Complete Genome Sequence of the Intracellular Bacterial Symbiont TC1 in the Anaerobic Ciliate
            <i>Trimyema compressum</i>

Shinzato, Naoya; Aoyama, Hiroaki; Saitoh, Seikoh; Nikoh, Naruo; Nakano, Kazuma; Shimoji, Makiko; Shinzato, Misuzu; Satou, Kazuhito; Teruya, Kuniko; Hirano, Takashi; Yamada, Takanori; Nobu, Masaru K.; Tamaki, Hideyuki; Shirai, Yumi; Park, Sanghwa; Narihiro, Takashi; Liu, Wen Tso; Kamagata, Yoichi

doi:10.1128/genomea.01032-16

Cited by 6 publications

(6 citation statements)

References 8 publications

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“…We have sequenced a large number of genomes using PacBio RS II and published many scientific publications with collaborators in Okinawa genome projects in a wide variety of area including medical area. For viral and prokaryotic genomes, we determined all eight RNA segments of influenza A virus as full-length sequences (data not published), 21 complete bacterial genomic sequences, and 2 entire bacterial biosynthetic gene clusters [ 17 – 21 , 30 – 34 , 36 , 41 – 44 ]. For eukaryotic genomes, we constructed almost-complete (totally 95% of 540 Mb in 11 chromosomes) genome sequences of azuki bean [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

“…mccartyi IBARAKI PacBio, SOLiD3 Chromosome 1,451,062 47.00 39 sets of >1000-bp identical sequence pairs NZ-AP014563 2014 [ 33 ] Endosymbiont of Bathymodiolus septemdierum str. Myojin Knoll PacBio, 454, Sanger, Illumina Chromosome 1,469,434 38.70 Subpopulation AP013042 2015 [ 34 ] Bacterial symbiont “TC1” of Trimyema compressum PacBio Chromosome 1,586,453 32.8 207 sets of >1000-bp identical sequence pairs, G+C content of 23.5% region CP014606 2016 [ 36 ] Plasmid 35,795 29.7 CP014607 Vigna. angularis cv.…”

Section: Noted Studies Using Pacbio Rs IImentioning

confidence: 99%

“…Therefore, we carried out new sequencing using PacBio RS II. As the result, two circular contigs representing a single chromosome (1,586,453 bp, G+C content of 32.8%) and a single plasmid (35,795 bp, G+C content of 29.7%) were obtained [ 36 ]. The genome contained 207 sets of >1000-bp identical sequence pairs and low G+C regions (2000 bp, G+C content of 23.5% minimum) (unpublished).…”

Section: Noted Studies Using Pacbio Rs IImentioning

confidence: 99%

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Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

et al. 2017

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PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II’s sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

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Section: Discussionmentioning

confidence: 99%

Section: Noted Studies Using Pacbio Rs IImentioning

confidence: 99%

Section: Noted Studies Using Pacbio Rs IImentioning

confidence: 99%

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Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

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“…By using a cultured strain, physiological and metabolic profiles have been investigated, showing that both types of endosymbionts could positively affect the host's fitness (8,12). Recently, the complete genome sequence of the bacterial endosymbiont of T. compressum strain S10, strain TC1, was successfully determined (18). Genomic information on endosymbionts could give insights into their functions and the evolution of microbe-microbe symbiotic associations.…”

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confidence: 99%

Tripartite Symbiosis of an Anaerobic Scuticociliate with Two Hydrogenosome-Associated Endosymbionts, a Holospora -Related Alphaproteobacterium and a Methanogenic Archaeon

Takeshita

Yamada

Kawahara

et al. 2019

Appl Environ Microbiol

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A number of anaerobic ciliates, unicellular eukaryotes, intracellularly possess methanogenic archaea and bacteria as symbiotic partners. Although this tripartite relationship is of interest in terms of the fact that each participant is from a different domain, the difficulty in culture and maintenance of those host species with symbiotic partners has disturbed both ecological and functional studies so far. In this study, we obtained a stable culture of a small anaerobic scuticociliate, strain GW7. By transmission electron microscopic observation and fluorescent in situ hybridization with domain-specific probes, we demonstrate that GW7 possesses both archaeal and bacterial endosymbionts in its cytoplasm. These endosymbionts are in dependently associated with hydrogenosomes, which are organelle producing hydrogen and ATP under anaerobic conditions. Clone library analyses targeting prokaryotic 16S rRNA genes, fluorescent in situ hybridization with endosymbiont-specific probes, and molecular phylogenetic analyses revealed the phylogenetic affiliations and intracellular localizations of these endosymbionts. The endosymbiotic archaeon is a methanogen belonging to the genus Methanoregula (order Methanomicrobiales); a member of this genus has previously been described as the endosymbiont of an anaerobic ciliate from the genus Metopus (class Armophorea), which is only distantly related to strain GW7 (class Oligohymenophorea). The endosymbiotic bacterium belongs to the family Holosporaceae of the class Alphaproteobacteria, which also comprises several endosymbionts of various aerobic ciliates. For this endosymbiotic bacterium, we propose a novel candidate genus and species, “Candidatus Hydrogenosomobacter endosymbioticus.” IMPORTANCE Tripartite symbioses between anaerobic ciliated protists and their intracellular archaeal and bacterial symbionts are not uncommon, but most reports have been based mainly on microscopic observations. Deeper insights into the function, ecology, and evolution of these fascinating symbioses involving partners from all three domains of life have been hampered by the difficulties of culturing anaerobic ciliates in the laboratory and the frequent loss of their prokaryotic partners during long-term cultivation. In the present study, we report the isolation of an anaerobic scuticociliate, strain GW7, which has been stably maintained in our laboratory for more than 3 years without losing either of its endosymbionts. Unexpectedly, molecular characterization of the endosymbionts revealed that the bacterial partner of GW7 is phylogenetically related to intranuclear endosymbionts of aerobic ciliates. This strain will enable future genomic, transcriptomic, and proteomic analyses of the interactions in this tripartite symbiosis and a comparison with endosymbioses in aerobic ciliates.

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“…Anaerobic ciliates are known to harbor endosymbiotic bacteria and archaea ( 24 , 25 , 34 ). Hirakata et al ( 5 ) investigated the prokaryotic community structure of the anaerobic ciliate, Metopus sp.…”

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confidence: 99%

Symbiosis Studies in Microbial Ecology

Kamagata

Narihiro

2016

Microb. Environ.

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Complete Genome Sequence of the Intracellular Bacterial Symbiont TC1 in the Anaerobic Ciliate Trimyema compressum

Cited by 6 publications

References 8 publications

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

Tripartite Symbiosis of an Anaerobic Scuticociliate with Two Hydrogenosome-Associated Endosymbionts, a Holospora -Related Alphaproteobacterium and a Methanogenic Archaeon

Symbiosis Studies in Microbial Ecology

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