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Genomes of the Hymenoptera Michael G View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital Repository @ Iowa State University Ecology, Evolution and Organismal Biology Ecology, Evolution and Organismal Biology Publications 2-2018 Genomes of the Hymenoptera Michael G. Branstetter U.S. Department of Agriculture Anna K. Childers U.S. Department of Agriculture Diana Cox-Foster U.S. Department of Agriculture Keith R. Hopper U.S. Department of Agriculture Karen M. Kapheim Utah State University See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/eeob_ag_pubs Part of the Behavior and Ethology Commons, Entomology Commons, and the Genetics and Genomics Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ eeob_ag_pubs/269. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Ecology, Evolution and Organismal Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Ecology, Evolution and Organismal Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Genomes of the Hymenoptera Abstract Hymenoptera is the second-most sequenced arthropod order, with 52 publically archived genomes (71 with ants, reviewed elsewhere), however these genomes do not capture the breadth of this very diverse order (Figure 1, Table 1). These sequenced genomes represent only 15 of the 97 extant families. Although at least 55 other genomes are in progress in an additional 11 families (see Table 2), stinging wasps represent 35 (67%) of the available and 42 (76%) of the in progress genomes. A more comprehensive catalog of hymenopteran genomes is needed for research into the evolutionary processes underlying the expansive diversity in terms of ecology, behavior, and physiological traits within this group. Additional sequencing is needed to generate an assembly for even 0.05% of the estimated 1 million hymenopteran species, and we recommend premier level assemblies for at least 0.1% of the >150,000 named species dispersed across the order. Given the haplodiploid sex determination in Hymenoptera, haploid male sequencing will help minimize genome assembly issues to enable higher quality genome assemblies. Disciplines Behavior and Ethology | Ecology and Evolutionary Biology | Entomology | Genetics and Genomics Comments This article is published as Branstetter, M., Childers, A.K., Cox-Foster, D., Hopper, K.R., Kapheim, K.M., Toth, A.L., Worley, K.C. 2017. Genomes of Hymenoptera. Current Opinion in Insect Science 25: 65-75. doi: 10.1016/j.cois.2017.11.008. Rights Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The onc tent of this document is not copyrighted. Authors Michael G. Branstetter, Anna K. Childers, Diana Cox-Foster, Keith R. Hopper, Karen M. Kapheim, Amy L. Toth, and Kim C. Worley This article is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/eeob_ag_pubs/269 Available online at www.sciencedirect.com ScienceDirect Genomes of the Hymenoptera 1 2 1 Michael G Branstetter , Anna K Childers , Diana Cox-Foster , 3 4 5 Keith R Hopper , Karen M Kapheim , Amy L Toth and 6 Kim C Worley Hymenoptera is the second-most sequenced arthropod order, Introduction with 52 publically archived genomes (71 with ants, reviewed The order Hymenoptera is both ancient and hyper- elsewhere), however these genomes do not capture the diverse, having fossils that date back to the Triassic breadth of this very diverse order (Figure 1, Table 1). These [1], and a richness that exceeds 150,000 described and sequenced genomes represent only 15 of the 97 extant one million estimated species [2,3]. One of the ‘big four’ families. Although at least 55 other genomes are in progress in insect orders, Hymenoptera comprise diverse species an additional 11 families (see Table 2), stinging wasps represent including sawflies and wood wasps (‘Symphyta’), para- 35 (67%) of the available and 42 (76%) of the in progress sitoid wasps (‘Parasitica’), and stinging wasps (Aculeata), genomes. A more comprehensive catalog of hymenopteran which includes the ubiquitous and ecologically dominant genomes is needed for research into the evolutionary ants, bees and social wasps. With an astonishing diversity processes underlying the expansive diversity in terms of of biologically interesting traits Hymenoptera have sig- ecology, behavior, and physiological traits within this group. nificant economic impact (e.g. biological control and Additional sequencing is needed to generate an assembly for pollination) and thus was one of the first insect orders even 0.05% of the estimated 1 million hymenopteran species, to benefit from genome sequencing [4]. Despite addi- and we recommend premier level assemblies for at least 0.1% tional genomes sequenced (Table 1) or in preparation > of the 150,000 named species dispersed across the order. (Figure 1, Table 2), genomic resources are lacking for Given the haplodiploid sex determination in Hymenoptera, most major lineages, which comprise 28 superfamilies, haploid male sequencing will help minimize genome assembly 97 families, and 8422 genera. Herein we discuss insights issues to enable higher quality genome assemblies. gained and opportunities for improvements for hyme- nopteran genomics (noting that ants are reviewed sepa- rately). Our proposed roadmap for future hymenopteran Addresses genome sequencing optimizes benefit to the research 1 Pollinating Insect-biology, Management, Systematics Research Unit, community. USDA-ARS, Logan, UT 84322, United States 2 Bee Research Laboratory, USDA-ARS, Beltsville, MD 20705, United States 3 Features of hymenopteran genomes Beneficial Insects Introduction Research Unit, USDA-ARS, Newark, DE 19713, United States Hymenopteran genomes possess some notable and 4 Utah State University, Department of Biology, Logan, UT 84322, United unique features. Hymenoptera are haplodiploid: unfertil- States 5 ized eggs produce haploid males and fertilized eggs Iowa State University, Department of Ecology, Evolution, and produce diploid females [5]. Haplodiploidy engenders Organismal Biology and Department of Entomology, Ames, IA 50011, United States interesting biology related to sex determination [6], con- 6 Human Genome Sequencing Center, and Department of Molecular and trol of sex ratios, and relatedness [7], but is also useful for Human Genetics, Baylor College of Medicine, One Baylor Plaza, whole genome sequencing. Enough DNA can sometimes Houston, TX 77030, United States be extracted from a single large haploid male to provide material for whole genome sequencing without genetic Current Opinion in Insect Science 2018, 25:65–75 variation (e.g. [8]). Another notable feature of some Hymenoptera is extremely high recombination rates, This review comes from a themed issue on Insect genomics especially in social species such as the honey bee, where Edited by Christopher Childers, Anna Childers and Stephen Richards recombination rates are among the highest known for any organism [9]. For a complete overview see the Issue and the Editorial Available online 22nd November 2017 Among sequenced examples, hymenopteran genomes are https://doi.org/10.1016/j.cois.2017.11.008 moderate in size (80% are between 180 and 340 Mb) with 2214-5745/ã 2017 Elsevier Inc. All rights reserved. a few exceptions [10,11,12 ]. Most possess 12,000– 20,000 genes (note counts are highly annotation-pipeline and assembly contiguity dependent [13 ]), with a rela- tively low content of repetitive and transposable ele- ments. One unusual feature is low GC content, which ranges from 30 to 45% depending on the species [8]. www.sciencedirect.com Current Opinion in Insect Science 2018, 25:65–75 66 Insect genomics Figure 1 Superfamily Name (common names) Family Genera Species Genomes Other Holometabola Pamphilioidea 2 11 333 0(0) SawfliesSymphyta* Wasps Parasitic Parasitica* Xyeloidea 1 5 63 0(1) Tenthredinoidea 7 547 7,169 1(0) ∼250 Mya Xiphydrioidea (wood wasps) 1 28 146 0(0) Hymen optera Siricoidea (horntails) 2 12 112 0(1) Cephoidea 1 21 160 1(1) Orussoidea (parasitic wood wasps) 1 16 82 1(0) Ichneumonoidea 2 2,632 43,230 5(4) Ceraphronoidea 2 27 603 0(0) Cynipoidea (gall wasps) 5 236 3,157 1(0) Platygastroidea 1 236 5,385 0(0) Proctotrupoidea∗ 8 39 450 0(0) Mymarommatoidea 1 3 10 0(0) ∼200 Mya Chalcidoidea (fairy wasps, fig wasps) 22 2,126 22,784 7(4) Apocrita (Wasp Waist) Diaprioidea 4 194 2,109 1(21) Evanioidea (ensign wasps) 3 29 1,130 0(0) Stephanoidea 1 11 342 0(1) Megalyroidea 1 8 43 0(0) Trigonalyoidea 1 16 92 0(0) Chrysidoidea∗ (cuckoo wasps) 7 222 6,532 0(7) Aculeata/Vespomorpha Vespoidea (yellow jackets, hornets, paper wasps) 2 272 5,004 2(12) Stinging Wasps Stinging ∼160 Mya Sierolomorphoidea 1 2 11 0(0) Aculeata (Wasp Sting) Pompiloidea (velvet ants, spider wasps) 4 347 9,223 0(0) Thynnoidea 2 69 1,065 0(0) Tiphioidea 1 53 1,000 0(0) Uncertain Placement Scolioidea 2 151 683 0(0) Paraphyletic Formicoidea (ants) 1 299 12,199 19(0) ∼ 145 Mya Apoidea∗ (sands wasps, beewolves) 4 266 9,697 0(2) Hymenoptera Genomes Apoidea: Anthophila (bees) 7 544 19,844 14(21) As of October 2017 Current Opinion in Insect Science Hymenoptera phylogeny and genome assemblies. Phylogeny based upon [83 ,88 ], with dotted lines marking lineages of uncertain placement, branches not to scale (=cladogram). Major groups shown on right, individual superfamilies listed with columns indicating the numbers of families, genera, species, genomes in NCBI (in progress). Although the reason for low GC content is not yet evolution of eusociality [8,12 ,18], social parasitism understood, it may be related to GC-biased gene conver- [19,20 ], venom function [19,20 ,21,22 ], and behavioral sion and high recombination rates [14].
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