BACs representing each other distinct loci hybridizing to help you probes SbRPG661, SbRPG373 and you may SbRPG851 were sequenced for the purpose out of matchmaking the latest lifetime of replication according to new divergence of your own Musa and you can 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 best hookup apps for iphone 2021 the Zingiberales (data not shown).
I together with assessed the degree of preservation ranging from genomic places nearby SbRPG661, SbRPG851 and you can SbRPG373 repeated family genes within the Musa and you will rice and found zero synteny inside regions anchored by such homologs. That it absence of synteny would-be explained from the duplication occurrences and you may subsequent gene losses or by the translocation of your focal genetics.
Discussion
1.8 Mb off Musa genomic succession showed that all the BACs analyzed have been gene steeped which have a reduced content out of transposable ability. Our very own analyses away from 443 Musa family genes predict showed that Musa genetics are apt to have a « rice-like » bimodal GC delivery with an extremely asymmetrical and you may long tail toward highest GC stuff such as earlier training [43, 44]. not, one minute class of « Arabidopsis-like » family genes was discovered with an overall reduced GC stuff no significant gradient along the coding sequence. Compared to an earlier assessment off yard and you may low-yard monocots [52, 53], our very own analyses recommend that Zingeberales genetics display some services with the genomes from both eudicots and members of the brand new Poaceae. This results signifies that brand new Musa genome is far more exactly like cereal genomes according to onion, asparagus as well as the basal-extremely monocot lineage, Acorus.