BACs symbolizing one another distinct loci hybridizing to probes SbRPG661, SbRPG373 and SbRPG851 have been sequenced with the aim regarding dating the brand new time of duplication relative to the fresh new divergence of your Musa and you may 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 in addition to reviewed the degree of conservation anywhere between genomic nations related SbRPG661, SbRPG851 and SbRPG373 recurring family genes for the Musa and rice and found zero synteny into the nations anchored by these types of homologs. So it absence of synteny is explained from the replication situations and you can subsequent gene losses or from the translocation of one’s focal family genes.
1.8 Mb of Musa genomic succession showed that all https://hookupranking.com/local-hookup/ BACs examined had been gene steeped that have a low posts out of transposable ability. Our analyses regarding 443 Musa genetics predict revealed that Musa family genes are apt to have a good “rice-like” bimodal GC delivery which have an incredibly asymmetrical and you will long tail on large GC articles such as earlier degree [43, 44]. Although not, a moment class of “Arabidopsis-like” genes was discover that have a total lowest GC articles with no significant gradient across the programming series. Compared to a past investigations off lawn and you will low-grass monocots [52, 53], our very own analyses recommend that Zingeberales genes express certain attributes into the genomes regarding one another eudicots and you can members of the Poaceae. That it impact means that the latest Musa genome is much more similar to cereal genomes according to onion, asparagus and basal-most monocot lineage, Acorus.