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Genomic features of the damselfly calopteryx splendens representing a sister clade to most insect orders

Published on Jan 30, 2017in Genome Biology and Evolution3.73
· DOI :10.1093/gbe/evx006
Panagiotis Ioannidis13
Estimated H-index: 13
(Swiss Institute of Bioinformatics),
Felipe A. Simão8
Estimated H-index: 8
(Swiss Institute of Bioinformatics)
+ 6 AuthorsEvgeny M. Zdobnov55
Estimated H-index: 55
(Swiss Institute of Bioinformatics)
Cite
Abstract
Insects comprise the most diverse and successful animal group with over one million described species that are found in almost every terrestrial and limnic habitat, with many being used as important models in genetics, ecology, and evolutionary research. Genome sequencing projects have greatly expanded the sampling of species from many insect orders, but genomic resources for species of certain insect lineages have remained relatively limited to date. To address this paucity, we sequenced the genome of the banded demoiselle, Calopteryx splendens, a damselfly (Odonata: Zygoptera) belonging to Palaeoptera, the clade containing the first winged insects. The 1.6 Gbp C. splendens draft genome assembly is one of the largest insect genomes sequenced to date and encodes a predicted set of 22,523 protein-coding genes. Comparative genomic analyses with other sequenced insects identified a relatively small repertoire of C. splendens detoxification genes, which could explain its previously noted sensitivity to habitat pollution. Intriguingly, this repertoire includes a cytochrome P450 gene not previously described in any insect genome. The C. splendens immune gene repertoire appears relatively complete and features several genes encoding novel multi-domain peptidoglycan recognition proteins. Analysis of chemosensory genes revealed the presence of both gustatory and ionotropic receptors, as well as the insect odorant receptor coreceptor gene (OrCo) and at least four partner odorant receptors (ORs). This represents the oldest known instance of a complete OrCo/OR system in insects, and provides the molecular underpinning for odonate olfaction. The C. splendens genome improves the sampling of insect lineages that diverged before the radiation of Holometabola and offers new opportunities for molecular-level evolutionary, ecological, and behavioral studies.
  • References (99)
  • Citations (18)
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References99
Newest
Published on Sep 1, 2016in Scientific Reports4.01
Atsushi Kasai14
Estimated H-index: 14
,
Takehiko I. Hayashi1
Estimated H-index: 1
+ 3 AuthorsKoichi Goka21
Estimated H-index: 21
Several reports suggested that rice seedling nursery-box application of some systemic insecticides (neonicotinoids and fipronil) is the cause of the decline in dragonfly species noted since the 1990s in Japan. We conducted paddy mesocosm experiments to investigate the effect of the systemic insecticides clothianidin, fipronil and chlorantraniliprole on rice paddy field biological communities. Concentrations of all insecticides in the paddy water were reduced to the limit of detection within 3 mo...
Published on Aug 1, 2016in Journal of Insect Physiology2.86
Francesca Frati9
Estimated H-index: 9
(University of Perugia),
Silvana Piersanti10
Estimated H-index: 10
(University of Perugia)
+ 1 AuthorsGianandrea Salerno19
Estimated H-index: 19
(University of Perugia)
Abstract Selection for the oviposition site represents the criterion for the behavioral process of habitat selection for the next generation. It is well known that in Odonata the most general cues are detected visually, but laboratory investigations on the coenagrionid Ischnura elegans showed through behavioral and electrophysiological assays that adults were attracted by olfactory cues emitted by prey and that males of the same species are attracted by female odor. The results of the present be...
Published on Jul 8, 2016in Nucleic Acids Research11.15
Zilong He4
Estimated H-index: 4
(CAS: Chinese Academy of Sciences),
Huangkai Zhang5
Estimated H-index: 5
(CAS: Chinese Academy of Sciences)
+ 3 AuthorsSongnian Hu44
Estimated H-index: 44
(CAS: Chinese Academy of Sciences)
Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its ‘dataset system’ contains not only the data to be visualized on the tree, but also ‘modifiers’ that control various aspects of the graphical annotation. Evolview is a single-page app...
Published on Jul 1, 2016in Acta Tropica2.63
Itsanun Wiwatanaratanabutr4
Estimated H-index: 4
(King Mongkut's Institute of Technology Ladkrabang),
Chongxing Zhang1
Estimated H-index: 1
(Academy of Medical Sciences, United Kingdom)
Wolbachia are inherited, endocytoplasmic bacteria that infect a wide range of arthropods. Here is the first systematic report on the study of Wolbachia infection in mosquitoes and their predators from both Thailand and China. In Thailand, 632 mosquito specimens (20 spp.) and 424 insect predators (23 spp.) were collected from the rice agroecosystem, mostly from the Central region, followed by the Northeast, the North and the South and were inhabiting rice fields, wetlands and ditches. In China, 9...
Published on Apr 1, 2016in Nature Communications11.88
Joshua B. Benoit32
Estimated H-index: 32
(UC: University of Cincinnati),
Zach N. Adelman25
Estimated H-index: 25
(VT: Virginia Tech)
+ 78 AuthorsJayendra Nath Shukla11
Estimated H-index: 11
(UK: University of Kentucky)
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...
Published on Apr 1, 2016in Nature Communications11.88
Jeffrey A. Rosenfeld20
Estimated H-index: 20
,
Darryl Reeves5
Estimated H-index: 5
+ 24 AuthorsJorge Gandara9
Estimated H-index: 9
The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding...
Published on Apr 1, 2016in Nature Communications11.88
Monika Gulia-Nuss6
Estimated H-index: 6
(UNR: University of Nevada, Reno),
Andrew B. Nuss8
Estimated H-index: 8
(UNR: University of Nevada, Reno)
+ 90 AuthorsKarine Megy12
Estimated H-index: 12
(University of Cambridge)
Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the ge...
Published on Feb 1, 2016in Current opinion in insect science3.78
Rahul V. Rane6
Estimated H-index: 6
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
Thomas J. Walsh111
Estimated H-index: 111
(CSIRO: Commonwealth Scientific and Industrial Research Organisation)
+ 4 AuthorsJohn G. Oakeshott48
Estimated H-index: 48
(CSIRO: Commonwealth Scientific and Industrial Research Organisation)
The size of gene families associated with xenobiotic detoxification in insects may be associated with the complexity of their diets and their propensities to develop insecticide resistance. We test these hypotheses by collating the annotations of cytochrome P450, carboxyl/cholinesterase and glutathione S-transferase genes in 65 insect species with data on their host use and history of insecticide resistance. We find 2–4 fold variation across the species in the numbers of these genes and, in some...
Published on Dec 1, 2015in Genome Biology14.03
Seth M. Barribeau18
Estimated H-index: 18
(ETH Zurich),
Ben M. Sadd20
Estimated H-index: 20
(ETH Zurich)
+ 21 AuthorsSilvio Erler15
Estimated H-index: 15
(MLU: Martin Luther University of Halle-Wittenberg)
Background Sociality has many rewards, but can also be dangerous, as high population density and low genetic diversity, common in social insects, is ideal for parasite transmission. Despite this risk, honeybees and other sequenced social insects have far fewer canonical immune genes relative to solitary insects. Social protection from infection, including behavioral responses, may explain this depauperate immune repertoire. Here, based on full genome sequences, we describe the immune repertoire ...
Published on Dec 1, 2015in Trends in Genetics10.63
Ryan M. Joseph3
Estimated H-index: 3
(Yale University),
John R. Carlson59
Estimated H-index: 59
(Yale University)
Chemoreception is essential for survival. Feeding, mating, and avoidance of predators depend on detection of sensory cues. Drosophila contains diverse families of chemoreceptors that detect odors, tastants, pheromones, and noxious stimuli, including receptors of the odor receptor (Or), gustatory receptor (Gr), ionotropic receptor (IR), Pickpocket (Ppk), and Trp families. We consider recent progress in understanding chemoreception in the fly, including the identification of new receptors, the dis...
Cited By18
Newest
Published on Jul 24, 2019in bioRxiv
Beatriz Willink6
Estimated H-index: 6
,
M. C. Duryea (Great Basin College)+ 1 AuthorsChristopher W. Wheat26
Estimated H-index: 26
(Stockholm University)
Pleiotropy (multiple phenotypic effects of single genes) and epistasis (gene interaction) play key roles in the development of complex phenotypes and might be especially important in polymorphic taxa. The development of discrete and heritable sympatric phenotypic polymorphisms often emerges from major-effect genes that interact with other loci and have pleiotropic effects on multiple traits and physiological functions. We quantified gene expression changes during ontogenetic colour development i...
Michael Thoma3
Estimated H-index: 3
(MPG: Max Planck Society),
Christine Missbach5
Estimated H-index: 5
(MPG: Max Planck Society)
+ 3 AuthorsBill S. Hansson60
Estimated H-index: 60
(MPG: Max Planck Society)
The insect odorant receptor (Or) gene family is among the largest multigene families in insect genomes, but its evolutionary origin and mode of expansion is still a matter of debate. We performed transcriptomic surveys of two wingless insect species, the silverfish Lepisma saccharina and Tricholepidion gertschi, and identified multiple Or gene family members in both species. A phylogenetic analysis suggests that the silverfish Ors do not fall into the clade comprised of more derived flying insec...
Published on Jul 9, 2019in Mbio6.75
Jacob L. Steenwyk5
Estimated H-index: 5
(Vandy: Vanderbilt University),
Xing-Xing Shen10
Estimated H-index: 10
(Vandy: Vanderbilt University)
+ 2 AuthorsAntonis Rokas53
Estimated H-index: 53
(Vandy: Vanderbilt University)
ABSTRACT The filamentous fungal family Aspergillaceae contains >1,000 known species, mostly in the genera Aspergillus and Penicillium . Several species are used in the food, biotechnology, and drug industries (e.g., Aspergillus oryzae and Penicillium camemberti), while others are dangerous human and plant pathogens (e.g., Aspergillus fumigatus and Penicillium digitatum). To infer a robust phylogeny and pinpoint poorly resolved branches and their likely underlying contributors, we used 81 genomes...
Published on Mar 22, 2019in bioRxiv
Mosè Manni11
Estimated H-index: 11
(University of Geneva),
Felipe A. Simão8
Estimated H-index: 8
(University of Geneva)
+ 6 AuthorsEvgeny M. Zdobnov55
Estimated H-index: 55
(University of Geneva)
The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemos...
Published on Apr 29, 2019in bioRxiv
Steven W. Miller7
Estimated H-index: 7
(UCSD: University of California, San Diego),
Artem Movsesyan (UCSD: University of California, San Diego)+ 2 AuthorsJames W. Posakony35
Estimated H-index: 35
(UCSD: University of California, San Diego)
Suppressor of Hairless [Su(H)], the transcription factor at the end of the Notch pathway in Drosophila, utilizes the Hairless protein to recruit two co-repressors, Groucho (Gro) and C-terminal Binding Protein (CtBP), indirectly. Hairless is present only in the Pancrustacea, raising the question of how Su(H) in other protostomes gains repressive function. We show that Su(H) from a wide array of arthropods, molluscs, and annelids includes motifs that directly bind Gro and CtBP; thus, direct co-rep...
Published on Apr 1, 2019in Current Opinion in Structural Biology7.05
Vikas Tiwari (NCBS: National Centre for Biological Sciences), Snehal D. Karpe3
Estimated H-index: 3
(NCBS: National Centre for Biological Sciences),
Ramanathan Sowdhamini27
Estimated H-index: 27
(NCBS: National Centre for Biological Sciences)
Olfactory receptors are important transmembrane proteins that enable organisms to perceive odours and react to them. Structural understanding of insect olfactory receptors is scarce. In this review, we discuss different transmembrane helix prediction methods, consensus methods, topology prediction methods which can enable topology prediction of these proteins. We discuss the current success rates by applying the algorithms on few G-protein coupled receptors of known structure and olfactory recep...
Published on Apr 1, 2019in Methods in Ecology and Evolution7.10
Feng Zhang1
Estimated H-index: 1
(CAS: Chinese Academy of Sciences),
Yinhuan Ding1
Estimated H-index: 1
(NAU: Nanjing Agricultural University)
+ 4 AuthorsYun‐Xia Luan1
Estimated H-index: 1
(SCNU: South China Normal University)
Published on Feb 1, 2019in Insect Biochemistry and Molecular Biology3.62
Hugh M. Robertson70
Estimated H-index: 70
(UIUC: University of Illinois at Urbana–Champaign),
Erica C.N. Robertson (UIUC: University of Illinois at Urbana–Champaign)+ 2 AuthorsNicholas J. Miller16
Estimated H-index: 16
(IIT: Illinois Institute of Technology)
Abstract We examined the genome of the soybean aphid, Aphis glycines , and an updated genome assembly of the pea aphid, Acyrthosiphon pisum , for members of the three major families of chemoreceptors, the Odorant Receptors (ORs), Gustatory Receptors (GRs) and Ionotropic Receptors (IRs), as well as the Odorant Binding Proteins (OBPs). The soybean aphid has 47 ORs, 61 GRs, 19 IRs, and 10 OBPs, compared with 87 ORs, 78 Grs, 19 IRs, and 18 OBPs in the pea aphid, with variable numbers of pseudogenes ...
Published on Jan 1, 2019in Methods of Molecular Biology
Robert M. Waterhouse35
Estimated H-index: 35
(Swiss Institute of Bioinformatics),
Mathieu Seppey3
Estimated H-index: 3
(Swiss Institute of Bioinformatics)
+ 1 AuthorsEvgeny M. Zdobnov55
Estimated H-index: 55
(Swiss Institute of Bioinformatics)
The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build "omics" resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of cr...
Published on Jan 1, 2019
Mathieu Seppey3
Estimated H-index: 3
,
Mosè Manni11
Estimated H-index: 11
,
Evgeny M. Zdobnov55
Estimated H-index: 55