PMC:4502367 / 17240-18643 JSONTXT

{"project":"2_test","denotations":[{"id":"25917918-21304975-43386562","span":{"begin":265,"end":269},"obj":"21304975"},{"id":"25917918-2231712-43386563","span":{"begin":415,"end":419},"obj":"2231712"},{"id":"25917918-23329690-43386564","span":{"begin":462,"end":466},"obj":"23329690"},{"id":"25917918-16093699-43386565","span":{"begin":831,"end":835},"obj":"16093699"},{"id":"25917918-21109532-43386566","span":{"begin":1128,"end":1132},"obj":"21109532"},{"id":"25917918-17984973-43386567","span":{"begin":1283,"end":1287},"obj":"17984973"}],"text":"Repeats and transposable elements identification\nRepetitive DNA was identified and annotated in SOAP assembled genomes of the four isolates described above to create a repertoire of repeats specific to the Zymoseptoria genus using the REPET pipeline (Flutre et al. 2011). To obtain more complete elements, repeat families in each species were clustered using Blastclust from the NCBI-BLAST package (Altschul et al. 1990), aligned using Mafft (Katoh and Standley 2013), and new consensuses were then created. These steps were iterated with decreasing values of identity percentage (from 100% to 75%) and coverage (from 100% to 30%) until there was no more clustering of the sequences. Next, the sequences were classified (TEclassifier.py script from REPET) using tBLASTx and BLASTx against the Repbase Update database (Jurka et al. 2005) and by the identification of structural features such as long terminal repeats (LTRs) or terminal inverted repeats (TIRs). The sequences were additionally translated into the six reading frames to perform a protein domain search on the conserved domain database (CDD) (Marchler-Bauer et al. 2011) using RPS-BLAST. Transposable element (TE) families of each strain were classified and named according to the nomenclature defined by Wicker et al. (2007). The 497 repeat families identified in this study are available in FASTA format in Supporting Information, File 1."}