PMC:4502367 / 24496-26281 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502367","sourcedb":"PMC","sourceid":"4502367","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502367","text":"Gene annotation using re-sequenced genomes and RNA-seq data from Z. pseudotritici, Z. ardabiliae, and Z. brevis\nRNA-sequencing data obtained from axenic cultures of Z. pseudotritici, Z. ardabiliae, and Z. brevis were filtered (Table S1) and assembled. The resulting transcriptomes include 35,132, 36,546, and 33,201 transcripts clustered into 12,027, 12,719, and 11,542 putative gene models for Z. pseudotritici, Z. ardabiliae, and Z. brevis, respectively (Table 1). The training set established for Z. tritici was also for the annotation of the three other Zymoseptoria species. For each species, EVM created a weighted consensus of the gene models, which after PASA corrections resulted in 11,044, 10,787, and 10,557 gene models for Z. pseudotritici, Z. ardabiliae, and Z. brevis, respectively (Table 1). The total number of predicted gene models in the re-sequenced Zymoseptoria species was similar; however, due to the fragmented genome assemblies of Z. pseudotritici, Z. ardabiliae, and Z. brevis, more partial gene models were predicted compared to models in Z. tritici (Table 1). Overall, the gene characteristics of these four species are very similar in accordance with the close phylogenetic relationships. Compared to Z. tritici, the functional annotation of the predicted gene models in Z. pseudotritici, Z. ardabiliae, and Z. brevis showed a larger proportion of sequences with an attributed function and a smaller proportion of sequences with no functional evidences. The four annotations are available from http://fungi.ensembl.org/Zymoseptoria_tritici/Info/Index (Z. tritici), http://genome.jgi.doe.gov/Zymps1/Zymps1.home.html (Z. pseudotritici), http://genome.jgi.doe.gov/Zymar1/Zymar1.home.html (Z.ardabiliae), and http://www.uniprot.org/taxonomy/1047168 (Z. brevis).","divisions":[{"label":"title","span":{"begin":0,"end":111}}],"tracks":[]}