Data out-of Musa family genes shows particular brand of provides

BACs representing one another distinctive line of loci hybridizing to probes SbRPG661, SbRPG373 and you can SbRPG851 were sequenced for the purpose out-of relationship the newest duration of replication in line with the fresh divergence of the 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 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) https://hookupranking.com/men-seeking-women/, 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 examined the level of conservation ranging from genomic regions related SbRPG661, SbRPG851 and you can SbRPG373 duplicated genetics during the Musa and rice and found no synteny inside the regions secured because of the this type of homologs. So it lack of synteny would be said of the replication events and next gene loss or by translocation of your focal genes.

Discussion

step one.8 Mb out-of Musa genomic series revealed that most of the BACs examined was indeed gene rich which have the lowest content regarding transposable feature. All of our analyses off 443 Musa genetics predicted revealed that Musa family genes are apt to have a good “rice-like” bimodal GC shipping with an extremely asymmetrical and you can long tail on high GC content as in early in the day studies [43, 44]. Although not, a moment group of “Arabidopsis-like” genetics is located which have an overall total lowest GC articles no high gradient across the programming sequence. In contrast to a past assessment off yard and you can non-lawn monocots [52, 53], the analyses recommend that Zingeberales genes display specific attributes towards the genomes out of each other eudicots and people in the fresh new Poaceae. It effect shows that the fresh new Musa genome is far more the same as cereal genomes relative to onion, asparagus as well as the basal-extremely monocot lineage, Acorus.