PMC:3558958 / 9660-12424 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3558958","sourcedb":"PMC","sourceid":"3558958","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3558958","text":"Genome sequencing and annotation\n\nGenome project history\nPaenibacillus sp.Y412MC10 was selected for sequencing on the basis of its biotechnological potential as part of the U.S. Department of Energy's Genomic Science program (formerly Genomics:GTL). The genome sequence is deposited in the Genomes On Line Database [42] (GOLD ID = Gc01127), and in GenBank (NCBI Reference Sequence = NC_013406). Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information and its association with MIGS identifiers is shown in Table 2.\nTable 2 Genome sequencing and project information\n\nGrowth conditions and DNA Isolation\nFor preparation of genomic DNA, liter cultures of Y412MC10 were grown from a single colony in YTP-2 medium at 37°C in flasks agitated at 200 rpm and collected by centrifugation. The cell concentrate was lysed using a combination of SDS and proteinase K, and genomic DNA was isolated using a phenol/chloroform extraction [43]. The genomic DNA was precipitated, and treated with RNase to remove residual contaminating RNA.\n\nGenome sequencing and assembly\nThe genome of Paenibacillus lautus Y412MC10 was sequenced at the Joint Genome Institute (JGI) [44] using Sanger sequencing with a combination of 6 kb and 34 kb DNA libraries and 454 FLX pyrosequencing done to a depth of 20× coverage [45]. Both libraries provided 5.8× coverage of the genome. Draft assemblies were based on 39,162 total reads. Solexa sequencing data was used to polish the assembly. All general aspects of library construction and sequencing performed at the JGI can be found at their website. The Phred/Phrap/Consed software package [46] was used to assemble 6-kb and fosmid libraries and to assess quality. Possible mis-assemblies were corrected; gaps between contigs were closed by 2,744 primer walks from sub-clones or 83 PCR end reads, 5 mini-libraries, and 10 PCR shatter libraries. The error rate of the completed genome sequence was 0.08, based on 49,558 total reads. Table 2 presents the project information and its association with MIGS version 2.0 compliance [47].\n\nGenome annotation\nGenes were identified using Prodigal [48] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [49]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [49], RNAMMer [50], Rfam [51], TMHMM [52], and signalP [52].\n","divisions":[{"label":"Title","span":{"begin":0,"end":32}},{"label":"Section","span":{"begin":34,"end":641}},{"label":"Title","span":{"begin":34,"end":56}},{"label":"Table caption","span":{"begin":588,"end":640}},{"label":"Title","span":{"begin":597,"end":638}},{"label":"Section","span":{"begin":640,"end":1096}},{"label":"Title","span":{"begin":640,"end":675}},{"label":"Section","span":{"begin":1098,"end":2120}},{"label":"Title","span":{"begin":1098,"end":1128}},{"label":"Section","span":{"begin":2122,"end":2763}},{"label":"Title","span":{"begin":2122,"end":2139}}],"tracks":[{"project":"MicrobeTaxon","denotations":[{"id":"T70","span":{"begin":57,"end":82},"obj":"http://purl.bioontology.org/ontology/NCBITAXON/481743"},{"id":"T71","span":{"begin":726,"end":734},"obj":"481743"},{"id":"T72","span":{"begin":1143,"end":1172},"obj":"481743"}],"namespaces":[{"prefix":"_base","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"attributes":[{"subj":"T70","pred":"source","obj":"MicrobeTaxon"},{"subj":"T71","pred":"source","obj":"MicrobeTaxon"},{"subj":"T72","pred":"source","obj":"MicrobeTaxon"}]},{"project":"2_test","denotations":[{"id":"23408395-19914934-140428068","span":{"begin":316,"end":318},"obj":"19914934"},{"id":"23408395-16056220-140428069","span":{"begin":1363,"end":1365},"obj":"16056220"},{"id":"23408395-18464787-140428070","span":{"begin":2116,"end":2118},"obj":"18464787"},{"id":"23408395-20211023-140423122","span":{"begin":2178,"end":2180},"obj":"20211023"},{"id":"23408395-9023104-140428071","span":{"begin":2328,"end":2330},"obj":"9023104"},{"id":"23408395-9023104-140428072","span":{"begin":2704,"end":2706},"obj":"9023104"},{"id":"23408395-17452365-140428073","span":{"begin":2718,"end":2720},"obj":"17452365"},{"id":"23408395-12520045-140428074","span":{"begin":2729,"end":2731},"obj":"12520045"},{"id":"23408395-11152613-140428075","span":{"begin":2741,"end":2743},"obj":"11152613"},{"id":"23408395-11152613-140428076","span":{"begin":2759,"end":2761},"obj":"11152613"}],"attributes":[{"subj":"23408395-19914934-140428068","pred":"source","obj":"2_test"},{"subj":"23408395-16056220-140428069","pred":"source","obj":"2_test"},{"subj":"23408395-18464787-140428070","pred":"source","obj":"2_test"},{"subj":"23408395-20211023-140423122","pred":"source","obj":"2_test"},{"subj":"23408395-9023104-140428071","pred":"source","obj":"2_test"},{"subj":"23408395-9023104-140428072","pred":"source","obj":"2_test"},{"subj":"23408395-17452365-140428073","pred":"source","obj":"2_test"},{"subj":"23408395-12520045-140428074","pred":"source","obj":"2_test"},{"subj":"23408395-11152613-140428075","pred":"source","obj":"2_test"},{"subj":"23408395-11152613-140428076","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"MicrobeTaxon","color":"#e4ec93","default":true},{"id":"2_test","color":"#d993ec"}]}]}}