripts are specific to one phase or the other. Comparison of our EST sequences against publicly available sequence databases indicates that ESTs from the adult and the juvenile libraries partition into different functional classes. Three conserved sequence elements were common to several of the ESTs and were also found within the genomic sequence of the carbonic anhydrase1 gene from A. acetabulum. To date, these conserved elements are specific to A. acetabulum.
Conclusions
Our data provide strong evidence that adult and juvenile phases in A. acetabulum vary significantly in gene expression. We discuss their possible roles in cell growth and morphogenesis as well as in phase change. We also discuss the potential role of the conserved elements found within the EST sequences in post-transcriptional regulation, particularly mRNA localization and/or stability.
doi:10.1186/1471-2229-4-3
PMCID: PMC385229  PMID: 15070428

Results 1-5 (5)