Dataset Information

Analyses of pig genomes provide insight into porcine demography and evolution.

ABSTRACT: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

SUBMITTER: Groenen MA

PROVIDER: S-EPMC3566564 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature

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Analyses of pig genomes provide insight into porcine demography and evolution.

Groenen Martien A M MA Archibald Alan L AL Uenishi Hirohide H Tuggle Christopher K CK Takeuchi Yasuhiro Y Rothschild Max F MF Rogel-Gaillard Claire C Park Chankyu C Milan Denis D Megens Hendrik-Jan HJ Li Shengting S Larkin Denis M DM Kim Heebal H Frantz Laurent A F LA Caccamo Mario M Ahn Hyeonju H Aken Bronwen L BL Anselmo Anna A Anthon Christian C Auvil Loretta L Badaoui Bouabid B Beattie Craig W CW Bendixen Christian C Berman Daniel D Blecha Frank F Blomberg Jonas J Bolund Lars L Bosse Mirte M Botti Sara S Bujie Zhan Z Bystrom Megan M Capitanu Boris B Carvalho-Silva Denise D Chardon Patrick P Chen Celine C Cheng Ryan R Choi Sang-Haeng SH Chow William W Clark Richard C RC Clee Christopher C Crooijmans Richard P M A RP Dawson Harry D HD Dehais Patrice P De Sapio Fioravante F Dibbits Bert B Drou Nizar N Du Zhi-Qiang ZQ Eversole Kellye K Fadista João J Fadista João J Fairley Susan S Faraut Thomas T Faulkner Geoffrey J GJ Fowler Katie E KE Fredholm Merete M Fritz Eric E Gilbert James G R JG Giuffra Elisabetta E Gorodkin Jan J Griffin Darren K DK Harrow Jennifer L JL Hayward Alexander A Howe Kerstin K Hu Zhi-Liang ZL Humphray Sean J SJ Hunt Toby T Hornshøj Henrik H Jeon Jin-Tae JT Jern Patric P Jones Matthew M Jurka Jerzy J Kanamori Hiroyuki H Kapetanovic Ronan R Kim Jaebum J Kim Jae-Hwan JH Kim Kyu-Won KW Kim Tae-Hun TH Larson Greger G Lee Kyooyeol K Lee Kyung-Tai KT Leggett Richard R Lewin Harris A HA Li Yingrui Y Liu Wansheng W Loveland Jane E JE Lu Yao Y Lunney Joan K JK Ma Jian J Madsen Ole O Mann Katherine K Matthews Lucy L McLaren Stuart S Morozumi Takeya T Murtaugh Michael P MP Narayan Jitendra J Nguyen Dinh Truong DT Ni Peixiang P Oh Song-Jung SJ Onteru Suneel S Panitz Frank F Park Eung-Woo EW Park Hong-Seog HS Pascal Geraldine G Paudel Yogesh Y Perez-Enciso Miguel M Ramirez-Gonzalez Ricardo R Reecy James M JM Rodriguez-Zas Sandra S Rohrer Gary A GA Rund Lauretta L Sang Yongming Y Schachtschneider Kyle K Schraiber Joshua G JG Schwartz John J Scobie Linda L Scott Carol C Searle Stephen S Servin Bertrand B Southey Bruce R BR Sperber Goran G Stadler Peter P Sweedler Jonathan V JV Tafer Hakim H Thomsen Bo B Wali Rashmi R Wang Jian J Wang Jun J White Simon S Xu Xun X Yerle Martine M Zhang Guojie G Zhang Jianguo J Zhang Jie J Zhao Shuhong S Rogers Jane J Churcher Carol C Schook Lawrence B LB

Nature 20121101 7424

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between Eu ...[more]

PMID: 23151582

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Project description:Spiders are a highly diverse group of arthropods that occur in most habitats on land. Notably, spiders have significant ecological impact as predators because of their extraordinary prey capture adaptations, venom and silk. Spider venom is among the most heterogeneous animal venoms and has pharmacological applications, while spider silk is characterized by great toughness with potential for biomaterial application. We describe the genome sequences of two spiders representing two major taxonomic groups, the social velvet spider Stegodyphus mimosarum (Araneomorphae), and the Brazilian white-knee tarantula Acanthoscurria geniculata (Mygalomorphae). We annotate genes using a combination of transcriptomic and in-depth proteomic analyses. The genomes are large (2.6 Gb and 6 Gb, respectively) with short exons and long introns and approximately 50% repeats, reminiscent of typical mammalian genomes. Phylogenetic analyses show that spiders and ticks are sister groups outgrouped by mites, and phylogenetic dating using a molecular clock dates separation of velvet spider and tarantula at 270 my. Based on the genomes and proteomes, we characterize the genetic basis of venom and silk production of both species in detail. Venom protein composition differs markedly between the two spiders, with lipases as the most abundant protein in the velvet spider and present only at low concentration in tarantula. Venom in both spiders contains proteolytic enzymes, and our analyses suggest that these enzymes target and process precursor peptides that subsequently mediate the toxic effects of venom. Complete analysis of silk genes reveal a diverse suite of silk proteins in the velvet spider including novel types of spidroins, and dynamic evolution of major ampullate spidroin genes, whereas silk protein diversity in tarantula is far less complex. The difference in silk proteins between species is consistent with a more complex silk gland morpholgy and use of three-dimentional capture webs consisting of multiple silk types in aranomorph spiders.

Dataset Information

Analyses of pig genomes provide insight into porcine demography and evolution.

Publications

Analyses of pig genomes provide insight into porcine demography and evolution.

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