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Results of this similarity search were later used to generate the taxonomic distribution of best matches for annotated genes.
Based upon the current genome annotation (2,838 annotated genes in total), each TSS covers 1.52 genes.
Using the parental genome assemblies, we identified 23,529 homeologous coding sequences using reciprocal best BLAST (best-to-best) hits (Supplementary Table 2) representing 72% of the annotated genes.
However, it should be noted that the best-performing workflow still resulted in a loss of over 200 previously annotated genes, when reanalyzing simulated V. vulnificus CMCP6 data.
The best predictions were considered as overlapping results with above annotation steps and were integrated together to yield a summary of the annotated genes.
Cufflinks predicted genes were annotated with all of the above and the best hit in A. thaliana; this information was already provided by Phytozome v7.0 for annotated genes.
Green bars represent annotated genes.
Matrix of Pearson's correlation coefficients based on RPKM values of all annotated genes.
Further, these studies have used only known or annotated genes in their analysis.
To validate and improve gene models, we manually curated inaccurately annotated genes: 335 genes were manually added, and 86 genes were reclassified as pseudogenes.
Kale transcriptome datasets revealed 37,149 annotated genes and several secondary metabolite biosynthetic genes.
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