Extended Data Fig. 4 in Isolation of an archaeon at the prokaryote eukaryote interface
| Main Authors: | Imachi, Hiroyuki, Nobu, Masaru K., Nakahara, Nozomi, Morono, Yuki, Ogawara, Miyuki, Takaki, Yoshihiro, Takano, Yoshinori, Uematsu, Katsuyuki, Ikuta, Tetsuro, Ito, Motoo, Matsui, Yohei, Miyazaki, Masayuki, Murata, Kazuyoshi, Saito, Yumi, Sakai, Sanae, Song, Chihong, Tasumi, Eiji, Yamanaka, Yuko, Yamaguchi, Takashi, Kamagata, Yoichi, Tamaki, Hideyuki, Takai, Ken |
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| Format: | info Image |
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, 2020
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| Online Access: |
https://zenodo.org/record/3609924 |
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3609924 |
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<dc schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"><creator>Imachi, Hiroyuki</creator><creator>Nobu, Masaru K.</creator><creator>Nakahara, Nozomi</creator><creator>Morono, Yuki</creator><creator>Ogawara, Miyuki</creator><creator>Takaki, Yoshihiro</creator><creator>Takano, Yoshinori</creator><creator>Uematsu, Katsuyuki</creator><creator>Ikuta, Tetsuro</creator><creator>Ito, Motoo</creator><creator>Matsui, Yohei</creator><creator>Miyazaki, Masayuki</creator><creator>Murata, Kazuyoshi</creator><creator>Saito, Yumi</creator><creator>Sakai, Sanae</creator><creator>Song, Chihong</creator><creator>Tasumi, Eiji</creator><creator>Yamanaka, Yuko</creator><creator>Yamaguchi, Takashi</creator><creator>Kamagata, Yoichi</creator><creator>Tamaki, Hideyuki</creator><creator>Takai, Ken</creator><date>2020-01-15</date><description>Extended Data Fig. 4 | Ribosomal protein- and 16S rRNA gene-based phylogeny of MK-D1. a, Phylogenomic tree of MK-D1 and select cultured archaea,eukaryotes and bacteria based on 31 ribosomal proteins conserved across the three domains (Supplementary Table 7). Ribosomal protein sequences of MK-D1,the organisms shown in the tree and MAGs of uncultured archaeal lineages (Supplementary Table 8) were aligned individually using MAFFT.MAG-derived sequences (except for Ca. Korarchaeum) were then removed for tree construction.After removing all-gap positions and concatenation,the maximum-likelihood tree was constructed using RAxML- NG.Bootstrap values around critical branching points are also shown.In total, 14,875 sites of the alignment were used for tree construction. b, A ribosomal protein-based phylogenomic tree constructed using MrBayes.Bayesian inference phylogenies were calculated using MrBayes 3.2.7a and a ribosomal protein concatenated alignment used for Fig.4a. c, Phylogenetic tree of MK-D1 and related archaea based on 16S rRNA genes.The 16S rRNA gene sequences were aligned using SINA against the Silva v.132 alignment and the maximumlikelihood tree was calculated using RAxML.</description><description>Published as part of Imachi, Hiroyuki, Nobu, Masaru K., Nakahara, Nozomi, Morono, Yuki, Ogawara, Miyuki, Takaki, Yoshihiro, Takano, Yoshinori, Uematsu, Katsuyuki, Ikuta, Tetsuro, Ito, Motoo, Matsui, Yohei, Miyazaki, Masayuki, Murata, Kazuyoshi, Saito, Yumi, Sakai, Sanae, Song, Chihong, Tasumi, Eiji, Yamanaka, Yuko, Yamaguchi, Takashi, Kamagata, Yoichi, Tamaki, Hideyuki & Takai, Ken, 2020, Nature 41586 on pages 1-23, DOI: 10.1038/s41586-019-1916-6, http://zenodo.org/record/3609900</description><identifier>https://zenodo.org/record/3609924</identifier><identifier>10.5281/zenodo.3609924</identifier><identifier>oai:zenodo.org:3609924</identifier><relation>doi:10.1038/s41586-019-1916-6</relation><relation>lsid:urn:lsid:plazi.org:pub:FFC1FFD3FFFCFFE3737FFF9B8B2FFFB6</relation><relation>url:http://publication.plazi.org/id/FFC1FFD3FFFCFFE3737FFF9B8B2FFFB6</relation><relation>url:https://zenodo.org/record/3609900</relation><relation>doi:10.5281/zenodo.3609923</relation><relation>url:https://zenodo.org/communities/biosyslit</relation><rights>info:eu-repo/semantics/openAccess</rights><source>Nature 41586 1-23</source><subject>Biodiversity</subject><subject>Taxonomy</subject><title>Extended Data Fig. 4 in Isolation of an archaeon at the prokaryote eukaryote interface</title><type>Other:info:eu-repo/semantics/other</type><type>Image:Image</type><recordID>3609924</recordID></dc>
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| format |
Other:info:eu-repo/semantics/other Other Image:Image Image |
| author |
Imachi, Hiroyuki Nobu, Masaru K. Nakahara, Nozomi Morono, Yuki Ogawara, Miyuki Takaki, Yoshihiro Takano, Yoshinori Uematsu, Katsuyuki Ikuta, Tetsuro Ito, Motoo Matsui, Yohei Miyazaki, Masayuki Murata, Kazuyoshi Saito, Yumi Sakai, Sanae Song, Chihong Tasumi, Eiji Yamanaka, Yuko Yamaguchi, Takashi Kamagata, Yoichi Tamaki, Hideyuki Takai, Ken |
| title |
Extended Data Fig. 4 in Isolation of an archaeon at the prokaryote eukaryote interface |
| publishDate |
2020 |
| topic |
Biodiversity Taxonomy |
| url |
https://zenodo.org/record/3609924 |
| contents |
Extended Data Fig. 4 | Ribosomal protein- and 16S rRNA gene-based phylogeny of MK-D1. a, Phylogenomic tree of MK-D1 and select cultured archaea,eukaryotes and bacteria based on 31 ribosomal proteins conserved across the three domains (Supplementary Table 7). Ribosomal protein sequences of MK-D1,the organisms shown in the tree and MAGs of uncultured archaeal lineages (Supplementary Table 8) were aligned individually using MAFFT.MAG-derived sequences (except for Ca. Korarchaeum) were then removed for tree construction.After removing all-gap positions and concatenation,the maximum-likelihood tree was constructed using RAxML- NG.Bootstrap values around critical branching points are also shown.In total, 14,875 sites of the alignment were used for tree construction. b, A ribosomal protein-based phylogenomic tree constructed using MrBayes.Bayesian inference phylogenies were calculated using MrBayes 3.2.7a and a ribosomal protein concatenated alignment used for Fig.4a. c, Phylogenetic tree of MK-D1 and related archaea based on 16S rRNA genes.The 16S rRNA gene sequences were aligned using SINA against the Silva v.132 alignment and the maximumlikelihood tree was calculated using RAxML. Published as part of Imachi, Hiroyuki, Nobu, Masaru K., Nakahara, Nozomi, Morono, Yuki, Ogawara, Miyuki, Takaki, Yoshihiro, Takano, Yoshinori, Uematsu, Katsuyuki, Ikuta, Tetsuro, Ito, Motoo, Matsui, Yohei, Miyazaki, Masayuki, Murata, Kazuyoshi, Saito, Yumi, Sakai, Sanae, Song, Chihong, Tasumi, Eiji, Yamanaka, Yuko, Yamaguchi, Takashi, Kamagata, Yoichi, Tamaki, Hideyuki & Takai, Ken, 2020, Nature 41586 on pages 1-23, DOI: 10.1038/s41586-019-1916-6, http://zenodo.org/record/3609900 |
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