CLC GENOMICS WORKBENCH 20 MANUAL MANUAL

Keywords: Clostridium autoethanogenum, Next generation sequencing, Acetogen, Manual annotation, Synthesis gas fermentation

CLC GENOMICS WORKBENCH 20 MANUAL FULL

As a result, different functions were assigned to gene products or previous functional annotations rejected because of missing evidence in various occasions.Ĭonclusions: We present a revised manually curated full genome sequence for Clostridium autoethanogenum DSM10061, which provides reliable information for genome-scale models that rely heavily on the accuracy of annotation, and represents an important step towards the manipulation and metabolic modelling of this industrially relevant acetogen.

CLC GENOMICS WORKBENCH 20 MANUAL SERIAL

Furthermore, we have completed a comprehensive manual curation to reduce errors in the annotation that occur through serial use of automated annotation pipelines in related species. It was also observed that many genes containing these sequencing errors were annotated in the published closed genome as encoding proteins containing frameshift mutations (18 instances) or were annotated despite the coding frame containing stop codons, which if genuine, would severely hinder the organism's ability to survive. This was corroborated by the observation that over 90 % occurred within homopolymer regions of greater than 4 nucleotides in length. These variations were confirmed by Sanger sequencing and subsequent analysis suggested that the discrepancies were sequencing errors in the published genome not true single nucleotide polymorphisms. Results: We performed next generation sequencing using Illumina MiSeq technology on the DSM10061 strain of Clostridium autoethanogenum and observed 243 single nucleotide discrepancies when compared to the published finished sequence (NCBI: GCA_000484505.1), with 59.1 % present in coding regions. However, crucial to metabolic modelling and directed pathway engineering is a reliable and comprehensively annotated genome sequence. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Minton1*īackground: Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. Wichlacz3, Craig Woods1, Rupert Norman1, Jochen Blom4, Alexander Goesman4, Charlie Hodgman1, David Barrett2, Neil R.Thomas3, Klaus Winzer1 and Nigel P.

Annan1, Ronja Breitkopf1, Bart Pander1, Pawel Piatek1, Peter Rowe1, Alexander T. Humphreys1, Samantha McLean1, Sarah Schatschneider2, Thomas Millat1, Anne M. Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacteriumĬhristopher M.

Clc genomics workbench 20 manual