Shin IT

References (6)

Title : Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein - Hashimoto_2016_Nat.Commun_7_12808
Author(s) : Hashimoto T , Horikawa DD , Saito Y , Kuwahara H , Kozuka-Hata H , Shin IT , Minakuchi Y , Ohishi K , Motoyama A , Aizu T , Enomoto A , Kondo K , Tanaka S , Hara Y , Koshikawa S , Sagara H , Miura T , Yokobori S , Miyagawa K , Suzuki Y , Kubo T , Oyama M , Kohara Y , Fujiyama A , Arakawa K , Katayama T , Toyoda A , Kunieda T
Ref : Nat Commun , 7 :12808 , 2016
Abstract : Tardigrades, also known as water bears, are small aquatic animals. Some tardigrade species tolerate almost complete dehydration and exhibit extraordinary tolerance to various physical extremes in the dehydrated state. Here we determine a high-quality genome sequence of Ramazzottius varieornatus, one of the most stress-tolerant tardigrade species. Precise gene repertoire analyses reveal the presence of a small proportion (1.2% or less) of putative foreign genes, loss of gene pathways that promote stress damage, expansion of gene families related to ameliorating damage, and evolution and high expression of novel tardigrade-unique proteins. Minor changes in the gene expression profiles during dehydration and rehydration suggest constitutive expression of tolerance-related genes. Using human cultured cells, we demonstrate that a tardigrade-unique DNA-associating protein suppresses X-ray-induced DNA damage by approximately 40% and improves radiotolerance. These findings indicate the relevance of tardigrade-unique proteins to tolerability and tardigrades could be a bountiful source of new protection genes and mechanisms.
ESTHER : Hashimoto_2016_Nat.Commun_7_12808
PubMedSearch : Hashimoto_2016_Nat.Commun_7_12808
PubMedID: 27649274
Gene_locus related to this paper: ramva-a0a1d1uki4 , ramva-a0a1d1uvm7 , ramva-a0a1d1ula4 , ramva-a0a1d1v5e3 , ramva-a0a1d1unv1 , ramva-a0a1d1vjq5 , ramva-a0a1d1vlp2 , ramva-a0a1d1vh75 , ramva-a0a1d1vzz5

Title : The amphioxus genome and the evolution of the chordate karyotype - Putnam_2008_Nature_453_1064
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
Ref : Nature , 453 :1064 , 2008
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.
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

Title : The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants - Rensing_2008_Science_319_64
Author(s) : Rensing SA , Lang D , Zimmer AD , Terry A , Salamov A , Shapiro H , Nishiyama T , Perroud PF , Lindquist EA , Kamisugi Y , Tanahashi T , Sakakibara K , Fujita T , Oishi K , Shin IT , Kuroki Y , Toyoda A , Suzuki Y , Hashimoto S , Yamaguchi K , Sugano S , Kohara Y , Fujiyama A , Anterola A , Aoki S , Ashton N , Barbazuk WB , Barker E , Bennetzen JL , Blankenship R , Cho SH , Dutcher SK , Estelle M , Fawcett JA , Gundlach H , Hanada K , Heyl A , Hicks KA , Hughes J , Lohr M , Mayer K , Melkozernov A , Murata T , Nelson DR , Pils B , Prigge M , Reiss B , Renner T , Rombauts S , Rushton PJ , Sanderfoot A , Schween G , Shiu SH , Stueber K , Theodoulou FL , Tu H , Van de Peer Y , Verrier PJ , Waters E , Wood A , Yang L , Cove D , Cuming AC , Hasebe M , Lucas S , Mishler BD , Reski R , Grigoriev IV , Quatrano RS , Boore JL
Ref : Science , 319 :64 , 2008
Abstract : We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
ESTHER : Rensing_2008_Science_319_64
PubMedSearch : Rensing_2008_Science_319_64
PubMedID: 18079367
Gene_locus related to this paper: phypa-a9rbi6 , phypa-a9rfh1 , phypa-a9rg19 , phypa-a9rgt9 , phypa-a9rhz9 , phypa-a9rkj1 , phypa-a9rns2 , phypa-a9rp52 , phypa-a9rq03 , phypa-a9ry17 , phypa-a9ry72 , phypa-a9s5n8 , phypa-a9s6w1 , phypa-a9s8c7 , phypa-a9s299 , phypa-a9san7 , phypa-a9sc75 , phypa-a9se75 , phypa-a9sg07 , phypa-a9skf7 , phypa-a9skr1 , phypa-a9skw1 , phypa-a9sl58 , phypa-a9slp7 , phypa-a9smq5 , phypa-a9sp13 , phypa-a9ssb0 , phypa-a9sse1 , phypa-a9ssf6 , phypa-a9st85 , phypa-a9sx74 , phypa-a9sy58 , phypa-a9syy4 , phypa-a9t0n4 , phypa-a9t0p4 , phypa-a9t1j2 , phypa-a9t5h1 , phypa-a9t7g6 , phypa-a9t8u8 , phypa-a9t9c9 , phypa-a9t9d9 , phypa-a0a7i4d2t7 , phypa-a9t498 , phypa-a9tbu4 , phypa-a9tc36 , phypa-a9tds0 , phypa-a9te64 , phypa-a9tfw2 , phypa-a9tin6 , phypa-a9tja4 , phypa-a9tmp3 , phypa-a9tmr4 , phypa-a9tql4 , phypa-a9tr83 , phypa-a9tsl1 , phypa-a9tsv6 , phypa-a9tu05 , phypa-a9tw81 , phypa-a9tyr8 , phypa-a9u0c9 , phypa-a9u0k3 , phypa-a9u0p4 , phypa-a9u2u7 , phypa-a9u3s0 , phypa-a9tfm7 , phypa-a9tfp6 , phypa-a9syg9 , phypa-a9tzk2 , phypa-a9tvg4 , phypa-a9t1y4 , phypa-a9tqt6 , phypa-a9st18 , phypa-a9tix9 , phypa-a0a2k1kfe3 , phypa-a9sqk3 , phypa-a0a2k1ie71 , phypa-a0a2k1kg29 , phypa-a0a2k1iji3

Title : The medaka draft genome and insights into vertebrate genome evolution - Kasahara_2007_Nature_447_714
Author(s) : Kasahara M , Naruse K , Sasaki S , Nakatani Y , Qu W , Ahsan B , Yamada T , Nagayasu Y , Doi K , Kasai Y , Jindo T , Kobayashi D , Shimada A , Toyoda A , Kuroki Y , Fujiyama A , Sasaki T , Shimizu A , Asakawa S , Shimizu N , Hashimoto S , Yang J , Lee Y , Matsushima K , Sugano S , Sakaizumi M , Narita T , Ohishi K , Haga S , Ohta F , Nomoto H , Nogata K , Morishita T , Endo T , Shin IT , Takeda H , Morishita S , Kohara Y
Ref : Nature , 447 :714 , 2007
Abstract : Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.
ESTHER : Kasahara_2007_Nature_447_714
PubMedSearch : Kasahara_2007_Nature_447_714
PubMedID: 17554307
Gene_locus related to this paper: fugru-3cxest , fugru-4cxest , fugru-4neur , fugru-ACHE , fugru-ACHEE , fugru-balip , fugru-BCHE , fugru-BCHEB , fugru-cxest , oryla-ACHE , oryla-BCHE , oryla-d2x2i4 , oryla-h2m6h1 , oryla-h2m7w4 , oryla-h2m361 , oryla-h2mbn6 , oryla-h2mfw1 , oryla-h2mhi0 , oryla-h2mhl7 , oryla-h2mpb5 , oryla-h2mqz5 , oryla-h2mvs7 , oryla-h2mz49 , oryla-h2n1l9 , oryla-nlgn2 , takru-1neur , takru-2bneur , takru-3bneur , takru-h2rke7 , takru-h2rmg3 , takru-h2rsj9 , takru-h2rw77 , takru-h2ryq0 , takru-h2sci9 , takru-h2se90 , takru-h2spg7 , takru-h2sxi1 , takru-h2ts55 , takru-h2ts56 , takru-h2uxa9 , takru-h2vaf1 , takru-nlgn2a , takru-nlgn3a , takru-nlgn4a , oryla-h2mff8 , oryla-h2m2f0 , oryla-h2ler5 , takru-h2tsm6 , takru-h2tq49 , takru-h2tq47 , takru-h2s286 , takru-h2tng4 , takru-h2tq50 , takru-h2tng3 , takru-h2tng2 , oryla-h2lj38 , oryla-h2mxe6 , takru-h2tq48 , oryla-h2lf11 , takru-h2u5j0 , takru-h2rpm8 , oryla-h2n273 , oryla-h2n271 , oryla-h2lum7 , takru-h2tpz2 , takru-h2u3j1 , oryla-h2mdv3 , takru-h2tzm9 , takru-h2u8u6 , oryla-h2lcw8 , oryla-h2lc35 , oryla-h2ln66 , oryla-h2m8k0 , oryla-h2mdj7 , oryla-h2lw61 , oryla-h2lxe3 , oryla-h2l8y7 , oryla-h2mr84 , oryla-h2mr95 , oryla-h2mcz6 , oryla-h2lxr5 , oryla-h2ly57 , oryla-a0a3p9kz03 , oryla-a0a3p9hfu1 , oryla-h2m307 , oryla-h2lch5 , oryla-h2ldw9 , oryla-a0a3b3ic40 , oryla-h2ldi5 , oryla-h2mun1 , oryla-a0a3p9jla3

Title : Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D - Matsuzaki_2004_Nature_428_653
Author(s) : Matsuzaki M , Misumi O , Shin IT , Maruyama S , Takahara M , Miyagishima SY , Mori T , Nishida K , Yagisawa F , Yoshida Y , Nishimura Y , Nakao S , Kobayashi T , Momoyama Y , Higashiyama T , Minoda A , Sano M , Nomoto H , Oishi K , Hayashi H , Ohta F , Nishizaka S , Haga S , Miura S , Morishita T , Kabeya Y , Terasawa K , Suzuki Y , Ishii Y , Asakawa S , Takano H , Ohta N , Kuroiwa H , Tanaka K , Shimizu N , Sugano S , Sato N , Nozaki H , Ogasawara N , Kohara Y , Kuroiwa T
Ref : Nature , 428 :653 , 2004
Abstract : Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support the lives of photosynthetic eukaryotes, including higher plants. Here we report the 16,520,305-base-pair sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome. We identified 5,331 genes in total, of which at least 86.3% were expressed. Unique characteristics of this genomic structure include: a lack of introns in all but 26 genes; only three copies of ribosomal DNA units that maintain the nucleolus; and two dynamin genes that are involved only in the division of mitochondria and plastids. The conserved mosaic origin of Calvin cycle enzymes in this red alga and in green plants supports the hypothesis of the existence of single primary plastid endosymbiosis. The lack of a myosin gene, in addition to the unexpressed actin gene, suggests a simpler system of cytokinesis. These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.
ESTHER : Matsuzaki_2004_Nature_428_653
PubMedSearch : Matsuzaki_2004_Nature_428_653
PubMedID: 15071595
Gene_locus related to this paper: cyam1-m1vi61 , cyam1-m1vhh9

Title : Comparative sequence analysis of a gene-dense region among closely related species of Drosophila melanogaster - Kawahara_2004_Genes.Genet.Syst_79_351
Author(s) : Kawahara Y , Matsuo T , Nozawa M , Shin IT , Kohara Y , Aigaki T
Ref : Genes Genet Syst , 79 :351 , 2004
Abstract : Comparative sequence analysis among closely related species is essential for investigating the evolution of non-coding sequences, which evolve more rapidly than protein-coding sequences. We sequenced the cytogenetic map 56F10-16, a gene-dense region of D. simulans and D. sechellia, closely related species to D. melanogaster. About 57 kb of the genomic sequences containing 19 genes were annotated from each species according to the corresponding region of the D. melanogaster genome. The order and orientation of genes were perfectly conserved among the three species, and no transposable elements were found. The rate of nucleotide substitutions in the non-coding sequences was lower than that at the fourfold-degenerate sites, implying functional constraints in the non-coding regions. The sequence information from three closely related species, allowed us to estimate the insertions and the deletions that may have occurred in the lineages of D. simulans and D. sechellia using the D. melanogaster sequence as an outgroup. The number of deletions was twice that of insertions for the introns of D. simulans. More remarkably, the deletion outnumbered insertions by 7.5 times for the intergenic sequences of D. sechellia. These results suggest that the non-coding sequences have been shortened by deletion biases. However, the deletion bias was lower than that previously estimated for pseudogenes, suggesting that the non-coding sequences are already rich in functional elements, possibly involved in the regulation of gene expression including transcription and pre-mRNA processing. These features of non-coding sequences may be common to other gene-dense regions contributing to the compactness of the Drosophila genome.
ESTHER : Kawahara_2004_Genes.Genet.Syst_79_351
PubMedSearch : Kawahara_2004_Genes.Genet.Syst_79_351
PubMedID: 15729003
Gene_locus related to this paper: drose-q5r272 , drosi-q5r291