Author Report for: Kuroki YNo contact information in database for Kuroki Y
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A and Rokhsar DS <64 more author(s)> Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS (- 64) Ref: Nature, 538:336, 2016 : PubMed ESTHER: Session_2016_Nature_538_336 PubMedSearch: Session 2016 Nature 538 336 PubMedID: 27762356 Gene_locus related to this paper: xenla-a0a1l8f4t7, xenla-a0a1l8fbc6, xenla-a0a1l8fct2, xenla-q2tap9, xenla-q4klb6, xenla-q5xh09, xenla-q6ax59, xenla-q6dcw6, xenla-q6irp4, xenla-q6pad5, xenla-q7sz70, xenla-Q7ZXQ6, xenla-q66kx1, xenla-q640y7, xenla-q642r3, xenla-Q860X9, xenla-BCHE2, xenla-a0a1l8g7v4, xenla-a0a1l8g1u7, xenla-a0a1l8fmc5, xenla-a0a1l8g467, xenla-a0a1l8g4e4, xenla-a0a1l8ga66, xenla-a0a1l8gaw4, xenla-a0a1l8gt68, xenla-a0a1l8h0b2, xenla-a0a1l8fdr1, xenla-a0a1l8fdt7, xenla-a0a1l8fi72, xenla-a0a1l8fi73, xenla-a0a1l8fi77, xenla-a0a1l8fi96, xenla-a0a1l8hc38, xenla-a0a1l8hn27, xenla-a0a1l8hry6, xenla-a0a1l8hw96, xenla-a0a1l8i2x6, xenla-a0a1l8hei7, xenla-a0a1l8gnd1, xenla-a0a1l8i2g3, xenla-a0a1l8hdn0, xenla-a0a1l8h622 Abstract To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression. 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: The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA and Boore JL <60 more 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 (- 60) Ref: Science, 319:64, 2008 : PubMed 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 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. Title: The medaka draft genome and insights into vertebrate genome evolution Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K and Kohara Y <28 more 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 (- 28) Ref: Nature, 447:714, 2007 : PubMed 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 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. Title: Human chromosome 11 DNA sequence and analysis including novel gene identification Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T and Sakaki Y <24 more author(s)> Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim DW, She X, Barlow KF, Bloom T, Bruford E, Chang JL, Cuomo CA, Eichler E, Fitzgerald MG, Jaffe DB, LaButti K, Nicol R, Park HS, Seaman C, Sougnez C, Yang X, Zimmer AR, Zody MC, Birren BW, Nusbaum C, Fujiyama A, Hattori M, Rogers J, Lander ES, Sakaki Y (- 24) Ref: Nature, 440:497, 2006 : PubMed ESTHER: Taylor_2006_Nature_440_497 PubMedSearch: Taylor 2006 Nature 440 497 PubMedID: 16554811 Gene_locus related to this paper: human-PRCP Abstract Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena. Title: DNA sequence and analysis of human chromosome 18 Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA and Lander ES <45 more author(s)> Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K, Fitzgerald MG, Yang X, Abouelleil A, Allen NR, Anderson S, Bloom T, Bugalter B, Butler J, Cook A, Decaprio D, Engels R, Garber M, Gnirke A, Hafez N, Hall JL, Norman CH, Itoh T, Jaffe DB, Kuroki Y, Lehoczky J, Lui A, Macdonald P, Mauceli E, Mikkelsen TS, Naylor JW, Nicol R, Nguyen C, Noguchi H, O'Leary SB, O'Neill K, Piqani B, Smith CL, Talamas JA, Topham K, Totoki Y, Toyoda A, Wain HM, Young SK, Zeng Q, Zimmer AR, Fujiyama A, Hattori M, Birren BW, Sakaki Y, Lander ES (- 45) Ref: Nature, 437:551, 2005 : PubMed ESTHER: Nusbaum_2005_Nature_437_551 PubMedSearch: Nusbaum 2005 Nature 437 551 PubMedID: 16177791 Gene_locus related to this paper: human-LIPG Abstract Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements. Title: DNA sequence and comparative analysis of chimpanzee chromosome 22 Watanabe H, Fujiyama A, Hattori M, Taylor TD, Toyoda A, Kuroki Y, Noguchi H, BenKahla A, Lehrach H and Sakaki Y <35 more author(s)> Watanabe H, Fujiyama A, Hattori M, Taylor TD, Toyoda A, Kuroki Y, Noguchi H, BenKahla A, Lehrach H, Sudbrak R, Kube M, Taenzer S, Galgoczy P, Platzer M, Scharfe M, Nordsiek G, Blocker H, Hellmann I, Khaitovich P, Paabo S, Reinhardt R, Zheng HJ, Zhang XL, Zhu GF, Wang BF, Fu G, Ren SX, Zhao GP, Chen Z, Lee YS, Cheong JE, Choi SH, Wu KM, Liu TT, Hsiao KJ, Tsai SF, Kim CG, S OO, Kitano T, Kohara Y, Saitou N, Park HS, Wang SY, Yaspo ML, Sakaki Y (- 35) Ref: Nature, 429:382, 2004 : PubMed ESTHER: Watanabe_2004_Nature_429_382 PubMedSearch: Watanabe 2004 Nature 429 382 PubMedID: 15164055 Gene_locus related to this paper: pantr-a0a2j8lmv7 Abstract Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized. | |||||||
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