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Innovative Assembly Strategy Contributes to Understanding The GigaScience Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola --Manuscript Draft-- Manuscript Number: GIGA-D-17-00182R2 Full Title: Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola Article Type: Research Funding Information: National Science Foundation Dr. Taras K Oleksyk (1432092) Ministry of Education and Science of the Dr. Stephen J O'Brien Russian Federation (Mega-grant 11.G34.31.0068) Saint Petersburg State University Dr. Stephen J O'Brien (1.50.1623.2013) Abstract: Solenodons are insectivores living in Hispaniola and Cuba that form an isolated branch in the tree of placental mammals highly divergent from other eulipothyplan insectivores The history, unique biology and adaptations of these enigmatic venomous species could be illuminated by the availability of genome data, but a whole genome assembly for solenodons has not been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation and reduced numbers have likely resulted in high homozygosity within the Hispaniolan solenodon (Solenodon paradoxus), thus we tested the performance of several assembly strategies on the genome of this genetically impoverished species. The string-graph based assembly strategy seemed a better choice compared to the conventional de Bruijn graph approach, due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of five individuals from the southern subspecies (S. p. woodi). In addition, we obtained additional sequence from one sample of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on venom genes, repeats, variable microsatellite loci and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single copy orthologs from 10 other mammals. We estimated that solenodons diverged from other extant mammals 73.6 Mya. Patterns of SNP variation allowed us to infer population demography, which supported a subspecies split within the Hispaniolan solenodon at least 300 Kya. Corresponding Author: Taras K Oleksyk, Ph.D. UniverSud Paris Mayaguez, Puerto Rico PUERTO RICO Corresponding Author Secondary Information: Corresponding Author's Institution: UniverSud Paris Corresponding Author's Secondary Institution: First Author: Kirill Grigorev, M.S. First Author Secondary Information: Order of Authors: Kirill Grigorev, M.S. Sergey Kliver, M.S. Pavel Dobrynin, Ph.D. Aleksey Komissarov, Ph.D. Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Walter Wolfsberger, M.S. Ksenia Krasheninnikova, Ph.D. Yashira M Afanador-Hernández, M.S. Adam L. Brandt, Ph.D. Liz A Paulino, B.S. Rosanna Carreras, Ph.D. Luis E Rodríguez, Ph.D. Adrell Núñez, DVM Jessica R. Brandt, Ph.D. Filipe Silva, M.S. Audrey J Majeske, Ph.D. David Hernández-Martich, Ph.D. Agostinho Antunes, Ph.D. Stephen J O'Brien Alfred L Roca, Ph.D. Juan Carlos Martinez-Cruzado, Ph.D. Taras K Oleksyk, Ph.D. Order of Authors Secondary Information: Response to Reviewers: Dear Dr. Edmunds Thank you very much for getting back to me so quickly. I carefully went through your comments and addressed all the issues you have raised. Here are the answers to your comments line-by-line. I hope that you will find these satisfactory, but if anything outstanding remains, please let me know as soon as possible. Sincerely yours Taras Oleksyk, UPR-M Line 134 Are there also voucher numbers? There are no voucher numbers, as the animals were released on location. Line 151 This is a bit sparse Information is added to M&M as requested Line 253 Make sure this citation remains Citations were fixed with the new addition of the GigaScience database Line 267 Missing citation in the references added E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics 29:2933-2935 (2013). Line 284 Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Can you make sure the scripts are in GigaDB or zenodo? I have asked access to the Progressive Cactus scripts. They are are here: https://zenodo.org/record/1189347#.Wp6Jt2aB3sE can this reference be added to GIGADB? Line 652 Citation missing in references Added citation 12 Line 682 Are there reference numbers for these as please include them? If there are voucher numbers and details please include these too The text was added: "All the required collection and permits had been obtained before any field work was started. The samples have been collected and exported in compliance with Export Permit No: VAPB-00909 (Dominican Republic Environment and Natural Resources Ministry Viceministry of Protected Areas and Biodiversity Department of Biodiversity) and imported in compliance with CITES/ESA Import permit number 14US84465A/9 (University of Illinois Board of Trustees)." Line 689 What model of HiSeq? 2500? 4000? How did library construction work? Did you use PE reads and what size? Added: "Sequences for S. p. woodi were generated by Illumina HiSeq 2000 (Illumina Inc) with 100bp paired-end reads." Line 730 Make sure this is cited correctly with the full DOI. The curators should give you this when you check the mockup (don't use that). Please also include the accession and zenodo details i f the code is going there Added the correct DOI to the database, also the accession numbers ENA: NKTL01000000 PROJECT: PRJNA368679 Additional information: http://doi.org/10.5281/zenodo.1185377 I would also ask to add and addition Zenodo repository here for Progressive Cactus scripts https://zenodo.org/record/1189347#.Wp6Jt2aB3sE Additional Information: Question Response Are you submitting this manuscript to a No special series or article collection? Experimental design and statistics Yes Full details of the experimental design and statistical methods used should be given in the Methods section, as detailed in our Minimum Standards Reporting Checklist. Information essential to interpreting the data presented should be made available in the figure legends. Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Have you included all the information requested in your manuscript? Resources Yes A description of all resources used, including antibodies, cell lines, animals and software tools, with enough information to allow them to be uniquely identified, should be included in the Methods section. Authors are strongly encouraged to cite Research Resource Identifiers (RRIDs) for antibodies, model organisms and tools, where possible. Have you included the information requested as detailed in our Minimum Standards Reporting Checklist? Availability of data and materials Yes All datasets and code on which the conclusions of the paper rely must be either included in your submission or deposited in publicly available repositories (where available and ethically appropriate), referencing such data using a unique identifier in the references and in the “Availability of Data and Materials” section of your manuscript. Have you have met the above requirement as detailed in our Minimum Standards Reporting Checklist? Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Manuscript Click here to download Manuscript Grigorev et al. GigaScience 2018.main_SCE.TKO.docx 1 Innovative assembly strategy contributes to understanding the evolution and conservation 2 genetics of the endangered Solenodon paradoxus from the island of Hispaniola 1 3 2 4 Kirill Grigorev a,1, Sergey Kliver b,1, Pavel Dobrynin b, Aleksey Komissarov b, Walter Wolfsberger 3 5 a,c, Ksenia Krasheninnikova b, Yashira M. Afanador-Hernández a, Adam L. Brandt d,e, Liz A. 4 f f f g d,h 5 6 Paulino , Rosanna Carreras , Luis E. Rodríguez , Adrell Núñez , Jessica R. Brandt , Filipe Silva i,j k a i,j d,l 6 7 , J. David Hernández-Martich , Audrey J. Majeske , Agostinho Antunes , Alfred L. Roca , 7 8 Stephen J. O’Brien b,m, Juan Carlos Martínez-Cruzado a and Taras K. Oleksyk a,c2 8 9 9 a 10 Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico 10 b 1111 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. 1212 Petersburg, Russia c 1313 Biology Department, Uzhhorod National University, Uzhhorod, Ukraine 14 d 14 Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 15 1615 USA e 1716 Division of Natural Sciences, St. Norbert College, De Pere, Wisconsin, USA 1817 f Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic 1918 g Department of Conservation and Science, Parque Zoologico Nacional (ZOODOM), Santo 2019 Domingo, Dominican Republic 21 h 2220 Department of Biology, Marian University, Fond du Lac, Wisconsin, USA 2321 i CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of 2422 Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 2523 Porto, Portugal 26 j 2724 Department of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 2825 Porto, Portugal 2926 k Instituto de Investigaciones Botánicas y Zoológicas, Universidad Autónoma de Santo Domingo, 3027 Santo Domingo, Dominican
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