What's in a Name?

Total Page:16

File Type:pdf, Size:1020Kb

What's in a Name? VolNATURE 464|8|Vol April 464 2010|8 April 2010 NEWS VOLCANIC LAKE TEEMS WITH LIFE Flamingos and microbes thrive in hostile waters. go.nature.com/kikEKu M. EUGENIA FARÍAS EUGENIA M. What’s in a name? Fly world is abuzz Proposed reorganization of Drosophila fruitfly genus might throw out its most celebrated member. The star subject of genetic research — the designate D. melanogaster as the Drosophila that would occur if the genus were split. Dro- Drosophila melanogaster fruitfly — may lose type species — the accepted standard of the sophila melanogaster fits within a subgenus its name. genus (see Nature 457, 368; 2009). Kim van called Sophophora, which includes some 350 This is an anticipated repercussion of a der Linde, an ecologist at Florida State Univer- members. Splitting this group off to form a decision last week by the London-based Inter- sity in Tallahassee, wanted to ensure that the new genus would require fewer renamings national Commission on Zoological Nomen- name D. melanogaster would not than would be needed if D. mel- V. NI clature. It had spent more than two years change if the genus were divided, anogaster became the type spe- U debating a petition that would have protected as she and other scientists advo- cies for Drosophila. In that case, the hallowed name while opening the way to a cate. The genus is extremely roughly 1,100 species would be NDIANA I major reorganization of the Drosophila genus, large, and genetic data suggest pushed off into new genera. which includes at least 1,450 species. that some of its member species “It was very difficult for the The commission, which oversees the naming are more closely related to flies commissioners,” says Ellinor of all species, rejected the petition, setting the outside the genus than they are Drosophila melanogaster Michel, the commission’s execu- stage for a likely renaming of D. melanogaster to other Drosophila species. faces genus reassignment. tive secretary. “It was a question and hundreds of related species. Among biolo- In the end, the commission of celebrity, as everyone knows gists who study various fruitfly species to link voted 23 to 4 to reject van der Linde’s petition. D. melanogaster.” genes to traits, the 1 April ruling was no joke. The designated type species will continue to If a researcher were to use current data to “Oh my God,” says Therese Markow, a genet- be Drosophila funebris, described in 1787 by publish a revision of the Drosophila genus, icist at the University of California, San Diego, Johann Fabricius. But the proposal forced the D. melanogaster would probably become Sopho- who was reached in the Sonoran Desert, where taxonomic world to face the possibility that the phora melanogaster. Van der Linde says that if she was collecting fruitflies. Markow, who is genus in its present form may be untenable. she and her co-authors from the petition can director of the university’s Drosophila Spe- In their written opinions, commission mem- agree, they may present the case for the change. cies Stock Center, added that extensive name bers gave several reasons for voting against “Something needs to happen,” she says. changes could “wreak havoc” in the Drosophila the new proposal. Many called it premature But even if the celebrity fly is renamed, literature and databases. because the science about the organization of Michel noted, it may still be referred to by its The naming debate began when a US sci- the Drosophila genus remains unsettled. Oth- original name. ■ entist filed a petition with the commission to ers sought to limit the naming disruptions Rex Dalton Animals thrive without oxygen at sea bottom Living exclusively oxygen-free named, belong to a phylum of that helps these loriciferans to survive in O AR was thought to be a lifestyle tiny bottom-dwellers called their environment. Instead of mitochondria, OV open only to viruses and Loricifera. Measuring less which rely on oxygen, the creatures have AN single-celled microorganisms. than 1 millimetre long, they organelles that resemble hydrogenosomes, D R. A group of Italian and Danish live at a depth of more than which some single-celled organisms use researchers has now found 3,000 metres in the anoxic to produce energy-storing molecules three species of multicellular sediments of the Atalante anaerobically. animal, or metazoan, that basin, a place so little explored Angelika Brandt, a deep-sea biologist apparently spend their entire that Danovaro likens his at Germany’s Zoological Museum in lives in oxygen-starved waters team’s sampling to “going to Hamburg, says that the work by Danovaro’s in a basin at the bottom of the the Moon to collect rocks”. group is “highly significant”. The discovery Mediterranean Sea. Researchers have previously of metazoans living without mitochondria The discovery “opens Some loriciferans live in found multicellular and oxygen, she says, suggests that animals a whole new realm to anoxic sediments. animals living in anoxic can occupy niches that once seemed too metazoans that we thought environments, but Danovaro extreme. ■ was off limits”, says Lisa Levin, a biological says that it was never clear whether those Janet Fang oceanographer at Scripps Institution of animals were permanent residents. The new Correction Oceanography in La Jolla, California. loriciferans, which he and his team reported The News Feature ‘The human race’ (Nature Roberto Danovaro from the Polytechnic this week (R. Danovaro et al. BMC Biol. 464, 668–669; 2010) misspelt the name of the University of Marche in Ancona, Italy, and doi:10.1186/1741-7007-8-30; 2010), seem architect of whole-genome shotgun sequencing. his colleagues pulled up the animals during to “reproduce and live all their life in anoxic It should be Gene Myers. This error has been three research cruises off the south coast of conditions”, he says. corrected online in the HTML and PDF versions Greece. The species, which have not yet been The researchers identified an adaptation of this story. 825 © 2010 Macmillan Publishers Limited. All rights reserved.
Recommended publications
  • Advances in Genetics, Development, and Evolution of Drosophila
    springer.com Seppo Lakovaara (Hrsg.) Advances in Genetics, Development, and Evolution of Drosophila In 1906 Castle, Carpenter, Clarke, Mast, and Barrows published a paper entitled "The effects of inbreeding, cross-breeding, and selection upon the fertility and variability of Drosophila." This article, 55 pages long and published in the Proceedings of the Amer• ican Academy, described experiments performed with Drosophila ampe• lophila Lov, "a small dipterous insect known under various popular names such as the little fruit fly, pomace fly, vinegar fly, wine fly, and pickled fruit fly." This study, which was begun in 1901 and published in 1906, was the first published experimental study using Drosophila, subsequently known as Drosophila melanogaster Meigen. Of course, Drosophila was known before the experiments of Cas• tles's group. The small flies swarming around grapes and wine pots have surely been known as long Softcover reprint of the original 1st ed. as wine has been produced. The honor of what was the first known misclassification of the 1982, X, 474 p. fruit flies goes to Fabricius who named them Musca funebris in 1787. It was the Swedish dipterist, C.F. Fallen, who in 1823 changed the name of ~ funebris to Drosophila funebris Gedrucktes Buch which was heralding the beginning of the genus Drosophila. Present-day Drosophila research Softcover was started just 80 years ago and first published only 75 years ago. Even though the history 119,99 € | £109.99 | $149.99 of Drosophila research is short, the impact and volume of study on Drosophila has been [1]128,39 € (D) | 131,99 € (A) | CHF tremendous during the last decades.
    [Show full text]
  • Invasive Fruit Flies (Diptera: Drosophilidae) Meet in a Biodiversity Hotspot
    J. Entomol. Res. Soc., 19(1): 61-69, 2017 ISSN:1302-0250 Invasive Fruit Flies (Diptera: Drosophilidae) Meet in a Biodiversity Hotspot Carla REGO1* António Franquinho AGUIAR2 Délia CRAVO2 Mário BOIEIRO1 1Centre for Ecology, Evolution and Environmental Changes (cE3c), Azorean Biodiversity Group and Department of Agrarian Sciences, University of Azores, Angra do Heroísmo, Azores, PORTUGAL 2Laboratório de Qualidade Agrícola, Camacha, Madeira, PORTUGAL e-mails: *[email protected], [email protected], [email protected], [email protected] ABSTRACT Oceanic islands’ natural ecosystems worldwide are severely threatened by invasive species. Here we discuss the recent finding of three exotic drosophilids in Madeira archipelago -Acletoxenus formosus (Loew, 1864), Drosophila suzukii (Matsumura, 1931) and Zaprionus indianus (Gupta, 1970). Drosophila suzukii and Z. indianus are invasive species responsible for severe economic losses in fruit production worldwide and became the dominant drosophilids in several invaded areas menacing native species. We found that these exotic species are relatively widespread in Madeira but, at present, seem to be restricted to human disturbed environments. Finally, we stress the need to define a monitoring program in the short-term to determine population spread and environmental damages inflicted by the two invasive drosophilids, in order to implement a sustainable and effective control management strategy. Key words: Biological invasions, Drosophila suzukii, invasive species, island biodiversity, Madeira archipelago, Zaprionus indianus. INTRODUCTION Oceanic islands are known to contribute disproportionately to their area for Global biodiversity and by harbouring unique evolutionary lineages and emblematic plants and animals (Grant,1998; Whittaker and Fernández-Palácios, 2007). Nevertheless, many of these organisms are particularly vulnerable to human-mediated changes in their habitats due to their narrow range size, low abundance and habitat specificity (Paulay, 1994).
    [Show full text]
  • Evolution of a Pest: Towards the Complete Neuroethology of Drosophila Suzukii and the Subgenus Sophophora Ian W
    bioRxiv preprint first posted online Jul. 28, 2019; doi: http://dx.doi.org/10.1101/717322. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. ARTICLES PREPRINT Evolution of a pest: towards the complete neuroethology of Drosophila suzukii and the subgenus Sophophora Ian W. Keesey1*, Jin Zhang1, Ana Depetris-Chauvin1, George F. Obiero2, Markus Knaden1‡*, and Bill S. Hansson1‡* Comparative analysis of multiple genomes has been used extensively to examine the evolution of chemosensory receptors across the genus Drosophila. However, few studies have delved into functional characteristics, as most have relied exclusively on genomic data alone, especially for non-model species. In order to increase our understanding of olfactory evolution, we have generated a comprehensive assessment of the olfactory functions associated with the antenna and palps for Drosophila suzukii as well as sev- eral other members of the subgenus Sophophora, thus creating a functional olfactory landscape across a total of 20 species. Here we identify and describe several common elements of evolution, including consistent changes in ligand spectra as well as relative receptor abundance, which appear heavily correlated with the known phylogeny. We also combine our functional ligand data with protein orthologue alignments to provide a high-throughput evolutionary assessment and predictive model, where we begin to examine the underlying mechanisms of evolutionary changes utilizing both genetics and odorant binding affinities. In addition, we document that only a few receptors frequently vary between species, and we evaluate the justifications for evolution to reoccur repeatedly within only this small subset of available olfactory sensory neurons.
    [Show full text]
  • Johnson Stander 2020
    Gene Regulatory Network Homoplasy Underlies Recurrent Sexually Dimorphic Fruit Fly Pigmentation Jesse Hughes, Rachel Johnson, and Thomas M. Williams The Department of Biology at the University of Dayton; 300 College Park, Dayton, OH 45469 ABSTRACT Widespread Dimorphism in Sophophora and Beyond Pigment Metabolic Pathway Utilization in H. duncani Species with dimorphic tergite pigmentation are Traits that appear discontinuously along phylogenies may be explained by independent ori- widespread throughout the Drosophila genus. (A-E) Female and (A’-E’) male expressions of H. duncani gins (homoplasy) or repeated loss (homology). While discriminating between these models Sophophora subgenus species groups and species pigment metabolic pathway genes, and (F and F’) cartoon is difficult, the dissection of gene regulatory networks (GRNs) which drive the development are indicated by the gray background. D. busckii and representation of the pigmentation phenotype. (G) of such repeatedly occurring traits can offer a mechanistic window on this fundamental Summary of the H. duncani pathway use includes robust D. funebris are included as non-Sophophora species problem. The GRN responsible for the male-specific pattern of Drosophila (D.) melano- expression of all genes, with dimorphic expressions of Ddc, from the Drosophila genus that respectively exhibit gaster melanic tergite pigmentation has received considerable attention. In this system, a ebony, tan, and yellow. (A, A’) pale, (B, B’) Ddc, (C, C’) monomorphic and dimorphic patterns of tergite metabolic pathway of pigmentation enzyme genes is expressed in spatial and sex-specific ebony, (D, D’) tan, and (E, E’) yellow. Red arrowheads pigmentation. The homologous A5 and A6 segment (i.e., dimorphic) patterns. The dimorphic expression of several genes is regulated by the indicate robust patterns of dimorphic expression in the tergites are indicated for each species, the segments Bab transcription factors, which suppress pigmentation enzyme expression in females, by dorsal abdominal epidermis.
    [Show full text]
  • The Mariner Transposable Element in the Drosophilidae Family
    Heredity 73 (1994) 377—385 Received 10 February 1994 The Genetical Society of Great Britain The mariner transposable element in the Drosophilidae family FREDERIC BRUNET, FABIENNE GODIN, JEAN A. DAVID & PIERRE CAPY* Laboratoire Populations, Genétique et Evolution, CNRS, 91198 Gif/Yvette Cedex, France Thedistribution of the mariner transposable element among Drosophilidae species was investi- gated using three differetìt techniques, i.e. squash blots, Southern blots and PCR amplification, using two sets of primers (one corresponding to the Inverted Terminal Repeats and the other to two conserved regions of the putative transposase). Our results and those of others show that the distribution of mariner is not uniform and does not follow the phylogeny of the host species. An analysis of geographical distribution, based on endemic species, shows that mariner is mainly present in Asia and Africa. At least two hypotheses may be proposed to explain the specific and geographical distributions of this element. Firstly, 'they may be the results of several horizontal transmissions between Drosophila species and/or between Drosophila species and one or several donor species outside the Drosophilidae family. Secondly, these particular distributions may correspond to the evolution of the mariner element from an ancestral copy which was present in the ancestor of the Drosophilidae family. Keywords:Drosophila,mariner, transposon, phylogeny. al., 1994). In all cases, the evolutionary history of these Introduction elements is not simple and more information is neces- Thedistribution of the mariner transposable elements sary about the variability within and between more or in Drosophila was previously investigated by less closely related species. Maruyama & Hartl (1991 a).
    [Show full text]
  • OPTIMIZATION of FRUIT FLY (Drosophila Melanogaster) CULTURE MEDIA for HIGHER YIELD of OFFSPRING
    OPTIMIZATION OF FRUIT FLY (Drosophila melanogaster) CULTURE MEDIA FOR HIGHER YIELD OF OFFSPRING By TEE SUI YEE A project report submitted to the Department of Biological Science Faculty of Science Universiti Tunku Abdul Rahman in partial fulfillment of the requirements for the degree of Bachelor of Science (Hons) Biotechnology May 2010 ABSTRACT OPTIMIZATION OF FRUIT FLY (Drosophila melanogaster) CULTURE MEDIA FOR HIGHER YIELD OF OFFSPRING Tee Sui Yee Drosophila melanogaster is one of the most widely used model organism in research on genetics and genome evolution. Mass culture of D. melanogaster is important to produce enough amounts of flies for research purposes. Various culture media have been formulated using simple and economic methods to produce large amounts of Drosophila. In this study, ten different culture media were formulated to culture inbred D. melanogaster and used as attractant to collect Kampar wild-type Drosophila species. Banana medium was used as the positive control medium and plain agar was used as the negative control medium. For inbred D. melanogaster, the number of pupal cases and hatched flies were calculated for two generations while only the number of pupal cases was calculated for wild-caught Drosophila species. The results were analyzed by using one-way ANOVA, Tukey’s HSD multiple range test and paired sample t- test. One-way ANOVA showed that there were significant differences (p≤ 0.05) in the numbers of inbred offspring and also the numbers of wild-caught Drosophila species among different culture media. For inbred D. melanogaster, the banana and egg medium managed to breed the highest number of offspring for both generations.
    [Show full text]
  • Downloaded Transcribed from an RNA Template Directly Onto a Consensus Sequences of Jockey Families Deposited in the Tambones Et Al
    Tambones et al. Mobile DNA (2019) 10:43 https://doi.org/10.1186/s13100-019-0184-1 RESEARCH Open Access High frequency of horizontal transfer in Jockey families (LINE order) of drosophilids Izabella L. Tambones1, Annabelle Haudry2, Maryanna C. Simão1 and Claudia M. A. Carareto1* Abstract Background: The use of large-scale genomic analyses has resulted in an improvement of transposable element sampling and a significant increase in the number of reported HTT (horizontal transfer of transposable elements) events by expanding the sampling of transposable element sequences in general and of specific families of these elements in particular, which were previously poorly sampled. In this study, we investigated the occurrence of HTT events in a group of elements that, until recently, were uncommon among the HTT records in Drosophila – the Jockey elements, members of the LINE (long interspersed nuclear element) order of non-LTR (long terminal repeat) retrotransposons. The sequences of 111 Jockey families deposited in Repbase that met the criteria of the analysis were used to identify Jockey sequences in 48 genomes of Drosophilidae (genus Drosophila, subgenus Sophophora: melanogaster, obscura and willistoni groups; subgenus Drosophila: immigrans, melanica, repleta, robusta, virilis and grimshawi groups; subgenus Dorsilopha: busckii group; genus/subgenus Zaprionus and genus Scaptodrosophila). Results: Phylogenetic analyses revealed 72 Jockey families in 41 genomes. Combined analyses revealed 15 potential HTT events between species belonging to different
    [Show full text]
  • Guidelines for the Capture and Management of Digital Zoological Names Information Francisco W
    Guidelines for the Capture and Management of Digital Zoological Names Information Francisco W. Welter-Schultes Version 1.1 March 2013 Suggested citation: Welter-Schultes, F.W. (2012). Guidelines for the capture and management of digital zoological names information. Version 1.1 released on March 2013. Copenhagen: Global Biodiversity Information Facility, 126 pp, ISBN: 87-92020-44-5, accessible online at http://www.gbif.org/orc/?doc_id=2784. ISBN: 87-92020-44-5 (10 digits), 978-87-92020-44-4 (13 digits). Persistent URI: http://www.gbif.org/orc/?doc_id=2784. Language: English. Copyright © F. W. Welter-Schultes & Global Biodiversity Information Facility, 2012. Disclaimer: The information, ideas, and opinions presented in this publication are those of the author and do not represent those of GBIF. License: This document is licensed under Creative Commons Attribution 3.0. Document Control: Version Description Date of release Author(s) 0.1 First complete draft. January 2012 F. W. Welter- Schultes 0.2 Document re-structured to improve February 2012 F. W. Welter- usability. Available for public Schultes & A. review. González-Talaván 1.0 First public version of the June 2012 F. W. Welter- document. Schultes 1.1 Minor editions March 2013 F. W. Welter- Schultes Cover Credit: GBIF Secretariat, 2012. Image by Levi Szekeres (Romania), obtained by stock.xchng (http://www.sxc.hu/photo/1389360). March 2013 ii Guidelines for the management of digital zoological names information Version 1.1 Table of Contents How to use this book ......................................................................... 1 SECTION I 1. Introduction ................................................................................ 2 1.1. Identifiers and the role of Linnean names ......................................... 2 1.1.1 Identifiers ..................................................................................
    [Show full text]
  • Extensive Morphological Divergence and Rapid Evolution of the Larval Neuromuscular Junction in Drosophila
    Extensive morphological divergence and rapid evolution of the larval neuromuscular junction in Drosophila Megan Campbella and Barry Ganetzkyb,1 aNeuroscience Training Program and bLaboratory of Genetics, University of Wisconsin, Madison, WI 53706 Contributed by Barry Ganetzky, January 20, 2012 (sent for review November 17, 2011) Although the complexity and circuitry of nervous systems undergo the evolution of synaptic morphology by analyzing NMJ pheno- evolutionary change, we lack understanding of the general types in different species of Drosophila. The overall body plan, principles and specific mechanisms through which it occurs. The musculature, and motor innervation pattern are precisely con- Drosophila larval neuromuscular junction (NMJ), which has been served among all species of Drosophila and are even shared with widely used for studies of synaptic development and function, is more distantly related groups of Diptera (3), despite enormous also an excellent system for studies of synaptic evolution because differences in size, habitat, food source, predation, and other the genus spans >40 Myr of evolution and the same identified aspects of their natural history and concomitant differences in synapse can be examined across the entire phylogeny. We have behavior. Moreover, the subgenus Drosophila by itself encom- now characterized morphology of the NMJ on muscle 4 (NMJ4) in passes at least 40 Myr of evolutionary history (4). The conserva- > Drosophila 20 species of . Although there is little variation within tion of body plan and muscle innervation over the evolutionary a species, NMJ morphology and complexity vary extensively be- history of Drosophila immediately raises the question of whether tween species. We find no significant correlation between NMJ NMJ morphology is also conserved or has undergone modifica- phenotypes and phylogeny for the species examined, suggesting tion in different species.
    [Show full text]
  • Names Are Key to the Big New Biology Patterson, D. J.1, Cooper, J.2, Kirk
    Names are key to the big new biology Patterson, D. J.1, Cooper, J.2, Kirk, P. M.3 , Pyle, R. L.4, Remsen, D. P.5 1. Biodiversity Informatics, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA. [email protected] 2. Landcare Research, PO Box 40, Lincoln 7640, New Zealand. [email protected] 3. CABI UK, Bakeham Lane, Egham, Surrey, TW20 9TY, United Kingdom. [email protected] 4. Department of Natural Sciences, Bishop Museum, 1525 Bernice St., Honolulu, Hawaii 96817, USA. [email protected] 5. GBIF, Universitetsparken 15, Copenhagen Ø, DK 2100, Denmark. [email protected]. Abstract Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution, ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a “big science”. Informatics devices will exploit this ‘big new biology’, revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory, and semantic Global Names Architecture. Patterson Cooper Kirk Pyle Remsen: Names are key to the big new biology 1 The value of taxonomy to a biology that is changing “New Biology” is a vision [1] of a discipline evolving to become considerably more data- intensive as it accommodates increasing amounts of under-analysed data from high-throughput molecular and environmental technologies, and from large-scale digitization programs such as the Biodiversity Heritage Library (BHL, http://www.biodiversitylibrary.org/).
    [Show full text]
  • Phylogeny of Drosophila and Related Genera Inferred from the Nucleotide Sequence of the Cu,Zn Sod Gene
    J Mol Evol (1994) 38:443454 Journal of Molecular Evolution © Springer-VerlagNew York Inc. 1994 Phylogeny of Drosophila and Related Genera Inferred from the Nucleotide Sequence of the Cu,Zn Sod Gene Jan Kwiatowski, 1,2 Douglas Skarecky, 1 Kevin Bailey, 1 Francisco J. Ayala 1 I Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92717, USA 2 Institute of Botany, Warsaw University, 00-478 Warsaw, Poland Received: 20 March 1993/Revised: 31 August 1993/Accepted: 30 September 1993 Abstract. The phylogeny and taxonomy of the dro- book of Genetics. Plenum Press, New York, pp. 421- sophilids have been the subject of extensive investiga- 469, 1975) phylogeny; are inconsistent in some impor- tions. Recently, Grimaldi (1990) has challenged some tant ways with Grimaldi's (Bull. Am. Museum Nat. Hist. common conceptions, and several sets of molecular da- 197:1-139, 1990) cladistic analysis; and also are in- ta have provided information not always compatible consistent with some inferences based on mitochondri- with other taxonomic knowledge or consistent with al DNA data. The Sod results manifest how, in addition each other. We present the coding nucleotide sequence to the information derived from nucleotide sequences, of the Cu,Zn superoxide dismutase gene (Sod) for 15 structural features (i.e., the deletion of an intron) can species, which include the medfly Ceratitis capitata help resolve phylogenetic issues. (family Tephritidae), the genera Chymomyza and Za- prionus, and representatives of the subgenera Dor- Key words: Superoxide dismutase gene -- Drosophi- silopha, Drosophila, Hirtodrosophila, Scaptodrosophi- la phylogeny -- Nucleotide sequence -- Medfly Ce- la, and Sophophora.
    [Show full text]
  • Long-Read Based Assembly and Synteny Analysis of a Reference
    Karageorgiou et al. BMC Genomics (2019) 20:223 https://doi.org/10.1186/s12864-019-5590-8 RESEARCH ARTICLE Open Access Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects Charikleia Karageorgiou*, Víctor Gámez-Visairas, Rosa Tarrío* and Francisco Rodríguez-Trelles* Abstract Background: Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup. Results: We generated a highly-contiguous ~ 129 Mb-long nuclear genome, consisting of six pseudochromosomes corresponding to the six chromosomes of a female haploid set, and a complete 15,764 bp-long mitogenome, and provide an account of their numbers and distributions of codifying and repetitive content. All 12 identified paracentric inversion differences in the subobscura subgroup would have originated by chromosomal breakage and repair, with some associated duplications, but no evidence of direct gene disruptions by the breakpoints. Between lineages, inversion fixation rates were 10 times higher in continental D. subobscura than in the two small oceanic- island endemics D. guanche and D. madeirensis. Within D. subobscura, we found contrasting ratios of chromosomal divergence to polymorphism between the A sex chromosome and the autosomes. Conclusions: We present the first high-quality, long-read sequencing of a D.
    [Show full text]