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Author Report for: Pollock DD

Title: The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I and Richardson MK <26 more author(s)> Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wuster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson MK (- 26)
Ref: Proc Natl Acad Sci U S A, 110:20651, 2013 : PubMed
Abstract


ESTHER: Vonk_2013_Proc.Natl.Acad.Sci.U.S.A_110_20651
PubMedSearch: Vonk 2013 Proc.Natl.Acad.Sci.U.S.A 110 20651
PubMedID: 24297900
Gene_locus related to this paper: ophha-v8p7p1.1, ophha-v8p7p1.3, ophha-v8n6c3, ophha-v8p9v2, ophha-v8p8q1, ophha-v8p760, ophha-v8pg65, ophha-v8pgg0, ophha-v8p9z4.2, ophha-v8nra3, ophha-v8p430, ophha-v8pbf0.2

Abstract

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection.



        

Title: Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B and Ray DA <38 more author(s)> St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ, Jr., Glenn TC, Green RE, Ray DA (- 38)
Ref: Genome Biol, 13:415, 2012 : PubMed
Abstract


ESTHER: St John_2012_Genome.Biol_13_415
PubMedSearch: St John 2012 Genome.Biol 13 415
PubMedID: 22293439
Gene_locus related to this paper: allmi-a0a151m601, allmi-a0a151mg34, allmi-a0a151n729.1, allmi-a0a151n729.2, allmi-a0a151n730, allmi-a0a151n794, allmi-a0a151nb42, allmi-a0a151p739, allmi-a0a151pfy5, allmi-a0a151nxh1, allmi-a0a151mjy2, allmi-a0a151m1n2, allmi-a0a151m6e2, allmi-a0a151nb40, allmi-a0a151pim9, allmi-a0a151pip0, allmi-a0a151pit2, allmi-a0a151ma81, allmi-a0a151nut3.1, allmi-a0a151nut3.2, allmi-a0a151mdf3, allmi-a0a151mwf8, allmi-a0a151new6, allmi-a0a151nc84, allmi-a0a151n0a8, allmi-a0a151nq31, allmi-a0a151mdb6, allsi-a0a1u7s7j5, allsi-a0a1u7rvh6, allmi-a0a151ly27, allmi-a0a151phf3, allsi-a0a1u7rrg3, allsi-a0a1u8cvq6, allsi-a0a1u8cyp8, allsi-a0a1u7s8q9

Abstract

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.



        

Title: The genome of the green anole lizard and a comparative analysis with birds and mammals
Alfoldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE and Lindblad-Toh K <40 more author(s)> Alfoldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K (- 40)
Ref: Nature, 477:587, 2011 : PubMed
Abstract


ESTHER: Alfoldi_2011_Nature_477_587
PubMedSearch: Alfoldi 2011 Nature 477 587
PubMedID: 21881562
Gene_locus related to this paper: anoca-h9g670, anoca-h9g675, anoca-h9g680, anoca-h9gbf2, anoca-h9gl37, anoca-h9gq07, anoca-h9gqa2, anoca-h9gqv4, anoca-h9gr08, anoca-h9glr3, anoca-h9gfq0, anoca-h9gfy1, anoca-h9g7n4, anoca-h9gpa2, anoca-h9g3p8

Abstract

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.



        

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
Abstract


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 of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L and Lindblad-Toh K <52 more author(s)> Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, Vandeberg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K (- 52)
Ref: Nature, 447:167, 2007 : PubMed
Abstract


ESTHER: Mikkelsen_2007_Nature_447_167
PubMedSearch: Mikkelsen 2007 Nature 447 167
PubMedID: 17495919
Gene_locus related to this paper: mondo-ACHE, mondo-b2bsf5, mondo-b2bsz5, mondo-BCHE, mondo-d2x2i6, mondo-d2x2i8, mondo-f6slk2, mondo-f6wu00, mondo-f6wuf2, mondo-f6xfj4, mondo-f6yt13, mondo-f7c7p0, mondo-f7ckd0, mondo-f7cvq8, mondo-f7cvr5, mondo-f7eil6, mondo-f7ez13, mondo-f7f0i7, mondo-f7fg16, mondo-f7gcv7, mondo-f7gep4, mondo-f7gly2, mondo-f6u7q2, mondo-f7fw54, mondo-f7dpf6, mondo-f6pgj5, mondo-f6yg68, mondo-f7g8u4, mondo-f7eyv1, mondo-f6pq73, mondo-f7cre0, mondo-f7fdj0, mondo-f7fdj5, mondo-f7ft63, mondo-f7ge99, mondo-f7gea2, mondo-f6pxq2, mondo-f7awc1, mondo-f7c412, mondo-f7ev24, mondo-f7b6s6, mondo-f6vcx0, mondo-f7g148, mondo-f6tlv9, mondo-f6tdm5, mondo-f7f3w0, mondo-f7fg39, mondo-f7d6c2, mondo-f6sdn0, mondo-f7gi08, mondo-f6xss6, mondo-f6sa37, mondo-f7gd97, mondo-f6z6x9

Abstract

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.