Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401 Alexey Fomenkov, a Zhiyi Sun, a Tamas Vincze, a Galina Dubinina, c Maria Orlova, b Sergey V. Tarlachkov, d,e Brian P. Anton, a Margarita Y. Grabovich, b Richard J. Roberts a a New England Biolabs, Ipswich, Massachusetts, USA b Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia c Federal State Institution, Federal Research Centre for Fundamentals of Biotechnology, Russian Academy of Sciences, Moscow, Russia d All-Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia e Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia ABSTRACT Here, we report the complete closed genome sequence and methylome analysis of Beggiatoa leptomitoformis strain D-401 (DSM 14945, UNIQEMU 779), which is quite different from the previously described Beggiatoa leptomitoformis neotype strain D-402 T (DSM 14946, UNIQEM U 779) with regard to morphology and lithotro- phic growth in the presence of thiosulfate. T he taxonomy of the genus Beggiatoa is still a work in progress. Despite the fact that many morphotypes of Beggiatoa have been described previously, only two species have been validated: Beggiatoa alba and Beggiatoa leptomitoformis. Previously, we reported the genome sequence of B. leptomitoformis strain D-402 T (1), after which we described this strain as a representative of a new species within the genus Beggiatoa (2). Since the isolates were initially described based on the morphological criteria alone and named Beggiatoa leptomitoformis, the species name was retained but its orthog- raphy was changed based on the rules of Appendix 9 of the International Code of Nomenclature of Prokaryotes (3) and validated as Beggiatoa leptomitoformis sp. nov. with the type strain D-402 T . Here, we report the genome sequence of a second strain, B. leptomitoformis D-401. Both strains differ in their morphology and physiology, especially their ability to grow lithotrophically in the presence of thiosulfate. While B. leptomitoformis D-402 T is able to accumulate elemental sulfur intracellularly, D-401 is not. Therefore, comparative genomic analysis of these strains could illuminate meta- bolic features associated with lithotrophic growth in Beggiatoa. B. leptomitoformis D-401 was sequenced using the Pacific Biosciences (PacBio) RS II sequencing platform. Briefly, SMRTbell libraries were constructed from genomic DNA sheared to a size ranging from 10 to 20 kb using the manufacturer’s instructions. DNA quality analysis and quantification were performed using the Qubit fluorimeter (Invit- rogen, Eugene, OR) and 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA). One 16-kb SMRTbell library was prepared according to the 20-kb PacBio sample preparation protocol, including additional separation on a BluePippin to remove fragments less than 7 kb. One size-selected and one non-size-selected library were sequenced by using C4-P6 chemistry using 2 single-molecule real-time (SMRT) cells with 240-minute col- lection times. Sequencing reads were processed, mapped, and assembled with the Pacific Biosciences SMRT analysis pipeline using the HGAP3 protocol and polished using Quiver (4). A total of 1.5 Gb of sequencing data was assembled into a single closed Received 12 March 2018 Accepted 22 March 2018 Published 26 April 2018 Citation Fomenkov A, Sun Z, Vincze T, Dubinina G, Orlova M, Tarlachkov SV, Anton BP, Grabovich MY, Roberts RJ. 2018. Complete genome sequence of the freshwater bacterium Beggiatoa leptomitoformis strain D-401. Genome Announc 6:e00311-18. https://doi .org/10.1128/genomeA.00311-18. Copyright © 2018 Fomenkov et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Alexey Fomenkov, fomenkov@neb.com. PROKARYOTES crossm Volume 6 Issue 17 e00311-18 genomea.asm.org 1