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BACs representing each other line of loci hybridizing in order to probes SbRPG661, SbRPG373 and you may SbRPG851 was indeed sequenced with the aim away from relationship this new duration of replication in accordance with the newest divergence of Musa and you will grain lineages
We also analyzed the 18,612 ginger (Zingiber officinale; Zingiberaceae, Zingiberales) EST-derived unigenes available on the TIGR Plant Transcript Assemblies web site (sequences generated by David Gang, University of Arizona) and found no evidence of large-scale duplication in the Ks distribution for paralogous pairs (Figure 8). Moreover, the modal Ks for reciprocal best matches between the Musa and Zingiber unigene sets is 0.78 (Figure 8), larger than the mode for Musa paralogous pairs. The age of the most recent common ancestor for the Musacaceae and Zingiberaceae is estimated at 87 Mya [3, 72, 73]. This implies an average synonymous substitution rate best hookup apps best of 4.5 per 10 9 years (0.78 synonymous substitutions per site/(2*87,000,000 years)), intermediate between rates estimated for the Poaceae (6.1–6.5 per 10 9 years) and palms in the order Arecales (2.61 per 10 9 years; . We must emphasize that all of these rate estimates are approximate, based on rough estimates of minimum divergence times. However, regardless of ambiguities in substitution rate calibrations, our results indicate that the predicted large-scale duplication that occurred in the Musa lineage (Ks = 0.55) post-dates the divergence of lineages leading to Zingiber and Musa (Ks = 0.78), but occurred well before the separation of Musa A and Musa B (Ks = 0.0410).
Ks values were also computed on 1,034 pairs of homologous genes identified between the Musa ESTs and the rice genome sequences. As expected, the distribution of Ks values between rice-Musa homologs form a single peak centred around Ks = 1.7 (Figure 8). Using this Ks value to estimate the age of the Poales-Zingiberales split is less straightforward than described above for the Musa-Zingiber split, because synonymous substitution rates clearly vary between these Commelinid monocot lineages.
BAC fingerprint analyses revealed that whereas SbRPG854 hybridized to a single locus in the Musa genome, SbRPG probes SbRPG132 hybridized to 6 regions, SbRPG663 hybridized to 5 loci, and two loci were identified for SbRPG373, SbRPG661 and SbRPG851 (Table 1 and Additional file 1). Pair-wise estimations of Ks, the number of synonymous substitutions per synonymous site, were 0.93 (± 0.25), 1.39 (± 0.19) and 1.43 (± 0.60) for Musa homologs of the coding regions of SbRPG661 (thioredoxin), SbRPG851 (phosphoglycerate kinase) and SbRPG373 (hypothetical protein), respectively. Phylogenetic analyses suggested that the SbRPG851 Musa homologs duplicated prior to the divergence of the Poales and the Zingiberales, (probably independent from the large-scale duplication described above), and the SbRPG661 and SbRPG373 Musa homologs are sister to each other in the gene tree, suggesting the duplications arose after the divergence of the Poales and the Zingiberales (data not shown).
We and additionally analyzed the level of preservation anywhere between genomic regions nearby SbRPG661, SbRPG851 and you may SbRPG373 duplicated genetics inside Musa and you can grain and found no synteny inside the countries secured of the these types of homologs. It lack of synteny would be informed me because of the duplication events and you will next gene losses otherwise from the translocation of the focal family genes.
step one.8 Mb out of Musa genomic succession showed that all the BACs examined had been gene steeped which have a low posts out of transposable ability. All of our analyses out-of 443 Musa family genes predict indicated that Musa genes tend to have a beneficial “rice-like” bimodal GC delivery which have an incredibly asymmetrical and you can long tail to the large GC blogs as in earlier in the day degree [43, 44]. not, a second category of “Arabidopsis-like” genes is actually receive with an overall total lower GC blogs without extreme gradient along the coding series. Weighed against a previous research from yard and you will non-lawn monocots [52, 53], the analyses advise that Zingeberales genes express some services to your genomes off each other eudicots and you can members of the fresh Poaceae. This effect signifies that the latest Musa genome is far more exactly like cereal genomes according to onion, asparagus together with basal-really monocot origin, Acorus.