Draft Genome Sequence of a Dictyoglomus Sp. from an Enrichment Culture of a New Zealand Geothermal Spring

Overview

Journal Genome Announc

Publisher American Society for Microbiology

Date 2018 Mar 17

PMID 29545298

Authors

Anna-Louise Reysenbach

John A Donaho

John F Kelley

Emily St John

Christina Turner

Mircea Podar

Matthew B Stott

Affiliations

Soon will be listed here.

Abstract

A draft genome of a novel sp., NZ13-RE01, was obtained from a New Zealand hot spring enrichment culture. The 1,927,012-bp genome is similar in both size and G+C content to other spp. Like its relatives, sp. NZ13-RE01 encodes many genes involved in complex carbohydrate metabolism.

References

Lowe T, Chan P . tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016; 44(W1):W54-7. PMC: 4987944. DOI: 10.1093/nar/gkw413. View

Brettin T, Davis J, Disz T, Edwards R, Gerdes S, Olsen G . RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015; 5:8365. PMC: 4322359. DOI: 10.1038/srep08365. View

Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y . dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012; 40(Web Server issue):W445-51. PMC: 3394287. DOI: 10.1093/nar/gks479. View

Overbeek R, Olson R, Pusch G, Olsen G, Davis J, Disz T . The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2013; 42(Database issue):D206-14. PMC: 3965101. DOI: 10.1093/nar/gkt1226. View

Li H . A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011; 27(21):2987-93. PMC: 3198575. DOI: 10.1093/bioinformatics/btr509. View

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D . Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19(9):1639-45. PMC: 2752132. DOI: 10.1101/gr.092759.109. View

Peng Y, Leung H, Yiu S, Chin F . IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012; 28(11):1420-8. DOI: 10.1093/bioinformatics/bts174. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

Konstantinidis K, Rossello-Mora R, Amann R . Uncultivated microbes in need of their own taxonomy. ISME J. 2017; 11(11):2399-2406. PMC: 5649169. DOI: 10.1038/ismej.2017.113. View

10.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

11.

Nishida H, Beppu T, Ueda K . Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae. Genomics. 2011; 98(5):370-5. DOI: 10.1016/j.ygeno.2011.08.001. View

12.

Wu Y, Tang Y, Tringe S, Simmons B, Singer S . MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014; 2:26. PMC: 4129434. DOI: 10.1186/2049-2618-2-26. View

13.

Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R . The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9:75. PMC: 2265698. DOI: 10.1186/1471-2164-9-75. View

14.

Coil D, Badger J, Forberger H, Riggs F, Madupu R, Fedorova N . Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12. Genome Announc. 2014; 2(1). PMC: 3931368. DOI: 10.1128/genomeA.00109-14. View

15.

Hoppert M, Valdez M, Enseleit M, Theilmann W, Valerius O, Braus G . Structure-functional analysis of the Dictyoglomus cell envelope. Syst Appl Microbiol. 2012; 35(5):279-90. DOI: 10.1016/j.syapm.2012.06.004. View

16.

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

17.

Brumm P, Gowda K, Robb F, Mead D . The Complete Genome Sequence of Hyperthermophile DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. Front Microbiol. 2017; 7:1979. PMC: 5167688. DOI: 10.3389/fmicb.2016.01979. View

18.

Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki E, Zaslavsky L . NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016; 44(14):6614-24. PMC: 5001611. DOI: 10.1093/nar/gkw569. View

19.

Brumm P, Hermanson S, Hochstein B, Boyum J, Hermersmann N, Gowda K . Mining Dictyoglomus turgidum for enzymatically active carbohydrases. Appl Biochem Biotechnol. 2010; 163(2):205-14. DOI: 10.1007/s12010-010-9029-6. View

20.

Parks D, Imelfort M, Skennerton C, Hugenholtz P, Tyson G . CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015; 25(7):1043-55. PMC: 4484387. DOI: 10.1101/gr.186072.114. View