BACs symbolizing each other type of loci hybridizing to probes SbRPG661, SbRPG373 and SbRPG851 was indeed sequenced with the aim of matchmaking the new time of duplication relative to this new divergence of your Musa and 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 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).
I also analyzed the degree of conservation ranging from genomic regions related SbRPG661, SbRPG851 and SbRPG373 recurring genes in the Musa and you will rice and found zero synteny in the places anchored by the such homologs. This absence of synteny might possibly be informed me by replication incidents and you can after that gene losses or by translocation of one’s focal family genes.
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step one.8 Mb of Musa genomic succession showed that all BACs examined was indeed gene steeped having the lowest content of transposable element. The analyses of 443 Musa genes predicted revealed that Musa genetics generally have an effective “rice-like” bimodal GC shipments having an extremely asymmetrical and you will long-tail toward high GC articles such as previous studies [43, 44]. Yet not, a second group of “Arabidopsis-like” genetics try found with an overall reasonable GC blogs with no significant gradient across the coding sequence. Compared to a past research off yard and non-lawn monocots [52, 53], all of our analyses advise that Zingeberales genetics express some attributes on genomes from each other eudicots and you can members of the new Poaceae. So it results suggests that the latest Musa genome is far more just like bookofsex cereal genomes relative to onion, asparagus while the basal-most monocot origin, Acorus.