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Furumizu C, Tanizawa Y, Nakamura Y. Letter to the Editor: Genome Annotation Matters-From Genes to Phylogenetic Inferences. Plant Cell Physiol 2024; 65:181-184. [PMID: 38035794 DOI: 10.1093/pcp/pcad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Affiliation(s)
- Chihiro Furumizu
- Natural Science Center for Basic Research and Development, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8527 Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530 Japan
| | - Yasuhiro Tanizawa
- National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
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Ara T, Kodama Y, Tokimatsu T, Fukuda A, Kosuge T, Mashima J, Tanizawa Y, Tanjo T, Ogasawara O, Fujisawa T, Nakamura Y, Arita M. DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata. Nucleic Acids Res 2024; 52:D67-D71. [PMID: 37971299 PMCID: PMC10767850 DOI: 10.1093/nar/gkad1046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/21/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023] Open
Abstract
The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data.
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Affiliation(s)
- Takeshi Ara
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuichi Kodama
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Toshiaki Tokimatsu
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Asami Fukuda
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehide Kosuge
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Mashima
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tomoya Tanjo
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Osamu Ogasawara
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takatomo Fujisawa
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Tanifuji G, Kamikawa R, Nakamura Y. A practical assembly guideline for genomes with various levels of heterozygosity. Brief Bioinform 2023; 24:bbad337. [PMID: 37798248 PMCID: PMC10555665 DOI: 10.1093/bib/bbad337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/06/2023] [Accepted: 09/03/2023] [Indexed: 10/07/2023] Open
Abstract
Although current long-read sequencing technologies have a long-read length that facilitates assembly for genome reconstruction, they have high sequence errors. While various assemblers with different perspectives have been developed, no systematic evaluation of assemblers with long reads for diploid genomes with varying heterozygosity has been performed. Here, we evaluated a series of processes, including the estimation of genome characteristics such as genome size and heterozygosity, de novo assembly, polishing, and removal of allelic contigs, using six genomes with various heterozygosity levels. We evaluated five long-read-only assemblers (Canu, Flye, miniasm, NextDenovo and Redbean) and five hybrid assemblers that combine short and long reads (HASLR, MaSuRCA, Platanus-allee, SPAdes and WENGAN) and proposed a concrete guideline for the construction of haplotype representation according to the degree of heterozygosity, followed by polishing and purging haplotigs, using stable and high-performance assemblers: Redbean, Flye and MaSuRCA.
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Affiliation(s)
| | - Mika Sakamoto
- Genome Informatics Laboratory, National Institute of Genetics
| | | | - Takuro Nakayama
- Division of Life Sciences Center for Computational Sciences, University of Tsukuba, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science
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Shitamori F, Nonogaki A, Motegi T, Matsumoto Y, Sakamoto M, Tanizawa Y, Nakamura Y, Yonezawa T, Momoi Y, Maeda S. Large-scale epidemiological study on feline autosomal dominant polycystic kidney disease and identification of novel PKD1 gene variants. J Feline Med Surg 2023; 25:1098612X231185393. [PMID: 37489504 PMCID: PMC10812055 DOI: 10.1177/1098612x231185393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
OBJECTIVES Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited disease in cats. In most cases, the responsible abnormality is a nonsense single nucleotide polymorphism in exon 29 of the PKD1 gene (chrE3:g.42858112C>A, the conventional PKD1 variant). The aim of this study was to conduct a large-scale epidemiological study of ADPKD caused by the conventional PKD1 variant in Japan and to search for novel polymorphisms by targeted resequencing of the PKD1 using a next-generation sequencer. METHODS A total of 1281 cats visiting the Veterinary Medical Center of the University of Tokyo were included in this study. DNA was extracted from the blood of each cat. We established a novel TaqMan real-time PCR genotyping assay for the conventional PKD1 variant, and all cases were examined for the presence of this variant. Targeted resequencing of all exons of the PKD1 was performed on the DNA of 23 cats with the conventional PKD1 variant, six cats diagnosed with cystic kidneys but without this variant, and 61 wild-type normal cats. RESULTS Among the 1281 cats examined in this study, 23 (1.8%) harboured the conventional PKD1 variant. The odds of having the conventional PKD1 variant were significantly higher in Persian cats, Scottish Folds and Exotic Shorthairs than in the other breeds, although the number of cases in each breed was small. Furthermore, we identified four variants unique to cats with cystic kidneys that were not found in wild-type normal cats, all of which were in exon 15. In particular, two (chrE:g.42848725delC, pGly1641fs and chrE:g.42850283C>T, pArg2162Trp) were candidate variants. CONCLUSIONS AND RELEVANCE This study revealed that the conventional PKD1 variant was prevalent in Scottish Fold, Persian and Exotic Shorthair breeds in Japan, and variants in exon 15 of PKD1, in addition to the conventional variant in exon 29, would be key factors in the pathogenesis of ADPKD in cats.
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Affiliation(s)
- Fumitaka Shitamori
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ayaka Nonogaki
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoki Motegi
- Veterinary Medical Center, The University of Tokyo, Tokyo, Japan
| | | | - Mika Sakamoto
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka, Japan
| | - Tomohiro Yonezawa
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Momoi
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Maeda
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Nozawa K, Terada M, Onishi M, Ozaki Y, Takano T, Fakhouri W, Novick D, Haro JM, Faris LH, Kawaguchi T, Tanizawa Y, Tsurutani J. Real-world treatment patterns and outcomes of abemaciclib for the treatment of HR + , HER2- metastatic breast cancer patients in Japan. Breast Cancer 2023:10.1007/s12282-023-01461-6. [PMID: 37217763 DOI: 10.1007/s12282-023-01461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/08/2023] [Indexed: 05/24/2023]
Abstract
INTRODUCTION This study described, in routine clinical practice in Japan, the patient characteristics, treatment patterns, and outcomes of female patients with HR + /HER2- metastatic breast cancer (MBC) who started abemaciclib treatment. METHODS Clinical charts were reviewed for patients starting abemaciclib in 12/2018-08/2021 with a minimum of 3 months follow-up data post-abemaciclib initiation regardless of abemaciclib discontinuation. Patient characteristics, treatment patterns, and tumor response were descriptively summarized. Kaplan-Meier curves estimated progression-free survival (PFS). RESULTS 200 patients from 14 institutions were included. At abemaciclib initiation, median age was 59 years, and the Eastern Cooperative Oncology Group performance status score was 0/1/2 for 102/68/5 patients (58.3/38.9/2.9%), respectively. Most had an abemaciclib starting dose of 150 mg (92.5%). The percentage of patients receiving abemaciclib as 1st, 2nd, or 3rd line treatment was 31.5%, 25.8%, and 25.2%, respectively. The most frequent endocrine therapy drugs used with abemaciclib were fulvestrant (59%) and aromatase inhibitors (40%). Evaluation of tumor response was available for 171 patients, 30.4% of whom had complete/partial response. Median PFS was 13.0 months (95% CI 10.1-15.8 months). CONCLUSIONS In a routine clinical practice setting in Japan, patients with HR + , HER2- MBC appear to benefit from abemaciclib treatment in terms of treatment response and median PFS, with the results broadly reflecting the evidence demonstrated in clinical trials.
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Affiliation(s)
- K Nozawa
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - M Terada
- Department of Breast Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - M Onishi
- Department of Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Y Ozaki
- Department of Breast Medical Oncology, Breast Oncology Center, The Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
| | - T Takano
- Department of Breast Medical Oncology, Breast Oncology Center, The Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
| | - W Fakhouri
- Eli Lilly and Company, Indianapolis, IN, USA
| | - D Novick
- Eli Lilly and Company, Indianapolis, IN, USA
| | - J M Haro
- Parc Sanitari Sant Joan de Déu, Universitat de Barcelona, Sant Boi de Llobregat, Barcelona, Spain
| | - L H Faris
- Parc Sanitari Sant Joan de Déu, Universitat de Barcelona, Sant Boi de Llobregat, Barcelona, Spain
| | - T Kawaguchi
- Eli Lilly and Company, Indianapolis, IN, USA
| | - Y Tanizawa
- Eli Lilly and Company, Indianapolis, IN, USA
| | - Junji Tsurutani
- Advanced Cancer Translational Research Institute, Showa University, Tokyo, Japan.
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Tazawa J, Kobayashi H, Tanizawa Y, Uchino A, Tanaka F, Urashima Y, Miura S, Sakamoto M, Ohkuma M, Tohno M. Clostridium folliculivorans sp. nov., isolated from soil samples of an organic paddy in Japan. Int J Syst Evol Microbiol 2023; 73. [PMID: 37103467 DOI: 10.1099/ijsem.0.005876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Two Gram-stain-negative, terminal endospore-forming, rod-shaped and aerotolerant bacterial strains designated D1-1T and B3 were isolated from soil samples of an organic paddy in Japan. Strain D1-1T grew at 15-37 °C, pH 5.0-7.3, and with up to 0.5 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene revealed that strain D1-1T belonged to the genus Clostridium and was closely related to Clostridium zeae CSC2T (99.7 % sequence similarity), Clostridium fungisolvens TW1T (99.7 %) and Clostridium manihotivorum CT4T (99.3 %). Strains D1-1T and B3 were whole-genome sequenced and indistinguishable, with an average nucleotide identity value of 99.7 %. The average nucleotide identity (below 91.1 %) and digital DNA-DNA hybridization (below 43.6 %) values between the two novel isolates and their corresponding relatives showed that strains D1-1T and B3 could be readily distinguished from their closely related species. A novel Clostridium species, Clostridium folliculivorans sp. nov., with type strain D1-1T (=MAFF 212477T=DSM 113523T), is proposed based on genotypic and phenotypic data.
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Affiliation(s)
- Junko Tazawa
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8666, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Akira Uchino
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8666, Japan
| | - Fukuyo Tanaka
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8604, Japan
| | - Yasufumi Urashima
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8666, Japan
| | - Shigenori Miura
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8666, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
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Ta KN, Shimizu-Sato S, Agata A, Yoshida Y, Taoka KI, Tsuji H, Akagi T, Tanizawa Y, Sano R, Nosaka-Takahashi M, Suzuki T, Demura T, Toyoda A, Nakamura Y, Sato Y. A leaf-emanated signal orchestrates grain size and number in response to maternal resources. Plant J 2023. [PMID: 36994645 DOI: 10.1111/tpj.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/25/2023] [Indexed: 05/13/2023]
Abstract
In plants, variations in seed size and number are outcomes of different reproductive strategies. Both traits are often environmentally influenced, suggesting that a mechanism exists to coordinate these phenotypes in response to available maternal resources. Yet, how maternal resources are sensed and influence seed size and number is largely unknown. Here, we report a mechanism that senses maternal resources and coordinates grain size and number in the wild rice Oryza rufipogon, a wild progenitor of Asian cultivated rice. We showed that FT-like 9 (FTL9) regulates both grain size and number and that maternal photosynthetic assimilates induce FTL9 expression in leaves to act as a long-range signal that increases grain number and reduces size. Our findings highlight a strategy that benefits wild plants to survive in a fluctuating environment. In this strategy, when maternal resources are sufficient, wild plants increase their offspring number while preventing an increase in offspring size by the action of FTL9, which helps expand their habitats. In addition, we found that a loss-of-function allele (ftl9) is prevalent among wild and cultivated populations, offering a new scenario in the history of rice domestication.
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Affiliation(s)
- Kim Nhung Ta
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Vietnam Japan University, Vietnam National University, Hanoi, Vietnam
| | - Sae Shimizu-Sato
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Ayumi Agata
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Yuri Yoshida
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Ken-Ichiro Taoka
- Kihara Institute for Biological Research, Yokohama City University, 244-0813, Yokohama, 641-12 Maioka, Totsuka, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, 244-0813, Yokohama, 641-12 Maioka, Totsuka, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, 700-8530, Okayama, Japan
| | - Yasuhiro Tanizawa
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Misuzu Nosaka-Takahashi
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Toshiya Suzuki
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Yutaka Sato
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
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Kurotani KI, Hirakawa H, Shirasawa K, Tanizawa Y, Nakamura Y, Isobe S, Notaguchi M. Genome Sequence and Analysis of Nicotiana benthamiana, the Model Plant for Interactions between Organisms. Plant Cell Physiol 2023; 64:248-257. [PMID: 36755428 PMCID: PMC9977260 DOI: 10.1093/pcp/pcac168] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/28/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
Nicotiana benthamiana is widely used as a model plant for dicotyledonous angiosperms. In fact, the strains used in research are highly susceptible to a wide range of viruses. Accordingly, these strains are subject to plant pathology and plant-microbe interactions. In terms of plant-plant interactions, N. benthamiana is one of the plants that exhibit grafting affinity with plants from different families. Thus, N. benthamiana is a good model for plant biology and has been the subject of genome sequencing analyses for many years. However, N. benthamiana has a complex allopolyploid genome, and its previous reference genome is fragmented into 141,000 scaffolds. As a result, molecular genetic analysis is difficult to perform. To improve this effort, de novo whole-genome assembly was performed in N. benthamiana with Hifi reads, and 1,668 contigs were generated with a total length of 3.1 Gb. The 21 longest scaffolds, regarded as pseudomolecules, contained a 2.8-Gb sequence, occupying 95.6% of the assembled genome. A total of 57,583 high-confidence gene sequences were predicted. Based on a comparison of the genome structures between N. benthamiana and N. tabacum, N. benthamiana was found to have more complex chromosomal rearrangements, reflecting the age of interspecific hybridization. To verify the accuracy of the annotations, the cell wall modification genes involved in grafting were analyzed, which revealed not only the previously indeterminate untranslated region, intron and open reading frame sequences but also the genomic locations of their family genes. Owing to improved genome assembly and annotation, N. benthamiana would increasingly be more widely accessible.
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Affiliation(s)
- Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Hideki Hirakawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Yasuhiro Tanizawa
- Research Organization of Information and Systems, National Institute of Genetics, Yata, Mishima, 411-8540 Japan
| | - Yasukazu Nakamura
- Research Organization of Information and Systems, National Institute of Genetics, Yata, Mishima, 411-8540 Japan
| | - Sachiko Isobe
- *Corresponding authors: Sachiko Isobe, E-mail, ; Michitaka Notaguchi, E-mail,
| | - Michitaka Notaguchi
- *Corresponding authors: Sachiko Isobe, E-mail, ; Michitaka Notaguchi, E-mail,
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Mochizuki T, Sakamoto M, Tanizawa Y, Seike H, Zhu Z, Zhou YJ, Fukumura K, Nagata S, Nakamura Y. Best Practices for Comprehensive Annotation of Neuropeptides of Gryllus bimaculatus. Insects 2023; 14:121. [PMID: 36835690 PMCID: PMC9960350 DOI: 10.3390/insects14020121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Genome annotation is critically important data that can support research. Draft genome annotations cover representative genes; however, they often do not include genes that are expressed only in limited tissues and stages, or genes with low expression levels. Neuropeptides are responsible for regulation of various physiological and biological processes. A recent study disclosed the genome draft of the two-spotted cricket Gryllus bimaculatus, which was utilized to understand the intriguing physiology and biology of crickets. Thus far, only two of the nine reported neuropeptides in G. bimaculatus were annotated in the draft genome. Even though de novo assembly using transcriptomic analyses can comprehensively identify neuropeptides, this method does not follow those annotations on the genome locus. In this study, we performed the annotations based on the reference mapping, de novo transcriptome assembly, and manual curation. Consequently, we identified 41 neuropeptides out of 43 neuropeptides, which were reported in the insects. Further, 32 of the identified neuropeptides on the genomic loci in G. bimaculatus were annotated. The present annotation methods can be applicable for the neuropeptide annotation of other insects. Furthermore, the methods will help to generate useful infrastructures for studies relevant to neuropeptides.
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Affiliation(s)
- Takako Mochizuki
- National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hitomi Seike
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Zhen Zhu
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Yi Jun Zhou
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Keisuke Fukumura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Shinji Nagata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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Tanizawa Y, Fujisawa T, Kodama Y, Kosuge T, Mashima J, Tanjo T, Nakamura Y. DNA Data Bank of Japan (DDBJ) update report 2022. Nucleic Acids Res 2022; 51:D101-D105. [PMID: 36420889 PMCID: PMC9825463 DOI: 10.1093/nar/gkac1083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/24/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) maintains database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), our primary mission is to collect and distribute nucleotide sequence data, as well as their study and sample information, in collaboration with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute. In addition to INSDC resources, the Center operates databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank), and human genetic and phenotypic data (JGA: Japanese Genotype-Phenotype Archive). These databases are built on the supercomputer of the National Institute of Genetics, whose remaining computational capacity is actively utilized by domestic researchers for large-scale biological data analyses. Here, we report our recent updates and the activities of our services.
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Affiliation(s)
- Yasuhiro Tanizawa
- To whom correspondence should be addressed. Tel: +55 981 6859; Fax: +55 981 6889;
| | - Takatomo Fujisawa
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuichi Kodama
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehide Kosuge
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Mashima
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tomoya Tanjo
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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11
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Kawamura S, Romani F, Yagura M, Mochizuki T, Sakamoto M, Yamaoka S, Nishihama R, Nakamura Y, Yamato KT, Bowman JL, Kohchi T, Tanizawa Y. MarpolBase Expression: A Web-Based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha. Plant Cell Physiol 2022; 63:1745-1755. [PMID: 36083565 PMCID: PMC9680858 DOI: 10.1093/pcp/pcac129] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/21/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
The liverwort Marchantia polymorpha is equipped with a wide range of molecular and genetic tools and resources that have led to its wide use to explore the evo-devo aspects of land plants. Although its diverse transcriptome data are rapidly accumulating, there is no extensive yet user-friendly tool to exploit such a compilation of data and to summarize results with the latest annotations. Here, we have developed a web-based suite of tools, MarpolBase Expression (MBEX, https://marchantia.info/mbex/), where users can visualize gene expression profiles, identify differentially expressed genes, perform co-expression and functional enrichment analyses and summarize their comprehensive output in various portable formats. Using oil body biogenesis as an example, we demonstrated that the results generated by MBEX were consistent with the published experimental evidence and also revealed a novel transcriptional network in this process. MBEX should facilitate the exploration and discovery of the genetic and functional networks behind various biological processes in M. polymorpha and promote our understanding of the evolution of land plants.
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Affiliation(s)
- Shogo Kawamura
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Masaru Yagura
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, 411-8540 Japan
| | - Takako Mochizuki
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, 411-8540 Japan
| | - Mika Sakamoto
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, 411-8540 Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Ryuichi Nishihama
- Faculty of Science and Technology, Tokyo University of Science, Noda, 278-8510 Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, 411-8540 Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology (BOST), Kindai University, Kinokawa, 649-6493 Japan
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne 3800, Australia
| | - Takayuki Kohchi
- *Corresponding authors: Takayuki Kohchi, E-mail, ; Yasuhiro Tanizawa, E-mail,
| | - Yasuhiro Tanizawa
- *Corresponding authors: Takayuki Kohchi, E-mail, ; Yasuhiro Tanizawa, E-mail,
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12
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Tamura K, Sakamoto M, Tanizawa Y, Mochizuki T, Matsushita S, Kato Y, Ishikawa T, Okuhara K, Nakamura Y, Bono H. A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan. DNA Res 2022; 30:6831280. [PMID: 36383440 PMCID: PMC9835750 DOI: 10.1093/dnares/dsac044] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Perilla frutescens (Lamiaceae) is an important herbal plant with hundreds of bioactive chemicals, among which perillaldehyde and rosmarinic acid are the two major bioactive compounds in the plant. The leaves of red perilla are used as traditional Kampo medicine or food ingredients. However, the medicinal and nutritional uses of this plant could be improved by enhancing the production of valuable metabolites through the manipulation of key enzymes or regulatory genes using genome editing technology. Here, we generated a high-quality genome assembly of red perilla domesticated in Japan. A near-complete chromosome-level assembly of P. frutescens was generated contigs with N50 of 41.5 Mb from PacBio HiFi reads. 99.2% of the assembly was anchored into 20 pseudochromosomes, among which seven pseudochromosomes consisted of one contig, while the rest consisted of less than six contigs. Gene annotation and prediction of the sequences successfully predicted 86,258 gene models, including 76,825 protein-coding genes. Further analysis showed that potential targets of genome editing for the engineering of anthocyanin pathways in P. frutescens are located on the late-stage pathways. Overall, our genome assembly could serve as a valuable reference for selecting target genes for genome editing of P. frutescens.
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Affiliation(s)
- Keita Tamura
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan,Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Mika Sakamoto
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takako Mochizuki
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Shuji Matsushita
- Agricultural Technology Research Center, Hiroshima Prefectural Technology Research Institute, Higashi-Hiroshima, Hiroshima 739-0151, Japan
| | - Yoshihiro Kato
- Mishima Foods Co., Ltd., Hiroshima City, Hiroshima 733-0036, Japan
| | - Takeshi Ishikawa
- Mishima Foods Co., Ltd., Hiroshima City, Hiroshima 733-0036, Japan
| | - Keisuke Okuhara
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan,PtBio Inc., Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hidemasa Bono
- To whom correspondence should be addressed. Tel. +81 82 424 4013.
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13
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Tohno M, Tanizawa Y, Sawada H, Sakamoto M, Ohkuma M, Kobayashi H. A novel species of lactic acid bacteria, Ligilactobacillus pabuli sp. nov., isolated from alfalfa silage. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we isolated a novel strain of lactic acid bacteria, AF129T, from alfalfa silage prepared locally in Morioka, Iwate, Japan. Polyphasic taxonomy was used to characterize the bacterial strain. The bacterium was rod-shaped, Gram-stain-positive, non-spore-forming and catalase-negative. The strain grew at various temperatures (15–40°C) and pH levels (4.0–8.0). The optimum growth conditions were a temperature of 30°C and a pH of 6.0. AF129T exhibited growth at salt (NaCl) concentrations of up to 6.5 % (w/v). The G+C content of the strain’s genomic DNA was 41.5 %. The major fatty acids were C16 : 0, C18 : 1ω9c, C19 : 0cyclo ω8c and summed feature 8. 16S rRNA gene sequencing revealed that AF129T represents a member of the genus
Ligilactobacillus
and it has higher sequence similarities with
Ligilactobacillus pobuzihii
(98.4 %),
Ligilactobacillus acidipiscis
(97.5 %) and
Ligilactobacillus salitolerans
(97.4 %). The digital DNA–DNA hybridization values for AF129T and phylogenetically related species of the genus
Ligilactobacillus
ranged from 19.8% to 24.1%. The average nucleotide identity of the strain with its closely related taxa was lower than the threshold (95 %–96 %) used for species differentiation. In the light of the above-mentioned physiological, genotypic, chemotaxonomic and phylogenetic evidence, we confirm that AF129T represents a member of the genus
Ligilactobacillus
and constitutes a novel species; we propose the name Ligilactobacillus pabuli sp. nov. for this species. The type strain is AF129T =MAFF 518002T =JCM 34518T=BCRC 81335T.
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Affiliation(s)
- Masanori Tohno
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroyuki Sawada
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
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14
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Bowman JL, Arteaga-Vazquez M, Berger F, Briginshaw LN, Carella P, Aguilar-Cruz A, Davies KM, Dierschke T, Dolan L, Dorantes-Acosta AE, Fisher TJ, Flores-Sandoval E, Futagami K, Ishizaki K, Jibran R, Kanazawa T, Kato H, Kohchi T, Levins J, Lin SS, Nakagami H, Nishihama R, Romani F, Schornack S, Tanizawa Y, Tsuzuki M, Ueda T, Watanabe Y, Yamato KT, Zachgo S. The renaissance and enlightenment of Marchantia as a model system. Plant Cell 2022; 34:3512-3542. [PMID: 35976122 PMCID: PMC9516144 DOI: 10.1093/plcell/koac219] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/21/2022] [Indexed: 05/07/2023]
Abstract
The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.
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Affiliation(s)
| | - Mario Arteaga-Vazquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Frederic Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Liam N Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Philip Carella
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Adolfo Aguilar-Cruz
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4442, New Zealand
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Liam Dolan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Ana E Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Kazutaka Futagami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | | | - Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Auckland 1142, New Zealand
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Jonathan Levins
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Sabine Zachgo
- Division of Botany, School of Biology and Chemistry, Osnabrück University, Osnabrück 49076, Germany
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15
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Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii KI, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima SY, Tanifuji G, Mock T, Nakamura Y. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. Sci Adv 2022; 8:eabi5075. [PMID: 35486731 PMCID: PMC9054022 DOI: 10.1126/sciadv.abi5075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Takuro Nakayama
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Ugo Cenci
- Université de Lille, CNRS, UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8
- SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Samuel Speak
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Krisztina Sarkozi
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Kaori Oyama
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Keitaro Kume
- Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Ken-ichiro Ishii
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yuichiro Kashiyama
- Graduate School of Engineering, Fukui University of Technology, Fukui, Japan
| | - Shigeki Mayama
- Advanced Support Center for Science Teachers, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
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16
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Iwasaki M, Kajiwara T, Yasui Y, Yoshitake Y, Miyazaki M, Kawamura S, Suetsugu N, Nishihama R, Yamaoka S, Wanke D, Hashimoto K, Kuchitsu K, Montgomery SA, Singh S, Tanizawa Y, Yagura M, Mochizuki T, Sakamoto M, Nakamura Y, Liu C, Berger F, Yamato KT, Bowman JL, Kohchi T. Identification of the sex-determining factor in the liverwort Marchantia polymorpha reveals unique evolution of sex chromosomes in a haploid system. Curr Biol 2021; 31:5522-5532.e7. [PMID: 34735792 PMCID: PMC8699743 DOI: 10.1016/j.cub.2021.10.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/02/2021] [Accepted: 10/08/2021] [Indexed: 12/18/2022]
Abstract
Sex determination is a central process for sexual reproduction and is often regulated by a sex determinant encoded on a sex chromosome. Rules that govern the evolution of sex chromosomes via specialization and degeneration following the evolution of a sex determinant have been well studied in diploid organisms. However, distinct predictions apply to sex chromosomes in organisms where sex is determined in the haploid phase of the life cycle: both sex chromosomes, female U and male V, are expected to maintain their gene functions, even though both are non-recombining. This is in contrast to the X-Y (or Z-W) asymmetry and Y (W) chromosome degeneration in XY (ZW) systems of diploids. Here, we provide evidence that sex chromosomes diverged early during the evolution of haploid liverworts and identify the sex determinant on the Marchantia polymorpha U chromosome. This gene, Feminizer, encodes a member of the plant-specific BASIC PENTACYSTEINE transcription factor family. It triggers female differentiation via regulation of the autosomal sex-determining locus of FEMALE GAMETOPHYTE MYB and SUPPRESSOR OF FEMINIZATION. Phylogenetic analyses of Feminizer and other sex chromosome genes indicate dimorphic sex chromosomes had already been established 430 mya in the ancestral liverwort. Feminizer also plays a role in reproductive induction that is shared with its gametolog on the V chromosome, suggesting an ancestral function, distinct from sex determination, was retained by the gametologs. This implies ancestral functions can be preserved after the acquisition of a sex determination mechanism during the evolution of a dominant haploid sex chromosome system.
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Affiliation(s)
- Miyuki Iwasaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Tomoaki Kajiwara
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yukiko Yasui
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Motoki Miyazaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shogo Kawamura
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Dierk Wanke
- Department Biologie I, Ludwig-Maximilians-University (LMU), München 80638, Germany
| | - Kenji Hashimoto
- Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Kazuyuki Kuchitsu
- Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Shilpi Singh
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Yasuhiro Tanizawa
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Masaru Yagura
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Takako Mochizuki
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart 70599, Germany
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology (BOST), Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
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17
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Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Ohkuma M, Kobayashi H. Lentilactobacillus fungorum sp. nov., isolated from spent mushroom substrates. Int J Syst Evol Microbiol 2021; 71. [PMID: 34913426 DOI: 10.1099/ijsem.0.005184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Japan, during a screening of lactic acid bacteria in spent mushroom substrates, an unknown bacterium was isolated and could not be assigned to any known species. Strain YK48GT is Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative. The isolate grew in 0-4 % (w/v) NaCl, at 15-37 °C (optimum, 30 °C) and at pH 4.0-8.0 (optimum, pH 6.0). The genomic DNA G+C content of strain YK48GT was 42.5 mol%. Based on its 16S rRNA gene sequence, strain YK48GT represented a member of the genus Lentilactobacillus and showed the highest pairwise similarity to Lentilactobacillus rapi DSM 19907T (97.86 %). Phylogenetic analyses based on amino acid sequences of 466 shared protein-encoding genes also revealed that the strain was phylogenetically positioned in the genus Lentilactobacillus but did not suggest an affiliation with previously described species. The average nucleotide identity and digital DNA-DNA hybridization values between strain YK48GT and the type strains of phylogenetically related species were 72.2-76.6% and 19.0-21.2 %, respectively, indicating that strain YK48GT represents a novel species within the genus Lentilactobacillus. Phenotypic data further confirmed the differentiation of strain YK48GT from other members of the genus Lentilactobacillus. According to the results of the polyphasic characterization presented in this study, strain YK48GT represents a novel species of the genus Lentilactobacillus, for which the name Lentilactobacillus fungorum sp. nov. is proposed. The type strain is YK48GT (=JCM 32598T=DSM 107968T).
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Affiliation(s)
- Masanori Tohno
- Institute of Livestock and Grassland Science, NARO, Nasushiobara, Tochigi 329-2793, Japan.,Research Center of Genetic Resources, Core Technology Research Headquarters, NARO, Tsukuba, Ibaraki, 305-8632, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoichiro Kojima
- Central Region Agricultural Research Center, NARO, Nasushiobara, Tochigi 329-2793, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, NARO, Nasushiobara, Tochigi 329-2793, Japan
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18
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Abstract
A rod-shaped, Gram-stain-negative, strictly anaerobic, catalase-negative and endospore-forming bacterial strain CSC2T was isolated from corn silage preserved in Tochigi, Japan. The strain CSC2T grew at 15-40 °C, at pH 5.0-7.7 and with up to 0.5 % (w/v) NaCl. The main cellular fatty acids were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal. The cellular polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidic acid, lysophosphatidylethanolamine, phosphatidylserine, lysophosphatidylcholine and two unidentified polar lipids. Phylogenetic analysis of the 16S rRNA gene showed that strain CSC2T was a member of the genus Clostridium and closely related to Clostridium polyendosporum DSM 57272T (95.6 % gene sequence similarity) and Clostridium fallax ATCC 19400T (95.3 %). The genomic DNA G+C content of strain CSC2T was 31.1 mol% (whole genome analysis). The average nucleotide identity based on blast and digital DNA-DNA hybridization values between strain CSC2T and the type strains of phylogenetically related species were below 71 and 24 %, respectively. On the basis of the genotypic, phenotypic and chemotaxonomic characteristics, it is proposed to designate strain CSC2T as representing Clostridium zeae sp. nov. The type strain is CSC2T (=MAFF212476T=JCM 33766T=DSM 111242T).
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Affiliation(s)
- Hisami Kobayashi
- Institute of Livestock and Grassland Science, NARO, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masaru Yagura
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- Institute of Livestock and Grassland Science, NARO, Nasushiobara, Tochigi 329-2793, Japan
- Research Center of Genetic Resources, Core Technology Research Headquarters, NARO, Tsukuba, Ibaraki, 305-8632, Japan
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19
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Kobayashi H, Tanizawa Y, Sakamoto M, Ohkuma M, Tohno M. Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999. Int J Syst Evol Microbiol 2021; 71. [PMID: 34379581 DOI: 10.1099/ijsem.0.004951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection (C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi. Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA-DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis.
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Affiliation(s)
- Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan.,Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8632, Japan
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20
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Abstract
During a study on the biodiversity of bacteria that inhabit woody biomass, we isolated a strain coded B40T from hardwood bark used as a compost ingredient in Japan. The strain, characterized as B40T, is a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative bacterium. This novel isolate showed growth at 30-50 °C, at pH 3.5-7.5 and in the presence of up to 4 % (w/v) NaCl. Its major fatty acids include C16:0, C18:1 ω9c and summed feature 8. The genomic DNA G+C content of strain B40T is 42.2 mol%. Results of 16S rRNA gene sequence-based phylogenetic analysis indicated that strain B40T belongs to the genus Lactobacillus and the closest neighbours of strain B40T are Lactobacillus gigeriorum 202T (95.7 %), Lactobacillus pasteurii CRBIP 24.76T (95.6 %), Lactobacillus psittaci DSM 15354T (95.4 %), Lactobacillus fornicalis TV1018T (95.4 %) and Lactobacillus jensenii ATCC 25258T (95.2 %). The amino acid sequence-based phylogenetic analyses of 489 shared protein-encoding genes showed that the strain forms a phylogenetically independent lineage in the genus Lactobacillus but could not be assigned to any known species. Strain B40T has an average nucleotide identify of <70.2 % and a digital DNA-DNA hybridization value of 19.2 % compared with the strains of other closely related Lactobacillus species. Differential genomic, phenotypic and chemotaxonomic properties, in addition to phylogenetic analyses, indicated that strain B40T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus corticis sp. nov. is proposed. The strain type is B40T (=JCM 32597T=DSM 107967T).
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Affiliation(s)
- Masanori Tohno
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.,Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization Nasushiobara, Tochigi, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yoichiro Kojima
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization Nasushiobara, Tochigi, Japan
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21
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Kajiya-Kanegae H, Ohyanagi H, Ebata T, Tanizawa Y, Onogi A, Sawada Y, Hirai MY, Wang ZX, Han B, Toyoda A, Fujiyama A, Iwata H, Tsuda K, Suzuki T, Nosaka-Takahashi M, Nonomura KI, Nakamura Y, Kawamoto S, Kurata N, Sato Y. OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species. Rice (N Y) 2021; 14:24. [PMID: 33661371 PMCID: PMC7933306 DOI: 10.1186/s12284-021-00468-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/17/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND OryzaGenome ( http://viewer.shigen.info/oryzagenome21detail/index.xhtml ), a feature within Oryzabase ( https://shigen.nig.ac.jp/rice/oryzabase/ ), is a genomic database for wild Oryza species that provides comparative and evolutionary genomics approaches for the rice research community. RESULTS Here we release OryzaGenome2.1, the first major update of OryzaGenome. The main feature in this version is the inclusion of newly sequenced genotypes and their meta-information, giving a total of 217 accessions of 19 wild Oryza species (O. rufipogon, O. barthii, O. longistaminata, O. meridionalis, O. glumaepatula, O. punctata, O. minuta, O. officinalis, O. rhizomatis, O. eichingeri, O. latifolia, O. alta, O. grandiglumis, O. australiensis, O. brachyantha, O. granulata, O. meyeriana, O. ridleyi, and O. longiglumis). These 19 wild species belong to 9 genome types (AA, BB, CC, BBCC, CCDD, EE, FF, GG, and HHJJ), representing wide genomic diversity in the genus. Using the genotype information, we analyzed the genome diversity of Oryza species. Other features of OryzaGenome facilitate the use of information on single nucleotide polymorphisms (SNPs) between O. sativa and its wild progenitor O. rufipogon in rice research, including breeding as well as basic science. For example, we provide Variant Call Format (VCF) files for genome-wide SNPs of 33 O. rufipogon accessions against the O. sativa reference genome, IRGSP1.0. In addition, we provide a new SNP Effect Table function, allowing users to identify SNPs or small insertion/deletion polymorphisms in the 33 O. rufipogon accessions and to search for the effect of these polymorphisms on protein function if they reside in the coding region (e.g., are missense or nonsense mutations). Furthermore, the SNP Viewer for 446 O. rufipogon accessions was updated by implementing new tracks for possible selective sweep regions and highly mutated regions that were potentially exposed to selective pressures during the process of domestication. CONCLUSION OryzaGenome2.1 focuses on comparative genomic analysis of diverse wild Oryza accessions collected around the world and on the development of resources to speed up the identification of critical trait-related genes, especially from O. rufipogon. It aims to promote the use of genotype information from wild accessions in rice breeding and potential future crop improvements. Diverse genotypes will be a key resource for evolutionary studies in Oryza, including polyploid biology.
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Affiliation(s)
- Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Science, The University of Tokyo, Bunkyo 1-1-1, Tokyo, 113-8657, Japan
| | - Hajime Ohyanagi
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Biological and Environmental Sciences & Engineering Division, Thuwal, 23955-6900, Saudi Arabia
| | - Toshinobu Ebata
- Dynacom Co., Ltd., World Business Garden, Marive East 25F, 2-6-1, Nakase, Mihama-ku, Chiba-shi, Chiba, 261-7125, Japan
| | - Yasuhiro Tanizawa
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Akio Onogi
- Institute of Crop Science, NARO, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Zi-Xuan Wang
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, China
| | - Bin Han
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, China
| | - Atsushi Toyoda
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Asao Fujiyama
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Science, The University of Tokyo, Bunkyo 1-1-1, Tokyo, 113-8657, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Toshiya Suzuki
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | | | - Ken-Ichi Nonomura
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Shoko Kawamoto
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Nori Kurata
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Yutaka Sato
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
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22
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Maeno S, Nishimura H, Tanizawa Y, Dicks L, Arita M, Endo A. Unique niche-specific adaptation of fructophilic lactic acid bacteria and proposal of three Apilactobacillus species as novel members of the group. BMC Microbiol 2021; 21:41. [PMID: 33563209 PMCID: PMC7871557 DOI: 10.1186/s12866-021-02101-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/20/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Fructophilic lactic acid bacteria (FLAB) found in D-fructose rich niches prefer D-fructose over D-glucose as a growth substrate. They need electron acceptors for growth on D-glucose. The organisms share carbohydrate metabolic properties. Fructobacillus spp., Apilactobacillus kunkeei, and Apilactobacillus apinorum are members of this unique group. Here we studied the fructophilic characteristics of recently described species Apilactobacillus micheneri, Apilactobacillus quenuiae, and Apilactobacillus timberlakei. RESULTS The three species prefer D-fructose over D-glucose and only metabolize D-glucose in the presence of electron acceptors. The genomic characteristics of the three species, i.e. small genomes and thus a low number of coding DNA sequences, few genes involved in carbohydrate transport and metabolism, and partial deletion of adhE gene, are characteristic of FLAB. The three species thus are novel members of FLAB. Reduction of genes involved in carbohydrate transport and metabolism in accordance with reduction of genome size were the common characteristics of the family Lactobacillaceae, but FLAB markedly reduced the gene numbers more than other species in the family. Pan-genome analysis of genes involved in metabolism displayed a lack of specific carbohydrate metabolic pathways in FLAB, leading to a unique cluster separation. CONCLUSIONS The present study expanded FLAB group. Fructose-rich environments have induced similar evolution in phylogenetically distant FLAB species. These are examples of convergent evolution of LAB.
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Affiliation(s)
- Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Hiroya Nishimura
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Leon Dicks
- Department of Microbiology, University of Stellenbosch, Matieland, Stellenbosch, 7602, South Africa
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan.
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23
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D''Ignazio A, Fujia K, Marrelli D, Marano L, Kamiya S, Hikage M, Tanizawa Y, Bando E, Roviello F, Terashima M. Risk factors for para-aortic nodes metastasis: Preliminary analysis from far Eastern and Western centers. Eur J Surg Oncol 2020. [DOI: 10.1016/j.ejso.2020.06.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Udagawa C, Sasaki Y, Tanizawa Y, Suemizu H, Ohnishi Y, Nakamura Y, Tokino T, Zembutsu H. Whole-exome sequencing of 79 xenografts as a potential approach for the identification of genetic variants associated with sensitivity to cytotoxic anticancer drugs. PLoS One 2020; 15:e0239614. [PMID: 32986753 PMCID: PMC7521756 DOI: 10.1371/journal.pone.0239614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022] Open
Abstract
Chemotherapy response remains unpredictable in most patients with cancer. In this study, we performed whole-exome sequencing of 79 cancer xenografts derived from human cancer tissues to identify genetic predictors of chemosensitivity to nine cytotoxic anticancer drugs. Xenografts were harvested from 12 organs with cancer and implanted into nude mice. The mice were exposed to one of nine cytotoxic anticancer drugs (5-fluorouracil, nimustine, adriamycin, cyclophosphamide, cisplatin, mitomycin C, methotrexate, vincristine, and vinblastine) to assess the correlation between chemosensitivity response and variant allele frequency. We found 162 candidate variants that were possibly associated with chemosensitivity to one or more of the nine anticancer drugs (P < 0.01). In a subgroup analysis of breast and gastric cancer xenografts, 78 and 67 variants, respectively, were possibly associated with chemosensitivity. This approach may help to contribute to the development of personalized treatments that may allow for the prescription of optimal chemotherapy regimens among patients with cancer.
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Affiliation(s)
- Chihiro Udagawa
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Sasaki
- Biology, Department of Liberal Arts and Sciences Center for Medical Education, Sapporo Medical University, Sapporo, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Japan
| | - Hiroshi Suemizu
- Laboratory Animal Research Department, Central Institute for Experimental Animals, Kawasaki, Japan
| | - Yasuyuki Ohnishi
- Laboratory Animal Research Department, Central Institute for Experimental Animals, Kawasaki, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima, Japan
| | - Takashi Tokino
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Hitoshi Zembutsu
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
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25
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Tanizawa Y, Kobayashi H, Nomura M, Sakamoto M, Arita M, Nakamura Y, Ohkuma M, Tohno M. Lactobacillus buchneri subsp. silagei subsp. nov., isolated from rice grain silage. Int J Syst Evol Microbiol 2020; 70:3111-3116. [PMID: 32250236 DOI: 10.1099/ijsem.0.004138] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Two Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacteria, designated strains SG162T and NK01, were isolated from Japanese rice grain silage and total mixed ration silage, respectively. They were initially identified as Lactobacillus buchneri based on the 16S rRNA gene sequence similarities. However, the two strains were separated into a distinct clade from L. buchneri DSM 20057T (=JCM 1115T) through whole-genome sequence-based characterization, forming an infraspecific subgroup together with strains CD034 and S42, whose genomic sequences were available in the public sequence database. Strains within the subgroup shared 99.4-99.7 % average nucleotide identity (ANI) and 97.5-99.0 % digital DNA-DNA hybridization (dDDH) with each other, albeit 96.9-97.0 % ANI and 76.0-76.6 % dDDH against DSM 20057T. Strains SG162T and NK01 could utilize more substrates as sole carbon sources than DSM 20057T, potentially owing to the abundance of genes involved in carbon metabolism, especially the Entner-Doudoroff pathway. The inability of γ-aminobutyric acid (GABA) production was evidenced by the lack of glutamate decarboxylase and glutamate/GABA antiporter genes in the new subgroup strains. Strain SG162T grew at 10-45 °C (optimum, 30 °C), pH 3.5-8.0, and 0-8 % (w/v) NaCl. Its genomic DNA G+C content was 44.1 mol%. The predominant fatty acids were C16 : 0, C19 : 0 cyclo ω8c, and summed feature 8. On the basis of the polyphasic characterization findings, strains SG162T and NK01 represent a novel subspecies of L. buchneri, for which the name Lactobacillus buchneri subsp. silagei subsp. nov. is proposed. The type strain is SG162T (=JCM 32599T=DSM 107969T), and strains CD034 and S42 are also transferred to L. buchneri subsp. silagei.
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Affiliation(s)
- Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hisami Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Masaru Nomura
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0901, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
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Kobayashi H, Tanizawa Y, Sakamoto M, Nakamura Y, Ohkuma M, Tohno M. Reclassification of Clostridium diolis Biebl and Spröer 2003 as a later heterotypic synonym of Clostridium beijerinckii Donker 1926 (Approved Lists 1980) emend. Keis et al. 2001. Int J Syst Evol Microbiol 2020; 70:2463-2466. [DOI: 10.1099/ijsem.0.004059] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clostridium diolis
shares high similarity based on 16S rRNA gene sequences and fatty acid composition with
Clostridium beijerinckii
. In this study, the taxonomic status of
C. diolis
was clarified using genomic and phenotypic approaches. High similarity was detected among
C. diolis
DSM 15410T,
C. beijerinckii
DSM 791T and NCTC 13035T, showing average nucleotide identity on blast and in silico DNA–DNA hybridization values over 97 and 85 %, respectively. Results of investigations for substrate utilization and enzyme activity displayed no striking differences between
C. diolis
DSM 15410T and
C. beijerinckii
JCM 1390T. Based on the results, we propose the reclassification of
Clostridium diolis
as a later heterotypic synonym of
Clostridium beijerinckii
. The type strain is ATCC 25752T (=CIP 104308T=DSM 791T=JCM 1390T=LMG 5716T=NCTC 13035T).
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Affiliation(s)
- Hisami Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
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27
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Montgomery SA, Tanizawa Y, Galik B, Wang N, Ito T, Mochizuki T, Akimcheva S, Bowman JL, Cognat V, Maréchal-Drouard L, Ekker H, Hong SF, Kohchi T, Lin SS, Liu LYD, Nakamura Y, Valeeva LR, Shakirov EV, Shippen DE, Wei WL, Yagura M, Yamaoka S, Yamato KT, Liu C, Berger F. Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Curr Biol 2020; 30:573-588.e7. [PMID: 32004456 PMCID: PMC7209395 DOI: 10.1016/j.cub.2019.12.015] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
Abstract
Genome packaging by nucleosomes is a hallmark of eukaryotes. Histones and the pathways that deposit, remove, and read histone modifications are deeply conserved. Yet, we lack information regarding chromatin landscapes in extant representatives of ancestors of the main groups of eukaryotes, and our knowledge of the evolution of chromatin-related processes is limited. We used the bryophyte Marchantia polymorpha, which diverged from vascular plants circa 400 mya, to obtain a whole chromosome genome assembly and explore the chromatin landscape and three-dimensional genome organization in an early diverging land plant lineage. Based on genomic profiles of ten chromatin marks, we conclude that the relationship between active marks and gene expression is conserved across land plants. In contrast, we observed distinctive features of transposons and other repetitive sequences in Marchantia compared with flowering plants. Silenced transposons and repeats did not accumulate around centromeres. Although a large fraction of constitutive heterochromatin was marked by H3K9 methylation as in flowering plants, a significant proportion of transposons were marked by H3K27me3, which is otherwise dedicated to the transcriptional repression of protein-coding genes in flowering plants. Chromatin compartmentalization analyses of Hi-C data revealed that repressed B compartments were densely decorated with H3K27me3 but not H3K9 or DNA methylation as reported in flowering plants. We conclude that, in early plants, H3K27me3 played an essential role in heterochromatin function, suggesting an ancestral role of this mark in transposon silencing.
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Affiliation(s)
- Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Bence Galik
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Nan Wang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Tasuku Ito
- John Innes Centre, Colney lane, Norwich NR4 7UH, UK
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Svetlana Akimcheva
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, 3800 VIC, Australia
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Laurence Maréchal-Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Heinz Ekker
- Vienna BioCenter Core Facilities (VBCF), Next Generation Sequencing facility, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Li-Yu Daisy Liu
- Department of Agronomy, National Taiwan University, Taipei 106, Taiwan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Lia R Valeeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Republic of Tatarstan 420008, Russia
| | - Eugene V Shakirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Republic of Tatarstan 420008, Russia; Department of Biological Sciences, Marshall University, Huntington, WV 25701, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - Wei-Lun Wei
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Masaru Yagura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria.
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28
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Terashima M, Nakamura K, Hatakeyama K, Furukawa K, Fujiya K, kamiya S, Hikage M, Tanizawa Y, Bando E, Oshima K, Urakami K, Machida N, Yasui H, Yamaguchi K. Prediction of S-1 adjuvant chemotherapy efficacy in stage II/III gastric cancer treatment based on comprehensive gene expression analysis. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz247.147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Arimizu Y, Kirino Y, Sato MP, Uno K, Sato T, Gotoh Y, Auvray F, Brugere H, Oswald E, Mainil JG, Anklam KS, Döpfer D, Yoshino S, Ooka T, Tanizawa Y, Nakamura Y, Iguchi A, Morita-Ishihara T, Ohnishi M, Akashi K, Hayashi T, Ogura Y. Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains. Genome Res 2019; 29:1495-1505. [PMID: 31439690 PMCID: PMC6724679 DOI: 10.1101/gr.249268.119] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/03/2019] [Indexed: 01/15/2023]
Abstract
How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)–producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectively. The locus of enterocyte effacement (LEE)–encoded type 3 secretion system (T3SS) is the major virulence determinant of EPEC and is also possessed by major STEC lineages. Cattle are thought to be the primary reservoir of STEC and EPEC. However, genome sequences of bovine commensal E. coli are limited, and the emerging process of STEC and EPEC is largely unknown. Here, we performed a large-scale genomic comparison of bovine commensal E. coli with human commensal and clinical strains, including EPEC and STEC, at a global level. The analyses identified two distinct lineages, in which bovine and human commensal strains are enriched, respectively, and revealed that STEC and EPEC strains have emerged in multiple sublineages of the bovine-associated lineage. In addition to the bovine-associated lineage-specific genes, including fimbriae, capsule, and nutrition utilization genes, specific virulence gene communities have been accumulated in stx- and LEE-positive strains, respectively, with notable overlaps of community members. Functional associations of these genes probably confer benefits to these E. coli strains in inhabiting and/or adapting to the bovine intestinal environment and drive their evolution to highly virulent human pathogens under the bovine-adapted genetic background. Our data highlight the importance of large-scale genome sequencing of animal strains in the studies of zoonotic pathogens.
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Affiliation(s)
- Yoko Arimizu
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yumi Kirino
- Laboratory of Veterinary Radiology, Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Mitsuhiko P Sato
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Koichi Uno
- Japan Microbiological Laboratory, Sendai, Miyagi 983-0034, Japan
| | - Toshio Sato
- Japan Microbiological Laboratory, Sendai, Miyagi 983-0034, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Frédéric Auvray
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31300 Toulouse, France
| | - Hubert Brugere
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31300 Toulouse, France
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31300 Toulouse, France.,CHU de Toulouse, Hôpital Purpan, 31300 Toulouse, France
| | - Jacques G Mainil
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine and Institute for Fundamental and Applied Research in Animal Health (FARAH), University of Liège, 4000 Liège, Belgium
| | - Kelly S Anklam
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Dörte Döpfer
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Shuji Yoshino
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki 889-2155, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Tomoko Morita-Ishihara
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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30
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Nakamura Y, Tanaka Y, Tanaka M, Yamamoto K, Matsuguma M, Kajimura Y, Tokunaga Y, Yujiri T, Tanizawa Y. Significance of Granulocyte Colony-Stimulating Factor-Combined High-Dose Cytarabine, Cyclophosphamide, and Total Body Irradiation in Allogeneic Hematopoietic Cell Transplantation for Myeloid Malignant Neoplasms. Transplant Proc 2019; 51:896-900. [PMID: 30979482 DOI: 10.1016/j.transproceed.2019.01.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/08/2018] [Accepted: 01/17/2019] [Indexed: 11/19/2022]
Abstract
Allogeneic hematopoietic cell transplant (HCT) is a curative procedure for myeloid malignant neoplasms, but relapse after HCT remains critical. A conditioning regimen involving granulocyte colony-stimulating factor-combined high-dose cytarabine, cyclophosphamide, and total body irradiation (G-CSF-combined high-dose cytarabine/cyclophosphamide/total-body irradiation [HDCA/CY/TBI]) was reported to improve outcomes after cord blood transplant (CBT) for myeloid malignant neoplasms, but this regimen was not previously evaluated among patients undergoing bone marrow transplant (BMT) or peripheral blood stem cell transplant (PBSCT). METHODS We retrospectively analyzed 28 patients who underwent allogeneic HCT including BMT from a related (1 patient) or unrelated donor (9 patients), PBSCT from a related donor (7 patients), or single-unit CBT from an unrelated donor (11 patients) after a G-CSF-combined HDCA/CY/TBI regimen. RESULTS All patients achieved neutrophil and platelet engraftment, which were significantly more rapid in the BMT/PBSCT group than in the CBT group. Eighteen patients were alive at a median follow-up of 54.3 months. The 3-year relapse and nonrelapse mortality rates were 28.6% and 7.1%, respectively, which were similar between the BMT/PBSCT and CBT groups. Overall survival and disease-free survival at 5 years after HCT were 62.6% and 64.3%, respectively, which were also similar between the BMT/PBSCT and CBT groups. Only disease status at HCT had a significant impact on overall survival and disease-free survival (86.7% with standard risk vs 38.5% with high risk and 86.7% with standard risk vs 38.5% with high risk, respectively). CONCLUSION A G-CSF-combined HDCA/CY/TBI regimen is a promising conditioning in patients with myeloid malignant neoplasms who undergo not only CBT but also BMT or PBSCT.
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Affiliation(s)
- Y Nakamura
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan.
| | - Y Tanaka
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan
| | - M Tanaka
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan
| | - K Yamamoto
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan
| | - M Matsuguma
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan
| | - Y Kajimura
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan
| | - Y Tokunaga
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan
| | - T Yujiri
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan
| | - Y Tanizawa
- Third Department of Internal Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan
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31
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Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Nakamura Y, Ohkuma M, Kobayashi H. Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates. Int J Syst Evol Microbiol 2019; 69:964-969. [DOI: 10.1099/ijsem.0.003224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43T, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43T was 43.6 mol%. The predominant fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of
Lactobacillus acidipiscis
(sequence similarity, 97.6 %) and
Lactobacillus pobuzihii
(97.4 %) were most closely related to YK43T. The average nucleotide identities were 74.1 % between strain YK43T and
L. acidipiscis
DSM 15836T and 74.0 % between YK43T and
L. pobuzihii
E100301T. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43T represents a novel species of the genus
Lactobacillus
, for which the name
Lactobacillus
salitolerans sp. nov. is proposed. The type strain is YK43T (=JCM 31331T = DSM 103433T).
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Affiliation(s)
- Masanori Tohno
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoichiro Kojima
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hisami Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
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32
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Makuuchi R, Fujiya K, Omori H, Irino T, Tanizawa Y, Bando E, Kawamura T, Terashima M. The optimal extent of lymph node dissection for Siewert type II adenocarcinoma of the esophagogastric junction. Eur J Surg Oncol 2019. [DOI: 10.1016/j.ejso.2018.10.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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33
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Abstract
Isolation of lactic acid bacteria (LAB) is the first and crucial step to study possible roles of LAB in the environment, especially in food fermentation. This is also important to use the organisms for further application. LAB are diverse bacterial group and have diverse growth characteristics. Culture condition of LAB is thus varied, and selection of a suitable culture medium is essential for the purposes. Identification is also an important step, since certain desirable and undesirable characteristics are shared within species. Identification was classically carried out by phenotypic characteristics but is usually performed by DNA sequence-based approaches. 16S rRNA gene sequencing is generally used for identification, and sequencing of housekeeping genes is used when needed. In addition, identification based on whole-genome sequence similarities is becoming common. Here we describe isolation and identification of LAB briefly.
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Affiliation(s)
- Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan.
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka Prefecture, Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka Prefecture, Japan
- RIKEN, Center for Sustainable Resource Science, Kanagawa, Japan
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34
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Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2019; 34:1037-1039. [PMID: 29106469 PMCID: PMC5860143 DOI: 10.1093/bioinformatics/btx713] [Citation(s) in RCA: 632] [Impact Index Per Article: 126.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/06/2017] [Indexed: 12/13/2022] Open
Abstract
Summary We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 min, with rich information such as pseudogenes, translation exceptions and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future. Availability and implementation The software is implemented in Python 3 and runs in both Python 2.7 and 3.4—on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan
| | - Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan
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35
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Abstract
DDBJ Fast Annotation and Submission Tool (DFAST) is a genome annotation pipeline for prokaryotes, which also assists data submission to the public sequence database. It is available both as a web service and as a stand-alone tool that runs on local machines. DFAST can annotate a typical-sized bacterial genome within 5 min. The default annotation workflow contains a gene prediction phase for protein coding sequence, rRNA, tRNA, and CRISPR, and a functional annotation phase to infer protein functions. DFAST generates result files in standard annotation formats and data files for submission to DNA Data Bank of Japan (DDBJ). In this chapter, the annotation workflow and applications of DFAST are introduced.
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Affiliation(s)
- Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan.
| | - Takatomo Fujisawa
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
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36
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Tanizawa Y, Tada I, Kobayashi H, Endo A, Maeno S, Toyoda A, Arita M, Nakamura Y, Sakamoto M, Ohkuma M, Tohno M. Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses. Int J Syst Evol Microbiol 2018; 68:3512-3517. [DOI: 10.1099/ijsem.0.003020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yasuhiro Tanizawa
- 1Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ipputa Tada
- 2Department of Genetics, School of Life Science, The Graduate University of Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Hisami Kobayashi
- 3Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi, 329-2793, Japan
| | - Akihito Endo
- 4Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Shintaro Maeno
- 4Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Atsushi Toyoda
- 1Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Masanori Arita
- 1Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- 5RIKEN, Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yasukazu Nakamura
- 1Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Mitsuo Sakamoto
- 6Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
- 7PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- 6Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- 3Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi, 329-2793, Japan
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Endo A, Maeno S, Tanizawa Y, Kneifel W, Arita M, Dicks L, Salminen S. Fructophilic Lactic Acid Bacteria, a Unique Group of Fructose-Fermenting Microbes. Appl Environ Microbiol 2018; 84:e01290-18. [PMID: 30054367 PMCID: PMC6146980 DOI: 10.1128/aem.01290-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Fructophilic lactic acid bacteria (FLAB) are a recently discovered group, consisting of a few Fructobacillus and Lactobacillus species. Because of their unique characteristics, including poor growth on glucose and preference of oxygen, they are regarded as "unconventional" lactic acid bacteria (LAB). Their unusual growth characteristics are due to an incomplete gene encoding a bifunctional alcohol/acetaldehyde dehydrogenase (adhE). This results in the imbalance of NAD/NADH and the requirement of additional electron acceptors to metabolize glucose. Oxygen, fructose, and pyruvate are used as electron acceptors. FLAB have significantly fewer genes for carbohydrate metabolism than other LAB, especially due to the lack of complete phosphotransferase system (PTS) transporters. They have been isolated from fructose-rich environments, including flowers, fruits, fermented fruits, and the guts of insects that feed on plants rich in fructose, and are separated into two groups on the basis of their habitats. One group is associated with flowers, grapes, wines, and insects, and the second group is associated with ripe fruits and fruit fermentations. Species associated with insects may play a role in the health of their host and are regarded as suitable vectors for paratransgenesis in honey bees. Besides their impact on insect health, FLAB may be promising candidates for the promotion of human health. Further studies are required to explore their beneficial properties in animals and humans and their applications in the food industry.
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Affiliation(s)
- Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan
| | | | - Wolfgang Kneifel
- Department of Food Sciences and Technology, University of Natural Resources and Life Science Vienna, Vienna, Austria
| | - Masanori Arita
- National Institute of Genetics, Shizuoka, Japan
- RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Leon Dicks
- Department of Microbiology, University of Stellenbosch, Stellenbosch, South Africa
| | - Seppo Salminen
- Functional Foods Forum, University of Turku, Turku, Finland
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Kondo M, Nagao Y, Mahbub MH, Tanabe T, Tanizawa Y. Factors predicting early postpartum glucose intolerance in Japanese women with gestational diabetes mellitus: decision-curve analysis. Diabet Med 2018; 35:1111-1117. [PMID: 29706019 DOI: 10.1111/dme.13657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2018] [Indexed: 02/05/2023]
Abstract
AIMS To identify factors predicting early postpartum glucose intolerance in Japanese women with gestational diabetes mellitus, using decision-curve analysis. METHODS A retrospective cohort study was performed. The participants were 123 Japanese women with gestational diabetes who underwent 75-g oral glucose tolerance tests at 8-12 weeks after delivery. They were divided into a glucose intolerance and a normal glucose tolerance group based on postpartum oral glucose tolerance test results. Analysis of the pregnancy oral glucose tolerance test results showed predictive factors for postpartum glucose intolerance. We also evaluated the clinical usefulness of the prediction model based on decision-curve analysis. RESULTS Of 123 women, 78 (63.4%) had normoglycaemia and 45 (36.6%) had glucose intolerance. Multivariable logistic regression analysis showed insulinogenic index/fasting immunoreactive insulin and summation of glucose levels, assessed during pregnancy oral glucose tolerance tests (total glucose), to be independent risk factors for postpartum glucose intolerance. Evaluating the regression models, the best discrimination (area under the curve 0.725) was obtained using the basic model (i.e. age, family history of diabetes, BMI ≥25 kg/m2 and use of insulin during pregnancy) plus insulinogenic index/fasting immunoreactive insulin <1.1. Decision-curve analysis showed that combining insulinogenic index/fasting immunoreactive insulin <1.1 with basic clinical information resulted in superior net benefits for prediction of postpartum glucose intolerance. CONCLUSIONS Insulinogenic index/fasting immunoreactive insulin calculated using oral glucose tolerance test results during pregnancy is potentially useful for predicting early postpartum glucose intolerance in Japanese women with gestational diabetes.
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Affiliation(s)
- M Kondo
- Division of Endocrinology, Metabolism, Haematological Sciences and Therapeutics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Y Nagao
- Division of Internal Medicine, Yamaguchi Red Cross Hospital, Yamaguchi-City, Yamaguchi, Japan
| | - M H Mahbub
- Division of Public Health and Preventive Medicine, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - T Tanabe
- Division of Public Health and Preventive Medicine, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Y Tanizawa
- Division of Endocrinology, Metabolism, Haematological Sciences and Therapeutics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
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Abstract
The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes. Functional comparison of the core genes of the two genera revealed a significant difference in the categories "amino acid transport and metabolism" representing their difference in niche specificity. Over-represented Bifidobacterium protein families were primarily involved in host interactions, the complex compound metabolism, and in stress responses. These findings coincide with the published information and validate our bias-resilient definition of the core genome.
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Affiliation(s)
- Maria Satti
- * Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- † Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Akihito Endo
- ‡ Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido 099-2493, Japan
| | - Masanori Arita
- † Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.,§ RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Shimizu T, Tanizawa Y, Mochizuki T, Nagasaki H, Yoshioka T, Toyoda A, Fujiyama A, Kaminuma E, Nakamura Y. Draft Sequencing of the Heterozygous Diploid Genome of Satsuma ( Citrus unshiu Marc.) Using a Hybrid Assembly Approach. Front Genet 2017; 8:180. [PMID: 29259619 PMCID: PMC5723288 DOI: 10.3389/fgene.2017.00180] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/06/2017] [Indexed: 12/19/2022] Open
Abstract
Satsuma (Citrus unshiu Marc.) is one of the most abundantly produced mandarin varieties of citrus, known for its seedless fruit production and as a breeding parent of citrus. De novo assembly of the heterozygous diploid genome of Satsuma ("Miyagawa Wase") was conducted by a hybrid assembly approach using short-read sequences, three mate-pair libraries, and a long-read sequence of PacBio by the PLATANUS assembler. The assembled sequence, with a total size of 359.7 Mb at the N50 length of 386,404 bp, consisted of 20,876 scaffolds. Pseudomolecules of Satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of Clementine, pummelo, and sweet orange. Gene prediction by modeling with MAKER-P proposed 29,024 genes and 37,970 mRNA; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. BUSCO scores for the assembled scaffold and predicted transcripts, and another analysis by BAC end sequence mapping indicated the assembled genome consistency was close to those of the haploid Clementine, pummel, and sweet orange genomes. The number of repeat elements and long terminal repeat retrotransposon were comparable to those of the seven citrus genomes; this suggested no significant failure in the assembly at the repeat region. A resequencing application using the assembled sequence confirmed that both kunenbo-A and Satsuma are offsprings of Kishu, and Satsuma is a back-crossed offspring of Kishu. These results illustrated the performance of the hybrid assembly approach and its ability to construct an accurate heterozygous diploid genome.
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Affiliation(s)
- Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Shimizu, Japan
| | - Yasuhiro Tanizawa
- Genome Informatics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Takako Mochizuki
- Genome Informatics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Hideki Nagasaki
- Genome Informatics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Terutaka Yoshioka
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Shimizu, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Eli Kaminuma
- Genome Informatics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
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Tohno M, Tanizawa Y, Irisawa T, Masuda T, Sakamoto M, Arita M, Ohkuma M, Kobayashi H. Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage. Int J Syst Evol Microbiol 2017; 67:3639-3644. [DOI: 10.1099/ijsem.0.002196] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Masanori Tohno
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi, 329-2793, Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Tomohiro Irisawa
- Department of Animal Science, Tokyo University of Agriculture, Atsugi, Kanagawa, 243-0034, Japan
| | - Takaharu Masuda
- Animal Industry Research Institute, Iwate Agricultural Research Center, Morioka, Iwate, 028-2711, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi, 329-2793, Japan
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Tada I, Tanizawa Y, Endo A, Tohno M, Arita M. Revealing the genomic differences between two subgroups in Lactobacillus gasseri. Biosci Microbiota Food Health 2017; 36:155-159. [PMID: 29038772 PMCID: PMC5633531 DOI: 10.12938/bmfh.17-006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/17/2017] [Indexed: 11/17/2022]
Abstract
Being an autochthonous species in humans, Lactobacillus gasseri is widely used as a probiotic for fermented products. We thoroughly compared the gene contents of 75 L. gasseri genomes and
identified two intraspecific groups by the average nucleotide identity (ANI) threshold of 94%. Group I, with 48 strains, possessed 53 group-specific genes including the gassericin T cluster (9 genes) and N-acyl
homoserine lactone lactonase. Group II, with 27 strains, including the type strain ATCC 33323, possessed group-specific genes with plasmid- or phage-related annotations. The genomic differences provide evidences for demarcating a
new probiotic group within L. gasseri.
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Affiliation(s)
- Ipputa Tada
- Department of Genetics, School of Life Science, The Graduate University of Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Akihito Endo
- Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Masanori Tohno
- National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Tochigi 329-2793, Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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Abstract
BACKGROUND Standard graphical tools for whole genome comparison require a reference genome. However, any reference is also subject to annotation biases and rearrangements, and may not serve as the standard except for those of extensively studied model species. To fully exploit the rapidly accumulating sequence data from the recent sequencing technologies, genome comparison without any reference has been anticipated. RESULTS We introduce a circular genome visualizer to compare complete genomes of closely related species. This tool visualizes the position of orthologous gene clusters rather than actual sequences or their features, thereby achieving the comparative view without using a single reference genome. The essential information is the matrix of orthologous gene clusters whose positions (not sequences) are color-coded in circular graphics. As a demonstration, comparison of 14 Lactobacillus paracasei strains and one L. casei strain revealed not only large-scale rearrangements but also genomic islands that are strain-specific. Comparison of 73 Helicobacter pylori strains confirmed their genetic consistency and also revealed the three general patterns of large-scale genome inversions. CONCLUSIONS From the ample sequence information in the GenBank/ENA/DDBJ repository, we can reconstruct a genomic consensus for particular species. By visualizing multiple strains at a glance, we can identify conserved as well as strain-specific regions in multiply sequenced genomes. Positional consistency for orthologous genes provides information orthogonal to major sequence features such as the GC content or sequence similarity of marker genes. The positional comparison is therefore useful for identifying large-scale genome rearrangements or gene transfers.
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Affiliation(s)
- Ipputa Tada
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540 Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
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44
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Tanizawa Y, Kobayashi H, Kaminuma E, Sakamoto M, Ohkuma M, Nakamura Y, Arita M, Tohno M. Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri. Biosci Microbiota Food Health 2017; 36:129-134. [PMID: 28748134 PMCID: PMC5510158 DOI: 10.12938/bmfh.16-026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/20/2017] [Indexed: 12/03/2022]
Abstract
Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573T to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide
metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus.
The availability of a reliable genome sequence will aid future investigations on the industrial applications of L. parakefiri in functional foods such as kefir grains.
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Affiliation(s)
- Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, 768 Senbonmatsu, Nasushiobara, Tochigi 329-2793, Japan
| | - Eli Kaminuma
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Mitsuo Sakamoto
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.,PRIME, Japan Agency for Medical Research and Development (AMED), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Masanori Tohno
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, 768 Senbonmatsu, Nasushiobara, Tochigi 329-2793, Japan
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Mochizuki T, Tanizawa Y, Fujisawa T, Ohta T, Nikoh N, Shimizu T, Toyoda A, Fujiyama A, Kurata N, Nagasaki H, Kaminuma E, Nakamura Y. DNApod: DNA polymorphism annotation database from next-generation sequence read archives. PLoS One 2017; 12:e0172269. [PMID: 28234924 PMCID: PMC5325239 DOI: 10.1371/journal.pone.0172269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/02/2017] [Indexed: 01/18/2023] Open
Abstract
With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.
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Affiliation(s)
- Takako Mochizuki
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yasuhiro Tanizawa
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takatomo Fujisawa
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tazro Ohta
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Naruo Nikoh
- Department of Liberal Arts, The Open University of Japan, Chiba, Chiba, Japan
| | - Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hideki Nagasaki
- Genome Informatics Group, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Eli Kaminuma
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
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Maeno S, Tanizawa Y, Kanesaki Y, Kubota E, Kumar H, Dicks L, Salminen S, Nakagawa J, Arita M, Endo A. Genomic characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation. Syst Appl Microbiol 2016; 39:516-526. [PMID: 27776911 DOI: 10.1016/j.syapm.2016.09.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 02/02/2023]
Abstract
Lactobacillus kunkeei is classified as a sole obligate fructophilic lactic acid bacterium that is found in fructose-rich niches, including the guts of honeybees. The species is differentiated from other lactobacilli based on its poor growth with glucose, enhanced growth in the presence of oxygen and other electron acceptors, and production of high concentrations of acetate from the metabolism of glucose. These characteristics are similar to phylogenetically distant Fructobacillus spp. In the present study, the genomic structure of L. kunkeei was characterized by using 16 different strains, and it had significantly less genes and smaller genomes when compared with other lactobacilli. Functional gene classification revealed that L. kunkeei had lost genes specifically involved in carbohydrate transport and metabolism. The species also lacked most of the genes for respiration, although growth was enhanced in the presence of oxygen. The adhE gene of L. kunkeei, encoding a bifunctional alcohol dehydrogenase (ADH)/aldehyde dehydrogenase (ALDH) protein, lacked the part encoding the ADH domain, which is reported here for the first time in lactic acid bacteria. The deletion resulted in the lack of ADH activity, implying a requirement for electron acceptors in glucose assimilation. These results clearly indicated that L. kunkeei had undergone a specific reductive evolution in order to adapt to fructose-rich environments. The reduction characteristics were similar to those of Fructobacillus spp., but distinct from other lactobacilli with small genomes, such as Lactobacillus gasseri and Lactobacillus vaginalis. Fructose-richness thus induced an environment-specific gene reduction in phylogenetically distant microorganisms.
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Affiliation(s)
- Shintaro Maeno
- Department of Food and Cosmetic Science, Tokyo University of Agriculture, Hokkaido, Japan
| | - Yasuhiro Tanizawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan; Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Yu Kanesaki
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Eri Kubota
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Himanshu Kumar
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Leon Dicks
- Department of Microbiology, University of Stellenbosch, Stellenbosch, South Africa
| | - Seppo Salminen
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Junichi Nakagawa
- Department of Food and Cosmetic Science, Tokyo University of Agriculture, Hokkaido, Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan; RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Akihito Endo
- Department of Food and Cosmetic Science, Tokyo University of Agriculture, Hokkaido, Japan.
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Terashima M, Hatakeyama K, Kusuhara M, Makuuchi R, Tokunaga M, Tanizawa Y, Bando E, Kawamura T, Hikage M, Kaji S, Ohshima K, Ohnami S, Urakami K, Yamaguchi K. Genetic analysis of gastric cancer with distinctive family history. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw371.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Tokunaga M, Makuuchi R, Tanizawa Y, Bando E, Kawamura T, Terashima M. Efficacy of staging laparoscopy for type 4 and large type 3 gastric cancer. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw371.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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49
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Makuuchi R, Hatakeyama K, Terashima M, Kusuhara M, Tokunaga M, Tanizawa Y, Bando E, Kawamura T, Hikage M, Kaji S, Ohshima K, Urakami K, Yamaguchi K. New approach to gastric cancer classification based on TP53 mutation. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw371.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Tanizawa Y, Bando E, Tokunaga M, Kawamura T, Makuuchi R, Kinugasa Y, Tsubosa Y, Uesaka K, Terashima M. 59. Efficacy of surgical treatment for responders to chemotherapy for gastric cancer with para-aortic lymph node metastasis. Eur J Surg Oncol 2016. [DOI: 10.1016/j.ejso.2016.06.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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