Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia:Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes

Kotak, Malini; Lin, Jonathan Y.; Isanapong, Jantiya; Rodrigues, Jorge L.  M.; Baltrus, David A.

doi:10.1128/MRA.01192-19

Title: Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia:Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes

Abstract

Here, we report the high-quality draft genome sequences of Opitutaceae sp. strains TAV3 and TAV4, which were isolated from the hindgut of the wood-feeding termite Reticulitermes flavipes. Using a combination of Illumina and PacBio sequencing, we constructed nearly complete assemblies totaling 5.84 and 5.91 Mbp in length for strains TAV3 and TAV4, respectively. In addition, we report an in silico analysis of potential lignocellulose-digesting enzymes present in these strains.

Authors:

Kotak, Malini ^[1];

^[2]; Isanapong, Jantiya ^[3];

^[4]; Baltrus, David A. ^[5]

Univ. of Texas, Arlington, TX (United States)
Univ. of California, Davis, CA (United States)
King Mongkut’s Univ. of Technology, Bangkok (Thailand)
Univ. of California, Davis, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Arizona, Tucson, AZ (United States)

Publication Date:: Thu Jan 09 00:00:00 EST 2020

Research Org.:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC); National Institutes of Health (NIH)

OSTI Identifier:: 1599847

Grant/Contract Number:: AC02-05CH11231; 1S10OD010786-01

Resource Type:: Accepted Manuscript

Journal Name:: Microbiology Resource Announcements

Additional Journal Information:: Journal Volume: 9; Journal Issue: 2; Journal ID: ISSN 2576-098X

Publisher:: SSPA - American Society for Microbiology

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Kotak, Malini, Lin, Jonathan Y., Isanapong, Jantiya, Rodrigues, Jorge L.  M., and Baltrus, David A. Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia:Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes.  United States: N. p., 2020. 
Web.  doi:10.1128/MRA.01192-19.

Copy to clipboard


                    Kotak, Malini, Lin, Jonathan Y., Isanapong, Jantiya, Rodrigues, Jorge L.  M., & Baltrus, David A. Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia:Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes.  United States.  https://doi.org/10.1128/MRA.01192-19

Copy to clipboard


                    Kotak, Malini, Lin, Jonathan Y., Isanapong, Jantiya, Rodrigues, Jorge L.  M., and Baltrus, David A. Thu .  
"Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia:Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes".  United States.  https://doi.org/10.1128/MRA.01192-19.  https://www.osti.gov/servlets/purl/1599847.

Copy to clipboard


                    
@article{osti_1599847,

  title        = {Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia:Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes},

  author       = {Kotak, Malini and Lin, Jonathan Y. and Isanapong, Jantiya and Rodrigues, Jorge L.  M. and Baltrus, David A.},

  abstractNote = {Here, we report the high-quality draft genome sequences of Opitutaceae sp. strains TAV3 and TAV4, which were isolated from the hindgut of the wood-feeding termite Reticulitermes flavipes. Using a combination of Illumina and PacBio sequencing, we constructed nearly complete assemblies totaling 5.84 and 5.91 Mbp in length for strains TAV3 and TAV4, respectively. In addition, we report an in silico analysis of potential lignocellulose-digesting enzymes present in these strains.},

  doi          = {10.1128/MRA.01192-19},

  journal      = {Microbiology Resource Announcements},

  number       = 2,

  volume       = 9,

  place        = {United States},

  year         = {Thu Jan 09 00:00:00 EST 2020},

  month        = {Thu Jan 09 00:00:00 EST 2020}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Accepted Manuscript (DOE)

Publisher's Version of Record

https://doi.org/10.1128/MRA.01192-19

Other availability

Search WorldCat to find libraries that may hold this journal

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

Symbiotic digestion of lignocellulose in termite guts
journal, February 2014

Brune, Andreas
Nature Reviews Microbiology, Vol. 12, Issue 3
DOI: 10.1038/nrmicro3182

Prokka: rapid prokaryotic genome annotation
journal, March 2014

Seemann, T.
Bioinformatics, Vol. 30, Issue 14
DOI: 10.1093/bioinformatics/btu153

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database
journal, August 2010

Park, Byung H.; Karpinets, Tatiana V.; Syed, Mustafa H.
Glycobiology, Vol. 20, Issue 12
DOI: 10.1093/glycob/cwq106

The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution
journal, October 2015

Brune, Andreas; Dietrich, Carsten
Annual Review of Microbiology, Vol. 69, Issue 1
DOI: 10.1146/annurev-micro-092412-155715

New Strategies for Cultivation and Detection of Previously Uncultured Microbes
journal, August 2004

Stevenson, B. S.; Eichorst, S. A.; Wertz, J. T.
Applied and Environmental Microbiology, Vol. 70, Issue 8
DOI: 10.1128/AEM.70.8.4748-4755.2004

Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii
journal, January 2012

Blifernez-Klassen, Olga; Klassen, Viktor; Doebbe, Anja
Nature Communications, Vol. 3, Issue 1
DOI: 10.1038/ncomms2210

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
journal, June 2017

Wick, Ryan R.; Judd, Louise M.; Gorrie, Claire L.
PLOS Computational Biology, Vol. 13, Issue 6
DOI: 10.1371/journal.pcbi.1005595

Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium
journal, May 2013

Isanapong, Jantiya; Sealy Hambright, W.; Willis, Austin G.
The ISME Journal, Vol. 7, Issue 9
DOI: 10.1038/ismej.2013.74

NCBI prokaryotic genome annotation pipeline
journal, June 2016

Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat
Nucleic Acids Research, Vol. 44, Issue 14
DOI: 10.1093/nar/gkw569

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
Nucleic Acids Research, Vol. 37, Issue Database
DOI: 10.1093/nar/gkn663

IND-enzymes: a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage
journal, May 2021

Sunny, Jithin S.; Nisha, Khairun; Natarajan, Anuradha
Extremophiles, Vol. 25, Issue 4
DOI: 10.1007/s00792-021-01231-2

Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea
journal, February 2021

Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier
Microbiology Resource Announcements, Vol. 10, Issue 5
DOI: 10.1128/mra.00297-20

Similar Records in DOE PAGES and OSTI.GOV collections:

High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes

Journal Article Isanapong, Jantiya ; Goodwin, Lynne A ; Bruce, David ; ... - Journal of Bacteriology

Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.
https://doi.org/10.1128/JB.00264-12
Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes

Journal Article Kotak, Malini ; Isanapong, Jantiya ; Goodwin, Lynne A. ; ... - Genome Announcements

The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated from the wood-feeding termite hindgut. Here, we report here its complete genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and 99,831 bp, respectively. In conclusion, genomic analysis reveals genes for methylotrophy, lignocellulose degradation, and ammonia and sulfate assimilation.
https://doi.org/10.1128/genomeA.00060-15

Full Text Available
Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes

Journal Article Tartar, Aurélien ; Wheeler, Marsha M. ; Zhou, Xuguo ; ... - Biotechnology for Biofuels

Background: Termite lignocellulose digestion is achieved through a collaboration of host plus prokaryotic and eukaryotic symbionts. In the present work, we took a combined host and symbiont metatranscriptomic approach for investigating the digestive contributions of host and symbiont in the lower termite Reticulitermes flavipes. Our approach consisted of parallel high-throughput sequencing from (i) a host gut cDNA library and (ii) a hindgut symbiont cDNA library. Subsequently, we undertook functional analyses of newly identified phenoloxidases with potential importance as pretreatment enzymes in industrial lignocellulose processing. Results: Over 10,000 expressed sequence tags (ESTs) were sequenced from the 2 libraries that aligned intomore »« less
https://doi.org/10.1186/1754-6834-2-25

Full Text Available
Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium

Journal Article Isanapong, Jantiya ; Hambright, Sealy ; Willis, Austin G. ; ... - The ISME Journal, 7(9):1803-1813

Termite hindguts are populated by a dense and diverse community of microbial symbionts working in concert to transform lignocellulosic plant material and derived residues into acetate, to recycle and fix nitrogen, and to remove oxygen. Although much has been learned about the breadth of microbial diversity in the hindgut, the ecophysiological roles of its members is less understood. In this study, we present new information about the ecophysiology of microorganism Diplosphaera colotermitum strain TAV2, an autochthonous member of the Reticulitermes flavipes gut community. An integrated high-throughput approach was used to determine the transcriptomic and proteomic profiles of cells grown undermore »« less
https://doi.org/10.1038/ismej.2013.74
Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

Journal Article Rossmassler, Karen ; Dietrich, Carsten ; Thompson, Claire ; ... - Microbiome

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential betweenmore »« less
Cited by 36
https://doi.org/10.1186/s40168-015-0118-1

Full Text Available

Similar Records

Title: Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia:Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes

Abstract

Citation Formats

Symbiotic digestion of lignocellulose in termite guts journal, February 2014

Prokka: rapid prokaryotic genome annotation journal, March 2014

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database journal, August 2010

The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution journal, October 2015

New Strategies for Cultivation and Detection of Previously Uncultured Microbes journal, August 2004

Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii journal, January 2012

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads journal, June 2017

Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium journal, May 2013

NCBI prokaryotic genome annotation pipeline journal, June 2016

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics journal, January 2009

IND-enzymes: a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage journal, May 2021

Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea journal, February 2021

Symbiotic digestion of lignocellulose in termite guts
journal, February 2014

Prokka: rapid prokaryotic genome annotation
journal, March 2014

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database
journal, August 2010

The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution
journal, October 2015

New Strategies for Cultivation and Detection of Previously Uncultured Microbes
journal, August 2004

Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii
journal, January 2012

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
journal, June 2017

Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium
journal, May 2013

NCBI prokaryotic genome annotation pipeline
journal, June 2016

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

IND-enzymes: a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage
journal, May 2021

Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea
journal, February 2021