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1.  Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface 
Genome Biology  2016;17:227.
Background
Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.
Results
The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates.
Conclusions
Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-016-1088-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-016-1088-8
PMCID: PMC5105290  PMID: 27832824
Chemoperception; Detoxification; Glycoside hydrolase; Horizontal gene transfer; Phytophagy; Xylophagy
2.  Early cave art and ancient DNA record the origin of European bison 
Nature Communications  2016;7:13158.
The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).
The ancestry of the European bison (wisent) remains a mystery. Here, Cooper and colleagues examine ancient DNA from fossil remains of extinct bison, and reveal the wisent originated through the hybridization of the extinct Steppe bison and ancestors of modern cattle.
doi:10.1038/ncomms13158
PMCID: PMC5071849  PMID: 27754477
3.  The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species 
Genome Biology  2016;17:192.
Background
The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control.
Results
The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT.
Conclusions
The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-016-1049-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-016-1049-2
PMCID: PMC5034548  PMID: 27659211
Medfly genome; Tephritid genomics; Insect orthology; Gene family evolution; Chromosomal synteny; Insect invasiveness; Insect adaptation; Medfly integrated pest management (IPM)
4.  Unique features of a global human ectoparasite identified through sequencing of the bed bug genome 
Benoit, Joshua B. | Adelman, Zach N. | Reinhardt, Klaus | Dolan, Amanda | Poelchau, Monica | Jennings, Emily C. | Szuter, Elise M. | Hagan, Richard W. | Gujar, Hemant | Shukla, Jayendra Nath | Zhu, Fang | Mohan, M. | Nelson, David R. | Rosendale, Andrew J. | Derst, Christian | Resnik, Valentina | Wernig, Sebastian | Menegazzi, Pamela | Wegener, Christian | Peschel, Nicolai | Hendershot, Jacob M. | Blenau, Wolfgang | Predel, Reinhard | Johnston, Paul R. | Ioannidis, Panagiotis | Waterhouse, Robert M. | Nauen, Ralf | Schorn, Corinna | Ott, Mark-Christoph | Maiwald, Frank | Johnston, J. Spencer | Gondhalekar, Ameya D. | Scharf, Michael E. | Peterson, Brittany F. | Raje, Kapil R. | Hottel, Benjamin A. | Armisén, David | Johan Crumière, Antonin Jean | Refki, Peter Nagui | Santos, Maria Emilia | Sghaier, Essia | Viala, Sèverine | Khila, Abderrahman | Ahn, Seung-Joon | Childers, Christopher | Lee, Chien-Yueh | Lin, Han | Hughes, Daniel S. T. | Duncan, Elizabeth J. | Murali, Shwetha C. | Qu, Jiaxin | Dugan, Shannon | Lee, Sandra L. | Chao, Hsu | Dinh, Huyen | Han, Yi | Doddapaneni, Harshavardhan | Worley, Kim C. | Muzny, Donna M. | Wheeler, David | Panfilio, Kristen A. | Vargas Jentzsch, Iris M. | Vargo, Edward L. | Booth, Warren | Friedrich, Markus | Weirauch, Matthew T. | Anderson, Michelle A. E. | Jones, Jeffery W. | Mittapalli, Omprakash | Zhao, Chaoyang | Zhou, Jing-Jiang | Evans, Jay D. | Attardo, Geoffrey M. | Robertson, Hugh M. | Zdobnov, Evgeny M. | Ribeiro, Jose M. C. | Gibbs, Richard A. | Werren, John H. | Palli, Subba R. | Schal, Coby | Richards, Stephen
Nature communications  2016;7:10165.
The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the last two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
doi:10.1038/ncomms10165
PMCID: PMC4740739  PMID: 26836814
5.  Genomics of Natural Populations: How Differentially Expressed Genes Shape the Evolution of Chromosomal Inversions in Drosophila pseudoobscura 
Genetics  2016;204(1):287-301.
Chromosomal rearrangements can shape the structure of genetic variation in the genome directly through alteration of genes at breakpoints or indirectly by holding combinations of genetic variants together due to reduced recombination. The third chromosome of Drosophila pseudoobscura is a model system to test hypotheses about how rearrangements are established in populations because its third chromosome is polymorphic for >30 gene arrangements that were generated by a series of overlapping inversion mutations. Circumstantial evidence has suggested that these gene arrangements are selected. Despite the expected homogenizing effects of extensive gene flow, the frequencies of arrangements form gradients or clines in nature, which have been stable since the system was first described >80 years ago. Furthermore, multiple arrangements exist at appreciable frequencies across several ecological niches providing the opportunity for heterokaryotypes to form. In this study, we tested whether genes are differentially expressed among chromosome arrangements in first instar larvae, adult females and males. In addition, we asked whether transcriptional patterns in heterokaryotypes are dominant, semidominant, overdominant, or underdominant. We find evidence for a significant abundance of differentially expressed genes across the inverted regions of the third chromosome, including an enrichment of genes involved in sensory perception for males. We find the majority of loci show additivity in heterokaryotypes. Our results suggest that multiple genes have expression differences among arrangements that were either captured by the original inversion mutation or accumulated after it reached polymorphic frequencies, providing a potential source of genetic variation for selection to act upon. These data suggest that the inversions are favored because of their indirect effect of recombination suppression that has held different combinations of differentially expressed genes together in the various gene arrangement backgrounds.
doi:10.1534/genetics.116.191429
PMCID: PMC5012393  PMID: 27401754
gene expression; inversions; expression inheritance; adaptation
6.  It’s More Than Stamp Collecting: How Genome Sequencing Can Unify Biological Research 
Trends in genetics : TIG  2015;31(7):411-421.
The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, whilst the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to “Big Science” survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need.
doi:10.1016/j.tig.2015.04.007
PMCID: PMC4490122  PMID: 26003218
7.  Genomic Signatures of Cooperation and Conflict in the Social Amoeba 
Current biology : CB  2015;25(12):1661-1665.
Summary
Cooperative systems are susceptible to invasion by selfish individuals that profit from receiving the social benefits but fail to contribute. These so-called “cheaters” can have a fitness advantage in the laboratory, but it is unclear whether cheating provides an important selective advantage in nature. We used a population genomic approach to examine the history of genes involved in cheating behaviors in the social amoeba Dictyostelium discoideum, testing whether these genes experience rapid evolutionary change as a result of conflict over spore-stalk fate. Candidate genes and surrounding regions showed elevated polymorphism, unusual patterns of linkage disequilibrium, and lower levels of population differentiation, but they did not show greater between-species divergence. The signatures were most consistent with frequency-dependent selection acting to maintain multiple alleles, suggesting that conflict may lead to stalemate rather than an escalating arms race. Our results reveal the evolutionary dynamics of cooperation and cheating and underscore how sequence-based approaches can be used to elucidate the history of conflicts that are difficult to observe directly.
doi:10.1016/j.cub.2015.04.059
PMCID: PMC4591038  PMID: 26051890
8.  Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts 
Genome Biology and Evolution  2016;8(5):1526-1542.
Wolbachia pipientis are obligate intracellular bacteria commonly found in many arthropods. They can induce various reproductive alterations in hosts, including cytoplasmic incompatibility, male-killing, feminization, and parthenogenetic development, and can provide host protection against some viruses and other pathogens. Wolbachia differ from many other primary endosymbionts in arthropods because they undergo frequent horizontal transmission between hosts and are well known for an abundance of mobile elements and relatively high recombination rates. Here, we compare the genomes of two closely related Wolbachia (with 0.57% genome-wide synonymous divergence) that differ in their reproductive effects on hosts. wVitA induces a sperm–egg incompatibility (also known as cytoplasmic incompatibility) in the parasitoid insect Nasonia vitripennis, whereas wUni causes parthenogenetic development in a different parasitoid, Muscidifurax uniraptor. Although these bacteria are closely related, the genomic comparison reveals rampant rearrangements, protein truncations (particularly in proteins predicted to be secreted), and elevated substitution rates. These changes occur predominantly in the wUni lineage, and may be due in part to adaptations by wUni to a new host environment, or its phenotypic shift to parthenogenesis induction. However, we conclude that the approximately 8-fold elevated synonymous substitution rate in wUni is due to a either an elevated mutation rate or a greater number of generations per year in wUni, which occurs in semitropical host species. We identify a set of genes whose loss or pseudogenization in the wUni lineage implicates them in the phenotypic shift from cytoplasmic incompatibility to parthenogenesis induction. Finally, comparison of these closely related strains allows us to determine the fine-scale mutation patterns in Wolbachia. Although Wolbachia are AT rich, mutation probabilities estimated from 4-fold degenerate sites are not AT biased, and predict an equilibrium AT content much less biased than observed (57–50% AT predicted vs. 76% current content at degenerate sites genome wide). The contrast suggests selection for increased AT content within Wolbachia genomes.
doi:10.1093/gbe/evw096
PMCID: PMC4898810  PMID: 27189996
endosymbiont; reproductive manipulation; mutational bias
9.  Metformin and patients on dialysis 
Australian Prescriber  2016;39(3):74-75.
doi:10.18773/austprescr.2016.041
PMCID: PMC4919177  PMID: 27345523
diabetes mellitus; haemodialysis; kidney disease; metformin
10.  Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont 
G3: Genes|Genomes|Genetics  2016;6(7):2113-2123.
Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum. The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain.
doi:10.1534/g3.116.028449
PMCID: PMC4938664  PMID: 27194801
Trichogramma; gene truncations; symbiosis; genome content; Rickettsiales
11.  Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas 
Science Advances  2016;2(4):e1501385.
Native American population history is reexamined using a large data set of pre-Columbian mitochondrial genomes.
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
doi:10.1126/sciadv.1501385
PMCID: PMC4820370  PMID: 27051878
Ancient DNA; Native America; colonization; Beringia
12.  Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution 
Genome Biology and Evolution  2016;8(6):1762-1775.
Metaseiulus occidentalis is an eyeless phytoseiid predatory mite employed for the biological control of agricultural pests including spider mites. Despite appearances, these predator and prey mites are separated by some 400 Myr of evolution and radically different lifestyles. We present a 152-Mb draft assembly of the M. occidentalis genome: Larger than that of its favored prey, Tetranychus urticae, but considerably smaller than those of many other chelicerates, enabling an extremely contiguous and complete assembly to be built—the best arachnid to date. Aided by transcriptome data, genome annotation cataloged 18,338 protein-coding genes and identified large numbers of Helitron transposable elements. Comparisons with other arthropods revealed a particularly dynamic and turbulent genomic evolutionary history. Its genes exhibit elevated molecular evolution, with strikingly high numbers of intron gains and losses, in stark contrast to the deer tick Ixodes scapularis. Uniquely among examined arthropods, this predatory mite’s Hox genes are completely atomized, dispersed across the genome, and it encodes five copies of the normally single-copy RNA processing Dicer-2 gene. Examining gene families linked to characteristic biological traits of this tiny predator provides initial insights into processes of sex determination, development, immune defense, and how it detects, disables, and digests its prey. As the first reference genome for the Phytoseiidae, and for any species with the rare sex determination system of parahaploidy, the genome of the western orchard predatory mite improves genomic sampling of chelicerates and provides invaluable new resources for functional genomic analyses of this family of agriculturally important mites.
doi:10.1093/gbe/evw048
PMCID: PMC4943173  PMID: 26951779
Metaseiulus Typhlodromus Galendromus occidentalis; western orchard predatory mite; genome assembly; Helitron rolling-circle transposons; parahaploid sex determination; Dicer-2 gene duplication
13.  The Knight and the King: two new species of giant bent-toed gecko (Cyrtodactylus, Gekkonidae, Squamata) from northern New Guinea, with comments on endemism in the North Papuan Mountains 
ZooKeys  2016;105-130.
The diverse biota of New Guinea includes many nominally widespread species that actually comprise multiple deeply divergent lineages with more localised histories of evolution. Here we investigate the systematics of the very large geckos of the Cyrtodactylus novaeguineae complex using molecular and morphological data. These data reveal two widespread and divergent lineages that can be distinguished from each other, and from type material of Cyrtodactylus novaeguineae, by aspects of size, build, coloration and male scalation. On the basis of these differences we describe two new species. Both have wide distributions that overlap extensively in the foothill forests of the North Papuan Mountains, however one is seemingly restricted to hill and lower montane forests on the ranges themselves, while the other is more widespread throughout the surrounding lowlands. The taxon endemic to the North Papuan Mountains is related to an apparently lowland form currently known only from Waigeo and Batanta Island far to the west – hinting at a history on island arcs that accreted to form the North Papuan Mountains.
doi:10.3897/zookeys.562.6052
PMCID: PMC4768470  PMID: 27006624
Arc accretion; Endemism; Indonesia; lizard; orogeny; Papua New Guinea; Papua Province; Sepik Basin
14.  Unique features of a global human ectoparasite identified through sequencing of the bed bug genome 
Benoit, Joshua B. | Adelman, Zach N. | Reinhardt, Klaus | Dolan, Amanda | Poelchau, Monica | Jennings, Emily C. | Szuter, Elise M. | Hagan, Richard W. | Gujar, Hemant | Shukla, Jayendra Nath | Zhu, Fang | Mohan, M. | Nelson, David R. | Rosendale, Andrew J. | Derst, Christian | Resnik, Valentina | Wernig, Sebastian | Menegazzi, Pamela | Wegener, Christian | Peschel, Nicolai | Hendershot, Jacob M. | Blenau, Wolfgang | Predel, Reinhard | Johnston, Paul R. | Ioannidis, Panagiotis | Waterhouse, Robert M. | Nauen, Ralf | Schorn, Corinna | Ott, Mark-Christoph | Maiwald, Frank | Johnston, J. Spencer | Gondhalekar, Ameya D. | Scharf, Michael E. | Peterson, Brittany F. | Raje, Kapil R. | Hottel, Benjamin A. | Armisén, David | Crumière, Antonin Jean Johan | Refki, Peter Nagui | Santos, Maria Emilia | Sghaier, Essia | Viala, Sèverine | Khila, Abderrahman | Ahn, Seung-Joon | Childers, Christopher | Lee, Chien-Yueh | Lin, Han | Hughes, Daniel S. T. | Duncan, Elizabeth J. | Murali, Shwetha C. | Qu, Jiaxin | Dugan, Shannon | Lee, Sandra L. | Chao, Hsu | Dinh, Huyen | Han, Yi | Doddapaneni, Harshavardhan | Worley, Kim C. | Muzny, Donna M. | Wheeler, David | Panfilio, Kristen A. | Vargas Jentzsch, Iris M. | Vargo, Edward L. | Booth, Warren | Friedrich, Markus | Weirauch, Matthew T. | Anderson, Michelle A. E. | Jones, Jeffery W. | Mittapalli, Omprakash | Zhao, Chaoyang | Zhou, Jing-Jiang | Evans, Jay D. | Attardo, Geoffrey M. | Robertson, Hugh M. | Zdobnov, Evgeny M. | Ribeiro, Jose M. C. | Gibbs, Richard A. | Werren, John H. | Palli, Subba R. | Schal, Coby | Richards, Stephen
Nature Communications  2016;7:10165.
The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
The bed bug, Cimex lectularius, is a ubiquitous human ectoparasite with global distribution. Here, the authors sequence the genome of the bed bug and identify reductions in chemosensory genes, expansion of genes associated with blood digestion and genes linked to pesticide resistance.
doi:10.1038/ncomms10165
PMCID: PMC4740739  PMID: 26836814
15.  Best Practices in Insect Genome Sequencing: What Works and What Doesn’t 
The last decade of decreasing DNA sequencing costs and proliferating sequencing services in core labs and companies has brought the de-novo genome sequencing and assembly of insect species within reach for many entomologists. However, sequence production alone is not enough to generate a high quality reference genome, and in many cases, poor planning can lead to extremely fragmented genome assemblies preventing high quality gene annotation and other desired analyses. Insect genomes can be problematic to assemble, due to combinations of high polymorphism, inability to breed for genome homozygocity, and small physical sizes limiting the quantity of DNA able to be isolated from a single individual. Recent advances in sequencing technology and assembly strategies are enabling a revolution for insect genome reference sequencing and assembly. Here we review historical and new genome sequencing and assembly strategies, with a particular focus on their application to arthropod genomes. We highlight both the need to design sequencing strategies for the requirements of the assembly software, and new long-read technologies that are enabling a return to traditional assembly approaches. Finally, we compare and contrast very cost effective short read draft genome strategies with the long read approaches that although entailing additional cost, bring a higher likelihood of success and the possibility of archival assembly qualities approaching that of finished genomes.
doi:10.1016/j.cois.2015.02.013
PMCID: PMC4465116  PMID: 26085980
16.  Hemichordate genomes and deuterostome origins 
Nature  2015;527(7579):459-465.
Acorn worms, also known as enteropneust (literally, ‘gut-breathing’) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal ‘gill’ slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.
doi:10.1038/nature16150
PMCID: PMC4729200  PMID: 26580012
17.  Does estrogen deficiency cause lacrimal gland inflammation and aqueous-deficient dry eye in mice? 
Experimental eye research  2014;127:153-160.
Researchers have proposed that estrogen deficiency will lead to a Sjögren's syndrome (SjS)-like lacrimal gland inflammation, aqueous tear deficiency and dry eye. The purpose of this study was to determine whether this proposal is correct. Lacrimal glands were obtained from adult, age-matched wild type (WT) and aromatase knockout (ArKO) mice, in which estrogen synthesis is completely eliminated. Tissues were also obtained from autoimmune MRL/Mp-lpr/lpr (MRL/lpr) mice as inflammation controls. Tear volumes in WT and ArKO mice were measured and glands were processed for molecular biological and histological evaluation. Our results demonstrate that estrogen absence does not lead to a SjS-like inflammation in lacrimal tissue or to an aqueous-deficient dry eye. There was no upregulation of genes associated with inflammatory pathways in lacrimal glands of male or female ArKO mice. Such inflammatory activity was prominent in autoimmune MRL/lpr tissues. We also found no evidence of inflammation in lacrimal gland tissue sections of estrogen-deficient mice, and tear volumes of ArKO males were actually increased as compared to those WT controls. Interestingly, our study did show that estrogen absence influences the expression of thousands of lacrimal gland genes, and that this impact is sex- and genotype-specific. Our findings demonstrate that estrogen absence is not a risk factor for the development of SjS-like lacrimal gland inflammation or for aqueous-deficient dry eye in mice.
doi:10.1016/j.exer.2014.07.017
PMCID: PMC4175142  PMID: 25084452
lacrimal gland; mice; estrogen; male; female; sex difference; inflammation; tear volume; gene expression
18.  Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature 
Cell Reports  2015;12(5):821-836.
Summary
Acute myeloid leukemia (AML) is characterized by recurrent mutations that affect the epigenetic regulatory machinery and signaling molecules, leading to a block in hematopoietic differentiation. Constitutive signaling from mutated growth factor receptors is a major driver of leukemic growth, but how aberrant signaling affects the epigenome in AML is less understood. Furthermore, AML cells undergo extensive clonal evolution, and the mutations in signaling genes are often secondary events. To elucidate how chronic growth factor signaling alters the transcriptional network in AML, we performed a system-wide multi-omics study of primary cells from patients suffering from AML with internal tandem duplications in the FLT3 transmembrane domain (FLT3-ITD). This strategy revealed cooperation between the MAP kinase (MAPK) inducible transcription factor AP-1 and RUNX1 as a major driver of a common, FLT3-ITD-specific gene expression and chromatin signature, demonstrating a major impact of MAPK signaling pathways in shaping the epigenome of FLT3-ITD AML.
Graphical Abstract
Highlights
•FLT3-ITD signaling is associated with a common gene expression signature•FLT3-ITD-specific gene expression is associated with a common chromatin signature•FLT3-ITD AML displays chronic activation of the inducible transcription factor AP-1•AP-1 cooperates with RUNX1 to shape the epigenome of FLT3-ITD AML
Cauchy et al. identify a specific gene expression and regulatory signature associated with aberrant signaling in acute myeloid leukemia with FLT3-ITD mutations. In FLT3-ITD AML, the inducible transcription factor AP-1 is chronically activated and cooperates with RUNX1, shaping the epigenome to transactivate specific target genes.
doi:10.1016/j.celrep.2015.06.069
PMCID: PMC4726916  PMID: 26212328
19.  Enhancement of insulin-mediated rat muscle glucose uptake and microvascular perfusion by 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside 
Background
Insulin-induced microvascular recruitment is important for optimal muscle glucose uptake. 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR, an activator of AMP-activated protein kinase), can also induce microvascular recruitment, at doses that do not acutely activate glucose transport in rat muscle. Whether low doses of AICAR can augment physiologic insulin action is unknown. In the present study we used the euglycemic hyperinsulinemic clamp to assess whether insulin action is augmented by low dose AICAR.
Methods
Anesthetized rats were studied during saline infusion or euglycemic insulin (3 mU/kg/min) clamp for 2 h in the absence or presence of AICAR for the last hour (5 mg bolus followed by 3.75 mg/kg/min). Muscle glucose uptake (R’g) was determined radioisotopically with 14C-2-deoxyglucose and muscle microvascular perfusion by contrast-enhanced ultrasound with microbubbles.
Results
AICAR did not affect blood glucose, or lower leg R’g, although it significantly (p < 0.05) increased blood lactate levels and augmented muscle microvascular blood volume via a nitric oxide synthase dependent pathway. Insulin increased femoral blood flow, whole body glucose infusion rate (GIR), R’g, hindleg glucose uptake, and microvascular blood volume. Addition of AICAR during insulin infusion increased lactate production, further increased R’g in Type IIA (fast twitch oxidative) and IIB (fast twitch glycolytic) fiber containing muscles, and hindleg glucose uptake, but decreased R’g in the Type I (slow twitch oxidative) fiber muscle. AICAR also decreased GIR due to inhibition of insulin-mediated suppression of hepatic glucose output. AICAR augmented insulin-mediated microvascular perfusion.
Conclusions
AICAR, at levels that have no direct effect on muscle glucose uptake, augments insulin-mediated microvascular blood flow and glucose uptake in white fiber type muscles. Agents targeted to endothelial AMPK activation are promising insulin sensitizers, however, the decrease in GIR and the propensity to increase blood lactate cautions against AICAR as an acute insulin sensitizer.
doi:10.1186/s12933-015-0251-y
PMCID: PMC4509722  PMID: 26194188
Muscle; Insulin; Glucose; Microcirculation; Microbubbles
20.  Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions 
Nature Communications  2015;6:7344.
Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.
Lucilia cuprina is a parasitic blowfly of major economic importance worldwide that feeds on the tissues of animals such as sheep. Here, the authors sequence the genome of L. cuprina and provide insights into the fly's molecular biology, interactions with the host animal and insecticide resistance.
doi:10.1038/ncomms8344
PMCID: PMC4491171  PMID: 26108605
21.  A Re-Appraisal of the Early Andean Human Remains from Lauricocha in Peru 
PLoS ONE  2015;10(6):e0127141.
The discovery of human remains from the Lauricocha cave in the Central Andean highlands in the 1960’s provided the first direct evidence for human presence in the high altitude Andes. The skeletons found at this site were ascribed to the Early to Middle Holocene and represented the oldest known population of Western South America, and thus were used in several studies addressing the early population history of the continent. However, later excavations at Lauricocha led to doubts regarding the antiquity of the site. Here, we provide new dating, craniometric, and genetic evidence for this iconic site. We obtained new radiocarbon dates, generated complete mitochondrial genomes and nuclear SNP data from five individuals, and re-analyzed the human remains of Lauricocha to revise the initial morphological and craniometric analysis conducted in the 1960’s. We show that Lauricocha was indeed occupied in the Early to Middle Holocene but the temporal spread of dates we obtained from the human remains show that they do not qualify as a single contemporaneous population. However, the genetic results from five of the individuals fall within the spectrum of genetic diversity observed in pre-Columbian and modern Native Central American populations.
doi:10.1371/journal.pone.0127141
PMCID: PMC4464891  PMID: 26061688
22.  The genomes of two key bumblebee species with primitive eusocial organization 
Sadd, Ben M | Barribeau, Seth M | Bloch, Guy | de Graaf, Dirk C | Dearden, Peter | Elsik, Christine G | Gadau, Jürgen | Grimmelikhuijzen, Cornelis JP | Hasselmann, Martin | Lozier, Jeffrey D | Robertson, Hugh M | Smagghe, Guy | Stolle, Eckart | Van Vaerenbergh, Matthias | Waterhouse, Robert M | Bornberg-Bauer, Erich | Klasberg, Steffen | Bennett, Anna K | Câmara, Francisco | Guigó, Roderic | Hoff, Katharina | Mariotti, Marco | Munoz-Torres, Monica | Murphy, Terence | Santesmasses, Didac | Amdam, Gro V | Beckers, Matthew | Beye, Martin | Biewer, Matthias | Bitondi, Márcia MG | Blaxter, Mark L | Bourke, Andrew FG | Brown, Mark JF | Buechel, Severine D | Cameron, Rossanah | Cappelle, Kaat | Carolan, James C | Christiaens, Olivier | Ciborowski, Kate L | Clarke, David F | Colgan, Thomas J | Collins, David H | Cridge, Andrew G | Dalmay, Tamas | Dreier, Stephanie | du Plessis, Louis | Duncan, Elizabeth | Erler, Silvio | Evans, Jay | Falcon, Tiago | Flores, Kevin | Freitas, Flávia CP | Fuchikawa, Taro | Gempe, Tanja | Hartfelder, Klaus | Hauser, Frank | Helbing, Sophie | Humann, Fernanda C | Irvine, Frano | Jermiin, Lars S | Johnson, Claire E | Johnson, Reed M | Jones, Andrew K | Kadowaki, Tatsuhiko | Kidner, Jonathan H | Koch, Vasco | Köhler, Arian | Kraus, F Bernhard | Lattorff, H Michael G | Leask, Megan | Lockett, Gabrielle A | Mallon, Eamonn B | Antonio, David S Marco | Marxer, Monika | Meeus, Ivan | Moritz, Robin FA | Nair, Ajay | Näpflin, Kathrin | Nissen, Inga | Niu, Jinzhi | Nunes, Francis MF | Oakeshott, John G | Osborne, Amy | Otte, Marianne | Pinheiro, Daniel G | Rossié, Nina | Rueppell, Olav | Santos, Carolina G | Schmid-Hempel, Regula | Schmitt, Björn D | Schulte, Christina | Simões, Zilá LP | Soares, Michelle PM | Swevers, Luc | Winnebeck, Eva C | Wolschin, Florian | Yu, Na | Zdobnov, Evgeny M | Aqrawi, Peshtewani K | Blankenburg, Kerstin P | Coyle, Marcus | Francisco, Liezl | Hernandez, Alvaro G | Holder, Michael | Hudson, Matthew E | Jackson, LaRonda | Jayaseelan, Joy | Joshi, Vandita | Kovar, Christie | Lee, Sandra L | Mata, Robert | Mathew, Tittu | Newsham, Irene F | Ngo, Robin | Okwuonu, Geoffrey | Pham, Christopher | Pu, Ling-Ling | Saada, Nehad | Santibanez, Jireh | Simmons, DeNard | Thornton, Rebecca | Venkat, Aarti | Walden, Kimberly KO | Wu, Yuan-Qing | Debyser, Griet | Devreese, Bart | Asher, Claire | Blommaert, Julie | Chipman, Ariel D | Chittka, Lars | Fouks, Bertrand | Liu, Jisheng | O’Neill, Meaghan P | Sumner, Seirian | Puiu, Daniela | Qu, Jiaxin | Salzberg, Steven L | Scherer, Steven E | Muzny, Donna M | Richards, Stephen | Robinson, Gene E | Gibbs, Richard A | Schmid-Hempel, Paul | Worley, Kim C
Genome Biology  2015;16(1):76.
Background
The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.
Results
We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.
Conclusions
These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0623-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-015-0623-3
PMCID: PMC4414376  PMID: 25908251
23.  Parallel Histories of Horizontal Gene Transfer Facilitated Extreme Reduction of Endosymbiont Genomes in Sap-Feeding Insects 
Molecular Biology and Evolution  2014;31(4):857-871.
Bacteria confined to intracellular environments experience extensive genome reduction. In extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. To understand the host’s role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid Pachypsylla venusta, a sap-feeding insect that harbors an ancient endosymbiont (Carsonella) with one of the most reduced bacterial genomes ever identified. Carsonella retains many genes required for synthesis of essential amino acids that are scarce in plant sap, but most of these biosynthetic pathways have been disrupted by gene loss. Host genes that are upregulated in psyllid cells housing Carsonella appear to compensate for endosymbiont gene losses, resulting in highly integrated metabolic pathways that mirror those observed in other sap-feeding insects. The host contribution to these pathways is mediated by a combination of native eukaryotic genes and bacterial genes that were horizontally transferred from multiple donor lineages early in the evolution of psyllids, including one gene that appears to have been directly acquired from Carsonella. By comparing the psyllid genome to a recent analysis of mealybugs, we found that a remarkably similar set of functional pathways have been shaped by independent transfers of bacterial genes to the two hosts. These results show that horizontal gene transfer is an important and recurring mechanism driving coevolution between insects and their bacterial endosymbionts and highlight interesting similarities and contrasts with the evolutionary history of mitochondria and plastids.
doi:10.1093/molbev/msu004
PMCID: PMC3969561  PMID: 24398322
amino acid biosynthesis; endosymbionts; lateral gene transfer; Pachypsylla venusta; psyllids
24.  AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome 
Insect molecular biology  2010;19(0 2):5-12.
AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.
doi:10.1111/j.1365-2583.2009.00930.x
PMCID: PMC4372297  PMID: 20482635
25.  A full-length cDNA resource for the pea aphid, Acyrthosiphon pisum 
Insect molecular biology  2010;19(0 2):23-31.
Large collections of full-length cDNAs are important resources for genome annotation and functional genomics. We report the creation of a collection of 50,599 full-length cDNA clones from the pea aphid, Acyrthosiphon pisum. Sequencing from 5’ and 3’ ends of the clones generated 97,828 high-quality expressed sequence tags (ESTs), representing approximately 9,000 genes. These sequences were imported to AphidBase and are shown to play crucial roles in both automatic gene prediction and manual annotation. Our detailed analyses demonstrated that the full-length cDNAs can further improve gene models and can even identify novel genes that are not included in the current version of the official gene set. This full-length cDNA collection can be utilized for a wide variety of functional studies, serving as a community resource for the study of the functional genomics of the pea aphid.
doi:10.1111/j.1365-2583.2009.00946.x
PMCID: PMC4370113  PMID: 20482637
full-length cDNA; aphid; functional genomics; EST analysis

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