Author Report for: Warren WCNo contact information in database for Warren WC
Gallant JR, Losilla M, Tomlinson C, Warren WC Ref: Genome Biol Evol, 9:3525, 2017 : PubMed ESTHER: Gallant_2017_Genome.Biol.Evol_9_3525 PubMedSearch: Gallant 2017 Genome.Biol.Evol 9 3525 PubMedID: 29240929 Gene_locus related to this paper: 9tele-a0a3b3qvg4, 9tele-a0a3b3t8w4, 9tele-a0a3b3s6z8, 9tele-a0a3b3r1d9, 9tele-a0a3b3sv81, 9tele-a0a3b3r9e0, 9tele-a0a3b3smy9, 9tele-a0a3b3r2i3, 9tele-a0a3b3rs87, 9tele-a0a3b3r308, 9tele-a0a3b3sjn6, 9tele-a0a3b3rr42 Abstract Several studies have begun to elucidate the genetic and developmental processes underlying major vertebrate traits. Few of these traits have evolved repeatedly in vertebrates, preventing the analysis of molecular mechanisms underlying these traits comparatively. Electric organs have evolved multiple times among vertebrates, presenting a unique opportunity to understand the degree of constraint and repeatability of the evolutionary processes underlying novel vertebrate traits. As there is now a completed genome sequence representing South American electric eels, we were motivated to obtain genomic sequence from a linage that independently evolved electric organs to facilitate future comparative analyses of the evolution and development of electric organs. We report here the sequencing and de novo assembly of the genome of the mormyrid Paramormyrops kingsleyae using short-read sequencing. In addition, we have completed a somatic transcriptome from 11 tissues to construct a gene expression atlas of predicted genes from this assembly, enabling us to identify candidate housekeeping genes as well as genes differentially expressed in the major somatic tissues of the mormyrid electric fish. We anticipate that this resource will greatly facilitate comparative studies on the evolution and development of electric organs and electroreceptors. Title: The cavefish genome reveals candidate genes for eye loss McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A and Warren WC <11 more author(s)> McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Retaux S, Rohner N, Searle SM, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC (- 11) Ref: Nat Commun, 5:5307, 2014 : PubMed ESTHER: McGaugh_2014_Nat.Commun_5_5307 PubMedSearch: McGaugh 2014 Nat.Commun 5 5307 PubMedID: 25329095 Gene_locus related to this paper: astmx-w5kyj0, astmx-w5l5v5, astmx-w5k377, astmx-w5kdz8, astmx-w5k5k8, astmx-w5kf08, astmx-w5lfx9, astmx-a0a3b1il55, astmx-w5k188, astmx-w5lig8, astmx-a0a3b1it79, astmx-a0a3b1kh87, astmx-w5kk92, astmx-w5kf44, astmx-a0a3b1ihb9, astmx-a0a3b1jet6, astmx-w5lug4, astmx-w5ln33, astmx-a0a3b1k1i9, astmx-w5l3f7 Abstract Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction. Title: Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment Scott JG, Warren WC, Beukeboom LW, Bopp D, Clark AG, Giers SD, Hediger M, Jones AK, Kasai S and Liu N <16 more author(s)> Scott JG, Warren WC, Beukeboom LW, Bopp D, Clark AG, Giers SD, Hediger M, Jones AK, Kasai S, Leichter CA, Li M, Meisel RP, Minx P, Murphy TD, Nelson DR, Reid WR, Rinkevich FD, Robertson HM, Sackton TB, Sattelle DB, Thibaud-Nissen F, Tomlinson C, van de Zande L, Walden KK, Wilson RK, Liu N (- 16) Ref: Genome Biol, 15:466, 2014 : PubMed ESTHER: Scott_2014_Genome.Biol_15_466 PubMedSearch: Scott 2014 Genome.Biol 15 466 PubMedID: 25315136 Gene_locus related to this paper: musdo-a0a1i8n2v5, musdo-a0a1i8n5k8 Abstract BACKGROUND: Adult house flies, Musca domestica L., are mechanical vectors of more than 100 devastating diseases that have severe consequences for human and animal health. House fly larvae play a vital role as decomposers of animal wastes, and thus live in intimate association with many animal pathogens. RESULTS: We have sequenced and analyzed the genome of the house fly using DNA from female flies. The sequenced genome is 691 Mb. Compared with Drosophila melanogaster, the genome contains a rich resource of shared and novel protein coding genes, a significantly higher amount of repetitive elements, and substantial increases in copy number and diversity of both the recognition and effector components of the immune system, consistent with life in a pathogen-rich environment. There are 146 P450 genes, plus 11 pseudogenes, in M. domestica, representing a significant increase relative to D. melanogaster and suggesting the presence of enhanced detoxification in house flies. Relative to D. melanogaster, M. domestica has also evolved an expanded repertoire of chemoreceptors and odorant binding proteins, many associated with gustation. CONCLUSIONS: This represents the first genome sequence of an insect that lives in intimate association with abundant animal pathogens. The house fly genome provides a rich resource for enabling work on innovative methods of insect control, for understanding the mechanisms of insecticide resistance, genetic adaptation to high pathogen loads, and for exploring the basic biology of this important pest. The genome of this species will also serve as a close out-group to Drosophila in comparative genomic studies. Title: Genome of the human hookworm Necator americanus Tang YT, Gao X, Rosa BA, Abubucker S, Hallsworth-Pepin K, Martin J, Tyagi R, Heizer E, Zhang X and Mitreva M <19 more author(s)> Tang YT, Gao X, Rosa BA, Abubucker S, Hallsworth-Pepin K, Martin J, Tyagi R, Heizer E, Zhang X, Bhonagiri-Palsikar V, Minx P, Warren WC, Wang Q, Zhan B, Hotez PJ, Sternberg PW, Dougall A, Gaze ST, Mulvenna J, Sotillo J, Ranganathan S, Rabelo EM, Wilson RK, Felgner PL, Bethony J, Hawdon JM, Gasser RB, Loukas A, Mitreva M (- 19) Ref: Nat Genet, 46:261, 2014 : PubMed ESTHER: Tang_2014_Nat.Genet_46_261 PubMedSearch: Tang 2014 Nat.Genet 46 261 PubMedID: 24441737 Gene_locus related to this paper: necam-w2tsu7 Abstract The hookworm Necator americanus is the predominant soil-transmitted human parasite. Adult worms feed on blood in the small intestine, causing iron-deficiency anemia, malnutrition, growth and development stunting in children, and severe morbidity and mortality during pregnancy in women. We report sequencing and assembly of the N. americanus genome (244 Mb, 19,151 genes). Characterization of this first hookworm genome sequence identified genes orchestrating the hookworm's invasion of the human host, genes involved in blood feeding and development, and genes encoding proteins that represent new potential drug targets against hookworms. N. americanus has undergone a considerable and unique expansion of immunomodulator proteins, some of which we highlight as potential treatments against inflammatory diseases. We also used a protein microarray to demonstrate a postgenomic application of the hookworm genome sequence. This genome provides an invaluable resource to boost ongoing efforts toward fundamental and applied postgenomic research, including the development of new methods to control hookworm and human immunological diseases. Title: Elephant shark genome provides unique insights into gnathostome evolution Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y and Warren WC <23 more author(s)> Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC (- 23) Ref: Nature, 505:174, 2014 : PubMed ESTHER: Venkatesh_2014_Nature_505_174 PubMedSearch: Venkatesh 2014 Nature 505 174 PubMedID: 24402279 Gene_locus related to this paper: calmi-ACHE, calmi-v9kt48, calmi-v9kmb8, calmi-v9kbr4, calmi-v9kn25, calmi-v9l873, calmi-v9kkm2, calmi-v9ku67, calmi-v9ki62, calmi-v9l0a5, calmi-v9kuk3, calmi-v9kdh1, calmi-v9kas4, calmi-v9keu1, calmi-v9kj52, calmi-v9kre8, calmi-v9ki07, calmi-v9kmn7, calmi-a0a4w3h3v0, calmi-a0a4w3hel5 Abstract The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the 'living fossil' coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity. Title: The duck genome and transcriptome provide insight into an avian influenza virus reservoir species Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y and Li N <40 more author(s)> Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim KW, Sheng Z, An Y, Searle S, Herrero J, Groenen MA, Crooijmans RP, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RH, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N (- 40) Ref: Nat Genet, 45:776, 2013 : PubMed ESTHER: Huang_2013_Nat.Genet_45_776 PubMedSearch: Huang 2013 Nat.Genet 45 776 PubMedID: 23749191 Gene_locus related to this paper: anapl-BCHE, anapl-r0lw36, anapl-r0m5n4, anapl-thioe, anapl-u3iqr9, anapl-r0l4n7, anapl-u3j4v8, anapl-u3icy5, anapl-u3ivv9, anapl-u3j4g1, anapl-u3j4i2, anapl-u3j4v5, anapl-r0kv25, anapl-u3ild2, anapl-u3imh5, anapl-b6dzk9, anapl-u3imp7, anapl-u3i5h5, anapl-u3id17, anapl-r0m1y3, anapl-r0lhc4, anapl-r0ktn0, anapl-r0l8l1, anapl-r0lin6, anapl-r0jhf3 Abstract The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 virus. Further, we show how the duck's defense mechanisms against influenza infection have been optimized through the diversification of its beta-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses. Title: The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits Schartl M, Walter RB, Shen Y, Garcia T, Catchen J, Amores A, Braasch I, Chalopin D, Volff JN and Warren WC <9 more author(s)> Schartl M, Walter RB, Shen Y, Garcia T, Catchen J, Amores A, Braasch I, Chalopin D, Volff JN, Lesch KP, Bisazza A, Minx P, Hillier L, Wilson RK, Fuerstenberg S, Boore J, Searle S, Postlethwait JH, Warren WC (- 9) Ref: Nat Genet, 45:567, 2013 : PubMed ESTHER: Schartl_2013_Nat.Genet_45_567 PubMedSearch: Schartl 2013 Nat.Genet 45 567 PubMedID: 23542700 Gene_locus related to this paper: xipma-m4a796, xipma-a0a3b5r0c8, xipma-m3zmg6, xipma-m3zml4, xipma-m4a704, xipma-a0a3b5r3p5, xipma-a0a3b5rfa0, xipma-m3zns4, xipma-m4a5i1, xipma-m3zxe7, xipma-a0a3b5r7u3, xipma-m3zyp9, xipma-m4a7a2, xipma-m4a1z8, xipma-a0a3b5qbj2, xipma-m4azu0, xipma-a0a3b5q4l7 Abstract Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, X. maculatus, offers a unique model to better understand the molecular biology of such traits. We report here the sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps identified an unexpected evolutionary stability of chromosomes in fish, in contrast to in mammals. Genes associated with viviparity show signatures of positive selection, identifying new putative functional domains and rare cases of parallel evolution. We also find that genes implicated in cognition show an unexpectedly high rate of duplicate gene retention after the teleost genome duplication event, suggesting a hypothesis for the evolution of the behavioral complexity in fish, which exceeds that found in amphibians and reptiles. Title: Insights into hominid evolution from the gorilla genome sequence Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T and Durbin R <61 more author(s)> Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R (- 61) Ref: Nature, 483:169, 2012 : PubMed ESTHER: Scally_2012_Nature_483_169 PubMedSearch: Scally 2012 Nature 483 169 PubMedID: 22398555 Gene_locus related to this paper: gorgo-g3qfr8, gorgo-g3qgi3, gorgo-g3r1s1, gorgo-g3r9p9, gorgo-a0a2i2zrx6, gorgo-g3re16, gorgo-g3s122, gorgo-a0a2i2y3x8 Abstract Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. Title: A high-resolution map of human evolutionary constraint using 29 mammals Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G and Kellis M <76 more author(s)> Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M (- 76) Ref: Nature, 478:476, 2011 : PubMed ESTHER: Lindblad-Toh_2011_Nature_478_476 PubMedSearch: Lindblad-Toh 2011 Nature 478 476 PubMedID: 21993624 Gene_locus related to this paper: cavpo-1plip, cavpo-2plrp, cavpo-h0v1b7, cavpo-h0v5v8, cavpo-h0vj36, cavpo-lipli, rabit-1hlip, rabit-1plip, rabit-g1t6x7, rabit-LIPH, myolu-l7n1c2, myolu-g1pqd9, cavpo-h0uyz6, cavpo-h0vi56, rabit-g1tbj4, myolu-g1p5c0, rabit-g1sds3, rabit-g1sye0, cavpo-h0v0r2, cavpo-h0v7s5, rabit-g1sp43, myolu-g1p4p3, cavpo-h0vw09, rabit-g1ssu3, myolu-g1pds0, rabit-g1sic4, cavpo-h0v2c4, myolu-g1pg61, myolu-g1pnb1, myolu-g1pu06, myolu-g1qa15, myolu-g1qfu0, rabit-g1sn99, rabit-g1snq9, rabit-g1sns7, rabit-g1tuu8, rabit-g1tzq7, cavpo-h0v2i2, cavpo-h0v2j0, cavpo-h0vsf5, cavpo-a0a286x8d3, cavpo-a0a286xbr3, cavpo-a0a286y0i8, cavpo-a0a286y4p3, myolu-g1q2n9, cavpo-h0v1p4, myolu-g1pan8, myolu-g1paq0, myolu-g1par4, myolu-g1prn3, myolu-g1q3i0, myolu-g1q463, myolu-g1pat6, myolu-g1q859, rabit-g1sul9, rabit-g1sun0, rabit-g1sup0, myolu-l7n125, myolu-g1pan2, rabit-g1sxd0, cavpo-h0v8j4, rabit-d5fit0, rabit-g1tkr5, myolu-g1nty6, myolu-g1p1p3, cavpo-h0vdd5, myolu-g1pdp2, rabit-g1tmm5, cavpo-h0vhq3, myolu-g1nth4, cavpo-h0vqx6, rabit-g1tqr7, myolu-g1p1e9, cavpo-h0v8y6, rabit-g1skt3, myolu-g1nzg3, cavpo-h0v5z0, rabit-g1sgz5, myolu-g1pkg5, rabit-g1tmw5, rabit-g1t134, cavpo-a0a286x9v5, myolu-g1qc57, myolu-g1q061, rabit-g1tnp4, rabit-g1tyf7, cavpo-h0w2w1, rabit-g1ta36, cavpo-h0w342, myolu-g1q4e3, rabit-g1sqa1, cavpo-h0uxk7, myolu-g1p353, cavpo-h0vpm0, rabit-a0a5f9cru6, cavpo-a0a286xtc0 Abstract The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease. Title: The draft genome of the parasitic nematode Trichinella spiralis Mitreva M, Jasmer DP, Zarlenga DS, Wang Z, Abubucker S, Martin J, Taylor CM, Yin Y, Fulton L and Wilson RK <11 more author(s)> Mitreva M, Jasmer DP, Zarlenga DS, Wang Z, Abubucker S, Martin J, Taylor CM, Yin Y, Fulton L, Minx P, Yang SP, Warren WC, Fulton RS, Bhonagiri V, Zhang X, Hallsworth-Pepin K, Clifton SW, McCarter JP, Appleton J, Mardis ER, Wilson RK (- 11) Ref: Nat Genet, 43:228, 2011 : PubMed ESTHER: Mitreva_2011_Nat.Genet_43_228 PubMedSearch: Mitreva 2011 Nat.Genet 43 228 PubMedID: 21336279 Gene_locus related to this paper: trisp-ACHE1, trisp-e5ryh1, trisp-e5s2p1, trisp-e5s3s1, trisp-e5s5l6, trisp-e5s7y8, trisp-e5s8m6, trisp-e5s9j3, trisp-e5s254, trisp-e5s773, trisp-e5sav1, trisp-e5sbp4, trisp-e5sgg4, trisp-e5sgu8, trisp-e5snw0, trisp-e5sr61, trisp-e5ss42, trisp-e5sgh2, 9bila-a0a0v0tgw4.1, 9bila-a0a0v0tws5 Abstract Genome evolution studies for the phylum Nematoda have been limited by focusing on comparisons involving Caenorhabditis elegans. We report a draft genome sequence of Trichinella spiralis, a food-borne zoonotic parasite, which is the most common cause of human trichinellosis. This parasitic nematode is an extant member of a clade that diverged early in the evolution of the phylum, enabling identification of archetypical genes and molecular signatures exclusive to nematodes. We sequenced the 64-Mb nuclear genome, which is estimated to contain 15,808 protein-coding genes, at approximately 35-fold coverage using whole-genome shotgun and hierarchal map-assisted sequencing. Comparative genome analyses support intrachromosomal rearrangements across the phylum, disproportionate numbers of protein family deaths over births in parasitic compared to a non-parasitic nematode and a preponderance of gene-loss and -gain events in nematodes relative to Drosophila melanogaster. This genome sequence and the identified pan-phylum characteristics will contribute to genome evolution studies of Nematoda as well as strategies to combat global parasites of humans, food animals and crops. Title: The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E and Currie CR <39 more author(s)> Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Fave MJ, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Munoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ, Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR (- 39) Ref: PLoS Genet, 7:e1002007, 2011 : PubMed ESTHER: Suen_2011_PLoS.Genet_7_e1002007 PubMedSearch: Suen 2011 PLoS.Genet 7 e1002007 PubMedID: 21347285 Gene_locus related to this paper: acrec-f4w848, acrec-f4wah1, acrec-f4wai9, acrec-f4wda7, acrec-f4wfh7, acrec-f4wk54, acrec-f4wng2, acrec-f4wpb7, acrec-f4wpb8, acrec-f4wpb9, acrec-f4x2j7, acrec-f4x3l5, acrec-f4x6y6, acrec-f4x7w5, acrec-f4x7w6, acrec-f4x378, acrec-f4x808, attce-h9hc46, solin-e9ige7, attce-w4wts9, attce-w4x506, attce-w4vya2, attce-w4vyi5, attce-w4wib4, attce-w4wkj3, attce-w4x3s7, attce-w4x3u4, attce-w4wu92, attce-w4w1m9, attce-w4x2m8, attce-w4w776, attce-w4x1t1, attce-a0a158nl98, attce-a0a158nmi0, attce-a0a158nqx5, attce-a0a158nr47.2, attce-a0a158ns84, attce-a0a158nvq4, attce-a0a158nij4, attce-a0a158nhg2, attce-a0a158nhn7, attce-a0a158nbh6, attce-a0a158ne04, attce-a0a158nyf0 Abstract Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses. Title: The genome of the Western clawed frog Xenopus tropicalis Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S and Rokhsar DS <38 more author(s)> Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS (- 38) Ref: Science, 328:633, 2010 : PubMed ESTHER: Hellsten_2010_Science_328_633 PubMedSearch: Hellsten 2010 Science 328 633 PubMedID: 20431018 Gene_locus related to this paper: xenla-q6pcj9, xentr-a9umk0, xentr-abhdb, xentr-ACHE, xentr-b0bm77, xentr-b1h0y7, xentr-b2guc4, xentr-b7zt03, xentr-b7ztj4, xentr-BCHE1, xentr-BCHE2, xentr-cxest2, xentr-d2x2k4, xentr-d2x2k6, xentr-f6rff6, xentr-f6v0g3, xentr-f6v2j6, xentr-f6v3z1, xentr-f6y4c8, xentr-f6yve5, xentr-f7a4y9, xentr-f7acc5, xentr-f7e2e2, xentr-LOC394897, xentr-ndrg1, xentr-q0vfb6, xentr-f7cpl7, xentr-f6yj44, xentr-f7ejk4, xentr-f6q8j8, xentr-f6z8f0, xentr-f7d709, xentr-b0bmb8, xentr-f7af63, xentr-a0a1b8y2w9, xentr-f7d4k9, xentr-f6r032, xentr-f6yvq3, xentr-a0a1b8y2z3, xentr-f7afg4, xentr-f6xb15, xentr-f7e1r2, xentr-a4ihf1, xentr-f7eue5, xentr-f6u7u3, xentr-f172a, xentr-f7equ8, xentr-f7dd89, xentr-a9jtx5 Abstract The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage. Title: A catalog of reference genomes from the human microbiome Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E and Zhu D <73 more author(s)> Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, Fitzgerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D (- 73) Ref: Science, 328:994, 2010 : PubMed ESTHER: Nelson_2010_Science_328_994 PubMedSearch: Nelson 2010 Science 328 994 PubMedID: 20489017 Gene_locus related to this paper: strp2-q04l35, strpn-AXE1, strpn-pepx Abstract The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented. Title: The genome of a songbird Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ and Wilson RK <72 more author(s)> Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK (- 72) Ref: Nature, 464:757, 2010 : PubMed ESTHER: Warren_2010_Nature_464_757 PubMedSearch: Warren 2010 Nature 464 757 PubMedID: 20360741 Gene_locus related to this paper: taegu-b5fyu7, taegu-BCHE, taegu-h0z4h9, taegu-h0z9w8, taegu-h0zat6, taegu-h0ze48, taegu-h0zha8, taegu-h0zkr8, taegu-h0zqp3, taegu-h0zz82, taegu-h0zqs1, taegu-h0yy64, taegu-h0yv40, taegu-h0yyt1, taegu-h0zcc8, taegu-h0z3k5, taegu-h0yw95, taegu-h0zkm7, taegu-h1a198, taegu-h0z6w2, taegu-h0zl93, taegu-h0zt33, taegu-h0yp71, taegu-h0ypu5, taegu-h1a048, taegu-h0ztq1, fical-u3kau2, 9pass-a0a093qu66, taegu-h0z7g0, fical-u3jnn0, taegu-h0zb80, taegu-h0zb89, taegu-h0z994, taegu-h0ztj6 Abstract The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour. Title: Genome analysis of the platypus reveals unique signatures of evolution Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L and Wilson RK <94 more author(s)> Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK (- 94) Ref: Nature, 453:175, 2008 : PubMed ESTHER: Warren_2008_Nature_453_175 PubMedSearch: Warren 2008 Nature 453 175 PubMedID: 18464734 Gene_locus related to this paper: ornan-f6s0q0, ornan-f6ty74, ornan-f6u2k2, ornan-f6uve1, ornan-f6vpb6, ornan-f6ybp3, ornan-f7bgu8, ornan-f7ct41, ornan-f7cza1, ornan-f7ejp8, ornan-f7exu1, ornan-f7f392, ornan-f7f9y6, ornan-f6ve87, ornan-f7f1d9, ornan-f6z3l1, ornan-f6r3f9, ornan-f6r3g8, ornan-f6vs71, ornan-f7g4v8 Abstract We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation. Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K and Wilson RK <111 more author(s)> Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, Van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK (- 111) Ref: Nature, 434:724, 2005 : PubMed ESTHER: Hillier_2005_Nature_434_724 PubMedSearch: Hillier 2005 Nature 434 724 PubMedID: 15815621 Gene_locus related to this paper: human-ABHD1, human-LDAH, human-ABHD18, human-KANSL3, human-PGAP1, human-PREPL Abstract Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions. | |||||||
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