In this work, we employed MicrobeCensus22 for de novo estimation of the average genome size (AGS) of microorganisms captured in shotgun metagenome sequences (Fig. 1a; Supplementary Data 1). Briefly, MicrobeCensus optimally aligns metagenomic reads to a set of 30 conserved single-copy gene (CSC...
Full size image The E. grandis genome encodes a large number of predicted protein-coding loci (36,376) of which 89% are expressed in vegetative and reproductive tissues (Extended Data Fig. 1) plus various classes of non-coding genes (Supplementary Information section 2). Of the 36,376 predi...
It also should be helpful in epidemiology and for the development of new vaccines. In 2011, an outbreak due to E. coli O104:H4 caused about 4000 cases with more than 40 deaths. The causative agent was quickly identified, and its genome sequenced. The incriminated food, however, was more...
(A) These two 15 bp genomic sequences (long rectangles) from Escherichia coli each generate three 8 bp reads (short rectangles). The reads can be further decomposed into a larger number of 4 bp kmers (ovals). The longest subsequence shared between the two large sequences is 5 bp long,...
metabolite (i.e., phenylpropanoids and flavonoids) synthesis in imparting the properties of aroma and environmental adaptation in this species. This study laid a foundation for further investigating the molecular mechanisms underlying the synthesis of specific compounds inT. mongolicus....
locustag ECPOOp \ --increment 10 --gffver 2 --centre CDC --compliant \ --genus Escherichia --species coli --strain POO247 --plasmid pECPOO247 \ --kingdom Bacteria --gcode 11 --usegenus \ --proteins /opt/prokka/db/trusted/Ecocyc-17.6 \ --evalue 1e-9 --rfam \ plasmid-closed....
Highly contiguous nanopore genome assembly of Chlamydomonas reinhardtii CC-1690. Microbiol. Resour. Announc. 9, e00726 (2020). Article PubMed PubMed Central Google Scholar Wang, J. et al. Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated ...
Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF: The complete genome sequence of Escherichia coli K-12. Science. 1997, 277 (5331): 1453-1462. 10.1126/science.277.5331.1453. CAS PubMed Google Scholar Andersson SG, ...
Full size table Figure 1 Read length distribution of BES after base calling, trimming for E. coli and vector sequences and removing redundancies. Full size image Assessment of the repetitive elements in the carp genome The proportion of the repetitive elements in the common carp genome was assess...
here we report a static description that provides a synthetic representation of the genome variability of the species in terms of a few parameters. We calculated the size of the totalS. pneumoniaegene pool accessible to the species, or pan-genome, using two different methodologies, namely the fin...