BACs symbolizing each other type of loci hybridizing in order to probes SbRPG661, SbRPG373 and you will SbRPG851 was sequenced with the aim of relationship this new time of duplication according to this new divergence of Musa and rice 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 K_s distribution for paralogous pairs (Figure 8). Moreover, the modal K_s 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 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 (K_s = 0.55) post-dates the divergence of lineages leading to Zingiber and Musa (K_s = 0.78), but occurred well before the separation of Musa A and Musa B (K_s = 0.0410).

K_s 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 K_s values between rice-Musa homologs form a single peak centred around K_s = 1.7 (Figure 8). Using this K_s 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 K_s, 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).

I and reviewed the amount of maintenance ranging from genomic regions surrounding SbRPG661, SbRPG851 and you will SbRPG373 recurring genetics during the Musa and you can grain and found zero synteny when you look at the places secured from the such homologs. Which absence of synteny could be free local hookup informed me by duplication incidents and you will further gene losses or by translocation of the focal genetics.

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step one.8 Mb away from Musa genomic sequence indicated that the BACs reviewed was indeed gene steeped which have a low posts off transposable function. The analyses regarding 443 Musa family genes predict showed that Musa genes generally have an effective “rice-like” bimodal GC delivery with a highly asymmetrical and you will long-tail toward higher GC posts as with early in the day degree [43, 44]. However, an extra family of “Arabidopsis-like” genetics is discover that have a complete reduced GC content and no extreme gradient over the programming series. Compared with a previous research off lawn and you will low-lawn monocots [52, 53], all of our analyses suggest that Zingeberales genetics express some qualities with the genomes regarding each other eudicots and you will members of the new Poaceae. This effect implies that brand new Musa genome is more like cereal genomes according to onion, asparagus additionally the basal-really monocot ancestry, Acorus.