Draft genome sequence of cellulolytic and xylanolytic Cellulomonas sp. B6 strain isolated from sub-tropical forest soil

FLORENCIA PICCINNI; YANINA MURUA; SILVINA GHIO; PAOLA TALIA; MÁXIMO RIVAROLA; ELEONORA CAMPOS

Genome Announcements

American Society for Microbiology

Año: 2016 vol. 4 p. 891 - 916

Cellulases and xylanases are widely used in textile, animal feed,food, and paper industries. They also play a key role in theproduction of cellulosic ethanol (1).Cellulomonas sp. strain B6 (available from Argentine collectionof microorganisms as IMIZA:CEB6) was isolated from the first10-cm layer of a preserved native subtropical forest soil sample(26°01=34==S 54°26=59==W) (2). It is a Gram-positive, rod-shaped,aerobic isolate that can grow on lignocellulosic biomass, such assugarcane residue, as a sole carbon source. Its secreted proteinextract presented cellulose- and xylan-degrading activities (ourunpublished data). Based on 16S rRNA analysis, strain B6 formeda cluster with Cellulomonas flavigena (accession no. AF140036.1)and Cellulomonas persica (accession no. NR_024913.1). The genomesof Cellulomonas flavigena DSM 20109 and B6 show anaverage nucleotide Identity (ANI) value of 81.99%, suggestingthat they are different species.Genomic DNA of Cellulomonas sp. strain B6 was extractedfrom a 24-h culture in LB broth by a commercial extraction kit(Wizard genomic DNA extraction kit; Promega) and sequencedusing the Illumina MiSeq platform. The data comprised 1,532,556paired-end reads of 500 bp, resulting in 83-fold genome coverage.The raw reads were subjected to trimming using Trimmomaticversion 0.33 (3) and assembled de novo using Celera Assemblerversion 8.2 (4), followed by the SPAdes genome assembler version3.5.0 (5), generating 279 contigs, with a total length of4,042,435 bp (N50, 24,612 bp) and a GC content of 75.1%, consistentwith the genus.Geneprediction and functional analysis were carried out using theRapid Annotations using Subsystems Technology (RAST) server version2.0 (6) and the NCBI Prokaryotic Genome Annotation Pipeline(http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). Usingthe NCBI pipeline, 3,691 genes, including 3,443 proteincodingsequences, 50 tRNA, and a set of full-length 5S, 23S, and16S rRNA gene sequences, were predicted. A noncoding RNA(ncRNA) of an RNase P (ATM99_11600) was also predicted. Similarresults were obtained by RAST. A comparison of a representativeset of FigFam protein-coding genes from Cellulomonas sp.B6 to other bacterial sequences available in RAST identified Cellulomonasflavigena DSM 20109 (score, 413) and Sanguibacterkeddieii DSM 10542 as the closest neighbors.Utilizing all functional annotations from CAZy (http://www.cazy.org/) (7) and dbCAN (http://csbl.bmb.uga.edu/dbCAN/)(8), 92 sequences encoding potential glycosyl hydrolases (GH)were identified, including six endo--1,4-glucanases (two GH5and four GH9), two exo-glucanases (GH6 and GH48), 11 -glucosidases (three GH1 and eight GH3), 10 endo-1,4--xylanases(eight GH10, one GH11, and one GH43), two -xylosidases (twoGH39 and one GH43:1), four -L-arabinofuranosidases (twoGH43 and two GH51), two endo-1,5--arabinosidases (GH43),and an -glucuronidase (GH67). These results are consistentwith the cellulolytic and xylanolytic activities of this bacterialisolate.The genome information will be useful for studies of microbialenzymes for industrial application in lignocellulosic biomass utilization.Accession number(s). This whole-genome shotgun projecthas been deposited at NCBI SRA database under the accession no.LNTD00000000. The version described in this paper is versionLNTD01000000.