Author Report for: Simakov ONo contact information in database for Simakov O
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 genomic substrate for adaptive radiation in African cichlid fish Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW and Di Palma F <65 more author(s)> Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alfoldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SC, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F (- 65) Ref: Nature, 513:375, 2014 : PubMed ESTHER: Brawand_2014_Nature_513_375 PubMedSearch: Brawand 2014 Nature 513 375 PubMedID: 25186727 Gene_locus related to this paper: oreni-i3j014, oreni-i3iw22, oreni-i3iwp5, oreni-i3j6k7, oreni-i3jhp1, oreni-i3jeq5, oreni-i3kf65, oreni-i3j210, oreni-i3j221, oreni-i3k9y3, oreni-i3k5p0, oreni-i3jwi4, oreni-i3jv26, oreni-i3k9m0, 9cich-a0a3p9d5c0, oreni-i3knk8, 9cich-a0a3b4hcr5, 9cich-a0a3p9dbr8, oreni-i3k1a6, oreni-i3jq62, 9cich-a0a3p9dgm2, neobr-a0a3q4g2a1, oreni-i3jdv9, neobr-a0a3q4hk25, oreni-i3jbm3, oreni-i3jbm2, oreni-i3jds8, 9cich-a0a3b4hbf8, 9cich-a0a3p9ars6, neobr-a0a3q4ghw9, oreni-i3kx89, 9cich-a0a3p9d359, oreni-i3kaa3, 9cich-a0a3p9bvw3 Abstract Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification. Title: Insights into bilaterian evolution from three spiralian genomes Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J and Rokhsar DS <16 more author(s)> Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS (- 16) Ref: Nature, 493:526, 2013 : PubMed ESTHER: Simakov_2013_Nature_493_526 PubMedSearch: Simakov 2013 Nature 493 526 PubMedID: 23254933 Gene_locus related to this paper: capte-r7t7t5, capte-r7tx98, capte-r7ua57, capte-r7ua73, capte-ACHE1, capte-ACHE2, capte-ACHE3, capte-ACHE4, helro-ACHE1, helro-ACHE1b, lotgi-ACHE1, lotgi-ACHE2, lotgi-v4aaa2, lotgi-v3zx52, lotgi-v4b4v9, capte-r7tuq9, capte-r7v997, capte-r7vgb9, lotgi-v3zwe9, capte-r7tu45, lotgi-v4bvy3, lotgi-v3zh31, capte-r7uie6, lotgi-v4b898, capte-r7u3w8, capte-r7uxb2, lotgi-v3za62, capte-r7ux79, capte-r7uq81, capte-r7vcc3, capte-r7ts12, capte-r7u1x0, capte-r7uhi1, capte-r7vei7, capte-r7v0v3, lotgi-v4bvi8, lotgi-v3zyd8, capte-r7tzy6, lotgi-v3z9i1, helro-t1fsg3, capte-x1yv75, capte-x2b306, lotgi-v3zcw8, capte-r7thp6, helro-t1fy80, lotgi-v4bky5, capte-r7tsq9, lotgi-v4ali9, lotgi-v4a9f2, lotgi-v3zjj3, helro-t1eej5, helro-t1g9b7, capte-r7tiy1, capte-r7tbl5, helro-t1exa6, lotgi-v4a5l7, helro-t1fm33, capte-r7ud05, capte-r7tql8, capte-r7u5g6, capte-r7u5z3, capte-r7ue07, lotgi-v3zk54, lotgi-v4a4r1, lotgi-v4aw76, lotgi-v4b250, lotgi-v4bbk1, lotgi-v3zq85, lotgi-v4a6s5, lotgi-v4amq2, lotgi-v4aqm2, lotgi-v4crq0, capte-r7tad7, capte-r7vgm6, lotgi-v4agl2, lotgi-v3zur2, lotgi-v4aui4, capte-r7tlv8, lotgi-v3zu07, helro-t1g0w9 Abstract Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome. Title: The dynamic genome of Hydra Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J and Steele RE <64 more author(s)> Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J, Wigge PA, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G, Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang JS, Ikeo K, Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz PR, Zhang X, Aufschnaiter R, Eder MK, Gorny AK, Salvenmoser W, Heimberg AM, Wheeler BM, Peterson KJ, Bottger A, Tischler P, Wolf A, Gojobori T, Remington KA, Strausberg RL, Venter JC, Technau U, Hobmayer B, Bosch TC, Holstein TW, Fujisawa T, Bode HR, David CN, Rokhsar DS, Steele RE (- 64) Ref: Nature, 464:592, 2010 : PubMed ESTHER: Chapman_2010_Nature_464_592 PubMedSearch: Chapman 2010 Nature 464 592 PubMedID: 20228792 Gene_locus related to this paper: 9burk-c9y6c0, 9burk-c9y8q9, 9burk-c9y9d4, 9burk-c9ya28, 9burk-c9yb37, 9burk-c9ycr9, 9burk-c9ydq0, 9burk-c9ydr2, 9burk-c9yew1, 9burk-c9yf78, 9burk-c9ygh2, 9burk-c9y7j2 Abstract The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction. Title: Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T and Rokhsar DS <18 more author(s)> Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS (- 18) Ref: Science, 329:223, 2010 : PubMed ESTHER: Prochnik_2010_Science_329_223 PubMedSearch: Prochnik 2010 Science 329 223 PubMedID: 20616280 Gene_locus related to this paper: volca-d8tmz1, volca-d8tne9, volca-d8tnn6, volca-d8tns6, volca-d8tr92, volca-d8u2d3, volca-d8u5r0, volca-d8u7s7, volca-d8u7s8, volca-d8u9w4, volca-d8u460, volca-d8uab7, volca-d8uai0, volca-d8uev0, volca-d8uhi9, volca-d8uiw9, volca-d8ujv0, volca-d8uf23, volca-d8tmz9, volca-d8u6e0 Abstract The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal-specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity. | |||||||
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