Draft genome of the red harvester ant Pogonomyrmex barbatus
Chris Smith,Christopher D. Smith,Hugh M. Robertson,Martin Helmkampf,Aleksey V. Zimin,Mark Yandell,Carson Holt,Hao Hu,Ehab Abouheif,Richard Benton,Elizabeth Cash,Vincent Croset,Cameron R. Currie,Eran Elhaik,Christine G. Elsik,Marie-Julie Favé,Vilaiwan M. Fernandes,Joshua D. Gibson,Dan Graur,Wulfila Gronenberg,Kirk J. Grubbs,Darren E. Hagen,Ana Sofia Ibarraran Viniegra,Brian R. Johnson,Reed M. Johnson,Abderrahman Khila,Jay W. Kim,Kaitlyn A. Mathis,Monica Munoz-Torres,Marguerite C. Murphy,Julie A. Mustard,Rin Nakamura,Oliver Niehuis,Surabhi Nigam,Rick P. Overson,Jennifer E. Placek,Rajendhran Rajakumar,Justin T. Reese,Garret Suen,Shu Tao,Candice W. Torres,Neil D. Tsutsui,Lumi Viljakainen,Florian Wolschin,Jürgen Gadau +44 more
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TLDR
Gene networks involved in generating key differences between the queen and worker castes show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor.Abstract:
We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.read more
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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.
TL;DR: MAKER2 is the first annotation engine specifically designed for second-generation genome projects, which scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality.
Journal ArticleDOI
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing
Doori Park,Je Won Jung,Beom-Soon Choi,Murukarthick Jayakodi,Jeong-Soo Lee,Jong-Sung Lim,Yeisoo Yu,Yong-Soo Choi,Myeong-Lyeol Lee,Yoonseong Park,Ik-Young Choi,Tae-Jin Yang,Owain R. Edwards,Gyoungju Nah,Hyung Wook Kwon +14 more
TL;DR: This first report of the whole genome sequence of A. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication, to contribute to a better understanding of the complex behaviors and natural biology of the Asian honey bee and to anticipate its future evolutionary trajectory.
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The monarch butterfly genome yields insights into long-distance migration
TL;DR: The monarch genome reveals a vertebrate-like opsin whose existence in insects is widespread; a full repertoire of molecular components for the monarch circadian clockwork; all members of the juvenile hormone biosynthetic pathway whose regulation shows unexpected sexual dimorphism; and a variant of the sodium/potassium pump that underlies a valuable chemical defense mechanism.
Journal ArticleDOI
Complementary Function and Integrated Wiring of the Evolutionarily Distinct Drosophila Olfactory Subsystems
Ana F. Silbering,Raphael Rytz,Yael Grosjean,Liliane Abuin,Pavan Ramdya,Gregory S.X.E. Jefferis,Richard Benton +6 more
TL;DR: Comprehensive comparative analysis of the Drosophila olfactory subsystems that express the ionotropic receptors (IRs) and odorant receptors (ORs) identifies ligands for most IR neuron classes, revealing their specificity for select amines and acids, which complements the broader tuning of ORs for esters and alcohols.
Journal ArticleDOI
Finding the missing honey bee genes: Lessons learned from a genome upgrade
Christine G. Elsik,Christine G. Elsik,Kim C. Worley,Anna K. Bennett,Martin Beye,Francisco Camara,Christopher P. Childers,Christopher P. Childers,Dirk C. de Graaf,Griet Debyser,Jixin Deng,Bart Devreese,Eran Elhaik,Jay D. Evans,Leonard J. Foster,Dan Graur,Roderic Guigó,Katharina J. Hoff,Michael Holder,Matthew E. Hudson,Greg J. Hunt,Huaiyang Jiang,Vandita Joshi,Radhika S. Khetani,Peter Kosarev,Christie Kovar,Jian Ma,Ryszard Maleszka,Robin F. A. Moritz,Monica Munoz-Torres,Monica Munoz-Torres,Terence Murphy,Donna M. Muzny,Irene Newsham,Justin T. Reese,Justin T. Reese,Hugh M. Robertson,Gene E. Robinson,Olav Rueppell,Victor V. Solovyev,Mario Stanke,Eckart Stolle,Jennifer M. Tsuruda,Matthias Van Vaerenbergh,Robert M. Waterhouse,Daniel B. Weaver,Charles W. Whitfield,Yuanqing Wu,Evgeny M. Zdobnov,Lan Zhang,Dianhui Zhu,Richard A. Gibbs +51 more
TL;DR: Improved honey bee genome assembly with a new gene annotation set and a number of genes similar to that of other insect genomes are reported, contrary to what was suggested in OGSv1.0.
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