Intron size, genome size and ploidy level in the Asteraceae.
Polyploidy is a key factor that plays an important role in the evolution of genome, and during the polyploidization, due to different balancing processes a variation in the nuclear DNA content occurs.(Pellicer.J.et.al, 2010). Polyploidy and hybridization is known to induce rapid genomic changes that include the loss and gain of DNA. The nuclear DNA content or the 2C value ranges from 0.431pg in Arabidopsis to 254.8 pg in Fritillaria assyriaca. (Bennett and Leitch,2003). The C-value is independent of the changes in ploidy this variation in the DNA content and its lack of correlation with the gene number is referred to as the c-value paradox or C-value enigma. A major source of increase in the genome size is polyploidy, but studies specifically with the natural polyploids of Asteraceae have shown that the total content of DNA increases with an average increase in the ploidy level, while the DNA content in the polyploid nucleus decreases.(Leitch and Bennett,2004). Differences in the size of introns have been linked to the differences in the nuclear DNA content and transposon copy number in plants. (Petrov,2001, Bennetzen,2002). With regard to the timing of the genomic changes it has been osbserved by many researchers that some changes in the genomic structure are exclusive to polyploidization. (Ozkan et.al,2001). The sequences unique to a single chromosome are rapidly lost following the polyploidization. (Ozkan. et.al,2001). A wide range of gene mapping studies have shown that genomes of the hybrid species are extensively restructured during the process of speciation. ( Rieseberg et.al 1995,1996, 2000)
Results and Discussion
The first of the project was focused on the computational analysis of the partial sequence data sets (EST derived datasets) from the diverse members of the family asteraceae with Arabidopsis as the out-group. If it is considered that the gene duplication occurs independently only in some lineages following speciation, and a putative orthologus is regarded as singly copy ortholog group only if it meets the criteria that include the Arabidopsis gene member had to be single copy, at least two of the gene members had to be single copy. As a result, 1343 alignments fit the definition of COS loci, of which 232 loci were helpful in designing the primer. In our investigation, we selected 192 primer pairs to test the amplification in eight taxa across the family asteraceae. Most of the primer pairs that is around 85 amplified in atleast one taxon, whereas around 65 amplified in atleast half of the taxa that are tested. The number of successful amplifications ranged from 67 in
Centaurea to 146 in Latuca, and 56 primer pairs were amplified in both the members of Carduoideae. Thirty nine prime pairs amplified fragments of the eight taxa tested, 26 are putatively single copy in all the individuals.
Results and Discussion
The first of the project was focused on the computational analysis of the partial sequence data sets (EST derived datasets) from the diverse members of the family asteraceae with Arabidopsis as the out-group. If it is considered that the gene duplication occurs independently only in some lineages following speciation, and a putative orthologus is regarded as singly copy ortholog group only if it meets the criteria that include the Arabidopsis gene member had to be single copy, at least two of the gene members had to be single copy. As a result, 1343 alignments fit the definition of COS loci, of which 232 loci were helpful in designing the primer. In our investigation, we selected 192 primer pairs to test the amplification in eight taxa across the family asteraceae. Most of the primer pairs that is around 85 amplified in atleast one taxon, whereas around 65 amplified in atleast half of the taxa that are tested. The number of successful amplifications ranged from 67 in
Centaurea to 146 in Latuca, and 56 primer pairs were amplified in both the members of Carduoideae. Thirty nine prime pairs amplified fragments of the eight taxa tested, 26 are putatively single copy in all the individuals.
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