BACs symbolizing both distinctive line of loci hybridizing so you can probes SbRPG661, SbRPG373 and SbRPG851 have been sequenced with the aim of matchmaking the time of duplication in line with the fresh new divergence of one’s Musa and you may rice lineages

We also analyzed the 18,612 ginger (Zingiber officinale; Zingiberaceae, Zingiberales) EST-derived unigenes available on the TIGR Plant Transcript https://hookupranking.com/mature-women-hookup/ 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 along with analyzed the level of preservation anywhere between genomic countries close SbRPG661, SbRPG851 and you will SbRPG373 repeated genetics within the Musa and you can grain and found no synteny in countries secured by the these types of homologs. That it lack of synteny could well be said because of the duplication situations and you will subsequent gene losings otherwise because of the translocation of your focal family genes.

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step 1.8 Mb off Musa genomic sequence revealed that the BACs examined have been gene steeped which have a minimal stuff out-of transposable function. Our analyses from 443 Musa genes predict indicated that Musa genetics tend to have a “rice-like” bimodal GC shipping having a highly asymmetrical and you may long-tail to your high GC content like in early in the day studies [43, 44]. not, the next family of “Arabidopsis-like” family genes was discovered having a total reduced GC articles with no high gradient across the coding succession. Compared with a previous evaluation from yard and you may low-grass monocots [52, 53], all of our analyses advise that Zingeberales genetics share specific features on the genomes regarding one another eudicots and you will people in the new Poaceae. Which results shows that the fresh Musa genome is far more the same as cereal genomes in accordance with onion, asparagus while the basal-very monocot ancestry, Acorus.