Author Report for: Satoh NNo contact information in database for Satoh N
Nishitsuji K, Arimoto A, Higa Y, Mekaru M, Kawamitsu M, Satoh N, Shoguchi E Ref: Sci Rep, 9:4607, 2019 : PubMed ESTHER: Nishitsuji_2019_Sci.Rep_9_4607 PubMedSearch: Nishitsuji 2019 Sci.Rep 9 4607 PubMedID: 30872679 Abstract The brown alga, Nemacystus decipiens ("ito-mozuku" in Japanese), is one of the major edible seaweeds, cultivated principally in Okinawa, Japan. N. decipiens is also a significant source of fucoidan, which has various physiological activities. To facilitate brown algal studies, we decoded the ~154 Mbp draft genome of N. decipiens Onna-1 strain. The genome is estimated to contain 15,156 protein-coding genes, ~78% of which are substantiated by corresponding mRNAs. Mitochondrial genes analysis showed a close relationship between N. decipiens and Cladosiphon okamuranus. Comparisons with the C. okamuranus and Ectocarpus siliculosus genomes identified a set of N. decipiens-specific genes. Gene ontology annotation showed more than half of these are classified as molecular function, enzymatic activity, and/or biological process. Extracellular matrix analysis revealed domains shared among three brown algae. Characterization of genes that encode enzymes involved in the biosynthetic pathway for sulfated fucan showed two sets of genes fused in the genome. One is a fusion of L-fucokinase and GDP-fucose pyrophosphorylase genes, a feature shared with C. okamuranus. Another fusion is between an ST-domain-containing gene and an alpha/beta hydrolase gene. Although the function of fused genes should be examined in future, these results suggest that N. decipiens is another promising source of fucoidan. Title: The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization Luo YJ, Takeuchi T, Koyanagi R, Yamada L, Kanda M, Khalturina M, Fujie M, Yamasaki S, Endo K, Satoh N Ref: Nat Commun, 6:8301, 2015 : PubMed ESTHER: Luo_2015_Nat.Commun_6_8301 PubMedSearch: Luo 2015 Nat.Commun 6 8301 PubMedID: 26383154 Gene_locus related to this paper: linun-a0a1s3h3d9, linun-a0a2r2mta8 Abstract The evolutionary origins of lingulid brachiopods and their calcium phosphate shells have been obscure. Here we decode the 425-Mb genome of Lingula anatina to gain insights into brachiopod evolution. Comprehensive phylogenomic analyses place Lingula close to molluscs, but distant from annelids. The Lingula gene number has increased to approximately 34,000 by extensive expansion of gene families. Although Lingula and vertebrates have superficially similar hard tissue components, our genomic, transcriptomic and proteomic analyses show that Lingula lacks genes involved in bone formation, indicating an independent origin of their phosphate biominerals. Several genes involved in Lingula shell formation are shared by molluscs. However, Lingula has independently undergone domain combinations to produce shell matrix collagens with EGF domains and carries lineage-specific shell matrix proteins. Gene family expansion, domain shuffling and co-option of genes appear to be the genomic background of Lingula's unique biomineralization. This Lingula genome provides resources for further studies of lophotrochozoan evolution. Title: The amphioxus genome and the evolution of the chordate karyotype Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A and Rokhsar DS <27 more author(s)> Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutierrez EL, Dubchak I, Garcia-Fernandez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin IT, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS (- 27) Ref: Nature, 453:1064, 2008 : PubMed ESTHER: Putnam_2008_Nature_453_1064 PubMedSearch: Putnam 2008 Nature 453 1064 PubMedID: 18563158 Gene_locus related to this paper: brafl-ACHE1, brafl-ACHE2, brafl-ACHEA, brafl-ACHEB, brafl-c3xqm2, brafl-c3xqm5, brafl-c3xtl0, brafl-c3xtl1, brafl-c3xut6, brafl-c3xut7, brafl-c3xvw5, brafl-c3xx27, brafl-c3xx28, brafl-c3xx30, brafl-c3xx32, brafl-c3xx36, brafl-c3xx38, brafl-c3xx39, brafl-c3xx40, brafl-c3xx41, brafl-c3xxt9, brafl-c3xyd7, brafl-c3xyd8, brafl-c3xyd9, brafl-c3xye0, brafl-c3xyt7, brafl-c3xzy1, brafl-c3xzy2, brafl-c3y1p9, brafl-c3y1t3, brafl-c3y2u3, brafl-c3y4l1, brafl-c3y6v9, brafl-c3y6y4, brafl-c3y7d7, brafl-c3y7s1, brafl-c3y8k5, brafl-c3y8t3, brafl-c3y8t4, brafl-c3y8t5, brafl-c3y8v8, brafl-c3y8w1.1, brafl-c3y8w2, brafl-c3y9i7, brafl-c3y9i8, brafl-c3y9l9, brafl-c3y9y3, brafl-c3y087, brafl-c3yan2, brafl-c3yaw4, brafl-c3ybw7, brafl-c3yc67, brafl-c3ydm8, brafl-c3yfm5, brafl-c3yfz8, brafl-c3ygc7, brafl-c3ygc9.1, brafl-c3ygd0, brafl-c3ygd1, brafl-c3ygd2.1, brafl-c3ygd4, brafl-c3ygg6, brafl-c3ygr1, brafl-c3yi63, brafl-c3yi64, brafl-c3yi67, brafl-c3yi68, brafl-c3yi69, brafl-c3yk61, brafl-c3ykb2, brafl-c3yla7, brafl-c3ylp9, brafl-c3ylq0, brafl-c3ylq1, brafl-c3ymu0, brafl-c3yne9, brafl-c3ypm6, brafl-c3yr72, brafl-c3yra8, brafl-c3ys59, brafl-c3yv27, brafl-c3ywf1, brafl-c3ywh9, brafl-c3yx17, brafl-c3yx19, brafl-c3yxb9, brafl-c3yxi7, brafl-c3yyq5, brafl-c3yz04, brafl-c3z1c7, brafl-c3z1u9, brafl-c3z1v0, brafl-c3z3n7, brafl-c3z5c8, brafl-c3z9f4, brafl-c3z066, brafl-c3z139, brafl-c3z975, brafl-c3zab8, brafl-c3zab9, brafl-c3zbr4, brafl-c3zci7, brafl-c3zcy8, brafl-c3zd14, brafl-c3zer1, brafl-c3zf44, brafl-c3zf47, brafl-c3zf48, brafl-c3zfs6, brafl-c3zhm6, brafl-c3ziv7.1, brafl-c3ziv7.2, brafl-c3zlg0, brafl-c3zlg2, brafl-c3zlg3, brafl-c3zli5, brafl-c3zme7, brafl-c3zme8, brafl-c3zmp8, brafl-c3zmv1, brafl-c3zmv2, brafl-c3znd6, brafl-c3znl2, brafl-c3zqg7, brafl-c3zqz2, brafl-c3zs46, brafl-c3zs49, brafl-c3zs56, brafl-c3zv54, brafl-c3zvv1, brafl-c3zwz6, brafl-c3zxg2, brafl-c3zxq3, brafl-c3yim2, brafl-c3zfs5, brafl-c3zfs3, brafl-c3xr79, brafl-c3y7r2, brafl-c3yj62, brafl-c3zg22, brafl-c3y2t9, brafl-c3y2u0, brafl-c3ycg1, brafl-c3ycg2, brafl-c3ycg4, brafl-c3z1l3, brafl-c3zn71, brafl-c3zj72, brafl-c3yf35, brafl-c3z474, brafl-c3zqr8, brafl-c3yde6 Abstract Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution. Title: Complete sequencing and characterization of 21,243 full-length human cDNAs Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H and Sugano S <144 more author(s)> Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Ohara O, Isogai T, Sugano S (- 144) Ref: Nat Genet, 36:40, 2004 : PubMed ESTHER: Ota_2004_Nat.Genet_36_40 PubMedSearch: Ota 2004 Nat.Genet 36 40 PubMedID: 14702039 Gene_locus related to this paper: human-ABHD1, human-ABHD4, human-ABHD12, human-ABHD16A, human-ACOT1, human-LDAH, human-ABHD18, human-CES1, human-CES4A, human-CES5A, human-CPVL, human-DAGLB, human-EPHX2, human-KANSL3, human-LIPA, human-LPL, human-MEST, human-NDRG1, human-NLGN1, human-NLGN4X, human-PRCP, human-PRSS16, human-SERAC1, human-TMEM53 Abstract As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at approximately 58% compared with a peak at approximately 42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs. Title: The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M and Rokhsar DS <77 more author(s)> Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-I T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS (- 77) Ref: Science, 298:2157, 2002 : PubMed ESTHER: Dehal_2002_Science_298_2157 PubMedSearch: Dehal 2002 Science 298 2157 PubMedID: 12481130 Gene_locus related to this paper: cioin-141645, cioin-147959, cioin-150181, cioin-154370, cioin-ACHE1, cioin-ACHE2, cioin-cxest, cioin-f6qcp0, cioin-f6r8z1, cioin-f6u176, cioin-f6vac9, cioin-f6x584, cioin-f6xa69, cioin-f6y403, cioin-h2xqb4, cioin-H2XTI0, cioin-F6T1M3, cioin-H2XUP7, cioin-CIN.7233, cioin-F6V269, cioin-Cin16330, cioin-h2xua2, cioin-f6vaa5, cioin-f6v9x6, cioin-f6swc9, cioin-f7amz2, cioin-f6s021, cioin-h2xxq9, cioin-h2xne6, cioin-f6ynr2 Abstract The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi. Title: A cDNA resource from the basal chordate Ciona intestinalis Satou Y, Yamada L, Mochizuki Y, Takatori N, Kawashima T, Sasaki A, Hamaguchi M, Awazu S, Yagi K and Satoh N <4 more author(s)> Satou Y, Yamada L, Mochizuki Y, Takatori N, Kawashima T, Sasaki A, Hamaguchi M, Awazu S, Yagi K, Sasakura Y, Nakayama A, Ishikawa H, Inaba K, Satoh N (- 4) Ref: Genesis, 33:153, 2002 : PubMed ESTHER: Satou_2002_Genesis_33_153 PubMedSearch: Satou 2002 Genesis 33 153 PubMedID: 12203911 Gene_locus related to this paper: cioin-141645, cioin-147959, cioin-150181, cioin-154370, cioin-ACHE1, cioin-ACHE2, cioin-cxest, cioin-F6V269 Title: The recently-described ascidian species Molgula tectiformis is a direct developer Tagawa K, Jeffery WR, Satoh N Ref: Zoolog Sci, 14:297, 1997 : PubMed ESTHER: Tagawa_1997_Zoolog.Sci_14_297 PubMedSearch: Tagawa 1997 Zoolog.Sci 14 297 PubMedID: 9256052 Abstract Molgula tectiformis is a new ascidian species recently described by Nishikawa (1991). In Otsuchi Bay, Iwate, Japan, they are easily obtainable from cages for culturing scallops. We report here that M. tectiformis is another example of a direct developer: their embryonic development is lacking the tadpole larva. The fertilized egg is orange and about 150 microns in diameter. At 18 degrees C, the egg cleaves at about 20 min intervals and gastrulation occurs about 5 hr after fertilization. In contrast to conventionally-developing ascidians, M. tectiformis does not form a tadpole larva. Immediately before hatching, three stolons or ampullae begin to extend from the tailless embryo. After hatching the stolons mediate the attachment of the juvenile body to the substratum. Histochemistry for tissue-specific enzyme activity did not detect muscle-specific acetyl-cholinesterase, endoderm-specific alkaline phosphatase, and pigment cell-specific tyrosinase. In addition, in situ hybridization could not prove the presence of muscle actin gene transcripts in the embryo. These results suggest that these larval tissues do not differentiate in M. tectiformis embryos. Because M. tectiformis is common and gravid year-around in Otsuchi Bay, this direct developer provides the opportunity for further analysis of molecular changes during evolution that cause an alternative mode of development. | |||||||
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