Abstracts (Alphabetized by Presenter)
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Supplemental Methods
Supplemental Methods Collection and Preparation After extraction, the DNA samples were sheared with a 1.5 blunt end needles (Jensen Global, Santa Barbara, CA, USA) and run through pulse field gel electrophoresis, in order to separate large DNA molecules, for 16 hours. Samples were checked with a spectrophotometer (Synergy H1 Hybrid Reader, BioTek Instruments Inc., Winooski, VT) and Qubit® fluorometer for quantification of our genomic DNA. Illumina and Pacbio Hybrid Assembly, Genome Size Estimation, and Quality Assessment All computational and bioinformatics analyses were conducted on the High Performance Computing (HPC) Cluster located that University of California, Irvine. Sequence data generated from two lanes of Illumina HiSeq 2500 were concatenated and raw sequence reads were assembled through PLATANUS v1.2.1 (1), which accounts for heterozygous diploid sequence data. Parameters used for PLATANUS was -m 256 (memory) and -t 48 (threads) for this initial assembly. Afterwards, contigs assembled from PLATANUS and reads from 40 SMRT cells of PacBio sequencing were assembled with a hybrid assembler DBG2OLC v1.0 (2). We used the following parameters in DBG2OLC: k 17 KmerCovTh 2 MinOverlap 20 AdaptiveTh 0.01 LD1 0 and RemoveChimera 1 and ran pbdagcon with default parameters. Without Illumina sequence reads, we also conducted a PacBio reads only assembly with FALCON v0.3.0 (https://github.com/PacificBiosciences/FALCON) with default parameters in order to assemble PacBio reads into contiguous sequences. The parameters we used were input type = raw, length_cutoff = 4000, length_cutoff_pr = 8000, with different cluster settings 32, 16, 32, 8, 64, and 32 cores, concurrency setting jobs were 32, and the remaining were default parameters. -
Evolutionary History and Whole Genome Sequence of Pejerrey (Odontesthes Bonariensis): New Insights Into Sex Determination in Fishes
Evolutionary History and Whole Genome Sequence of Pejerrey (Odontesthes bonariensis): New Insights into Sex Determination in Fishes by Daniela Campanella B.Sc. in Biology, July 2009, Universidad Nacional de La Plata, Argentina A Dissertation submitted to The Faculty of The Columbian College of Arts and Sciences of The George Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy January 31, 2015 Dissertation co-directed by Guillermo Ortí Louis Weintraub Professor of Biology Elisabet Caler Program Director at National Heart, Lung and Blood Institute, NIH The Columbian College of Arts and Sciences of The George Washington University certifies that Daniela Campanella has passed the Final Examination for the degree of Doctor of Philosophy as of December 12th, 2014. This is the final and approved form of the dissertation. Evolutionary History and Whole Genome Sequence of Pejerrey (Odontesthes bonariensis): New Insights into Sex Determination in Fishes Daniela Campanella Dissertation Research Committee: Guillermo Ortí, Louis Weintraub Professor of Biology, Dissertation Co-Director Elisabet Caler, Program Director at National Heart, Lung and Blood Institute, NIH, Dissertation Co-Director Hernán Lorenzi, Assistant Professor in Bioinformatics Department, J. Craig Venter Institute Rockville Maryland, Committee Member Jeremy Goecks, Assistant Professor of Computational Biology, Committee Member ! ""! ! Copyright 2015 by Daniela Campanella All rights reserved ! """! Dedication The author wishes to dedicate this dissertation to: My love, Ford, for his unconditional support and inspiration. For teaching me that admiration towards each other’s work is the fundamental fuel to go anywhere. My family and friends, for being there, meaning “there” everywhere and whenever. My grandpa Hugo, a pejerrey lover who knew how to fish, cook and enjoy the “silver arrows”. -
Draft Genome of the Mirrorwing Flyingfish (Hirundichthys Speculiger)
DATA REPORT published: 07 July 2021 doi: 10.3389/fgene.2021.695700 Draft Genome of the Mirrorwing Flyingfish (Hirundichthys speculiger) Pengwei Xu 1†, Chenxi Zhao 1†, Xinxin You 1,2†, Fan Yang 3, Jieming Chen 1,2, Zhiqiang Ruan 1,2, Ruobo Gu 2, Junmin Xu 2, Chao Bian 1,2* and Qiong Shi 1,2* 1 College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China, 2 Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China, 3 Marine Geological Department, Marine Geological Survey Institute of Hainan Province, Haikou, China Keywords: flying fish, whole genome sequencing, genome assembly, eevs, vision-related gene, phylogenetic tree SUMMARY Flying fishes are a group of Exocoetidae members with an intriguing epipelagic inhabitant. They have evolved numerous interesting characteristics. Here, we performed whole genome sequencing, de novo assembly and annotation of the representative mirrorwing flyingfish (Hirundichthys speculiger). We obtained a 1.04-Gb genome assembly using a hybrid approach from 99.21-Gb Illumina and 29.98-Gb PacBio sequencing reads. Its contig N50 and scaffold N50 values reached Edited by: 992.83 and 1,152.47 kb, respectively. The assembled genome was predicted to possess 23,611 Liang Guo, protein-coding genes, of which 23,492 (99.5%) were functionally annotated with public databases. South China Sea Fisheries Research A total of 42.02% genome sequences consisted of repeat elements, among them DNA transposons Institute, China accounted for the largest proportion (24.38%). A BUSCO (Benchmarking Universal Single Copy Reviewed by: Orthologs) evaluation demonstrated that the genome and gene completeness were 94.2% and Jitendra Kumar Sundaray, 95.7%, respectively. -
The Polycomb Orthologues in Teleost Fishes and Their Expression in the Zebrafish Model
G C A T T A C G G C A T genes Article The Polycomb Orthologues in Teleost Fishes and Their Expression in the Zebrafish Model Ludivine Raby, Pamela Völkel, Xuefen Le Bourhis and Pierre-Olivier Angrand * University Lille, CNRS, Inserm, CHU Lille, Centre Oscar Lambret, UMR 9020 - UMR 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France; [email protected] (L.R.); [email protected] (P.V.); [email protected] (X.L.B.) * Correspondence: [email protected]; Tel.: + 33-320-336-222 Received: 21 February 2020; Accepted: 26 March 2020; Published: 27 March 2020 Abstract: The Polycomb Repressive Complex 1 (PRC1) is a chromatin-associated protein complex involved in transcriptional repression of hundreds of genes controlling development and differentiation processes, but also involved in cancer and stem cell biology. Within the canonical PRC1, members of Pc/CBX protein family are responsible for the targeting of the complex to specific gene loci. In mammals, the Pc/CBX protein family is composed of five members generating, through mutual exclusion, different PRC1 complexes with potentially distinct cellular functions. Here, we performed a global analysis of the cbx gene family in 68 teleost species and traced the distribution of the cbx genes through teleost evolution in six fish super-orders. We showed that after the teleost-specific whole genome duplication, cbx4, cbx7 and cbx8 are retained as pairs of ohnologues. In contrast, cbx2 and cbx6 are present as pairs of ohnologues in the genome of several teleost clades but as singletons in others. -
ERSS Maylandia Zebra
Zebra Mbuna (Maylandia zebra) Ecological Risk Screening Summary U.S. Fish and Wildlife Service, February 2011 Revised, July 2018 Web Version, 8/3/2018 Photo: Bardrock. Licensed under CC BY-SA 4.0. Available: https://commons.wikimedia.org/wiki/File:Maylandia_zebra_-_ZOO_Edynburgh.JPG. (July 2018). 1 Native Range and Status in the United States Native Range From Froese and Pauly (2018): “Africa: Endemic to Lake Malawi [Malawi, Mozambique, Tanzania]. Occurs on the northwestern coast between Cape Manulo and Kande Islands. Also found on Jalo Reef, at Namalenje Islands, Cape Maclear, Monkey Bay, Boadzulu Islands and Nkopola. On the eastern part, occurs at Fort Maguire, Masinje on Likoma and Chisumulu Islands [Konings 1990].” 1 Status in the United States From Nico (2018): “Status: Reported from Nevada.” “The first report of this fish in Nevada was by a member of the American Cichlid Association, who observed several specimens of the "marmalade" form of P. zebra during a visit to Rogers Spring, a tributary of Lake Mead near Overton, Clark County, in July 1981 (Courtenay and Deacon 1982). Later records from Rogers Spring included a single male fish taken on 14 November 1981 (Courtenay, personal communication), and several individuals reportedly found in 1983 (Courtenay, personal communication). These records were apparently the basis for the listing of the species in later publications as introduced but not established in Nevada (e.g., Deacon and Williams 1984; Courtenay et al. 1984, 1986, 1991; Courtenay and Stauffer 1990; Vinyard 2001).” The most recent observation of M. zebra in Nevada occurred in 2001 (Nico 2018). This species is in trade in the United States. -
De Novo Transcriptome Analysis of Two Seahorse Species (Hippocampus Erectus and H
RESEARCH ARTICLE De Novo Transcriptome Analysis of Two Seahorse Species (Hippocampus erectus and H. mohnikei) and the Development of Molecular Markers for Population Genetics Qiang Lin1*, Wei Luo1, Shiming Wan2, Zexia Gao2 1 Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, 510275, China, 2 Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab. of Freshwater Animal a11111 Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China * [email protected] Abstract OPEN ACCESS Seahorse conservation has been performed utilizing various strategies for many decades, Citation: Lin Q, Luo W, Wan S, Gao Z (2016) De and the deeper understanding of genomic information is necessary to more efficiently pro- Novo Transcriptome Analysis of Two Seahorse tect the germplasm resources of seahorse species. However, little genetic information Species (Hippocampus erectus and H. mohnikei) and the Development of Molecular Markers for Population about seahorses currently exists in the public databases. In this study, high-throughput Genetics. PLoS ONE 11(4): e0154096. doi:10.1371/ RNA sequencing for two seahorse species, Hippocampus erectus and H. mohnikei, was journal.pone.0154096 carried out, and de novo assembly generated 37,506 unigenes for H. erectus and 36,113 Editor: Gao-Feng Qiu, Shanghai Ocean University, unigenes for H. mohnikei. Among them, 17,338 (46.23%) unigenes for H. erectus and CHINA 17,900 (49.57%) for H. mohnikei were successfully annotated based on the information Received: October 9, 2015 available from the public databases. -
De Novo Synthesis of a Sunscreen Compound in Vertebrates
De novo synthesis of a sunscreen compound in vertebrates Osborn, A. R., Almabruk, K. H., Holzwarth, G., Asamizu, S., LaDu, J., Kean, K. M., ... & Mahmud, T. (2015). De novo synthesis of a sunscreen compound in vertebrates. eLife, 4, e05919. doi:10.7554/eLife.05919 10.7554/eLife.05919 eLife Sciences Publications Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse SHORT REPORT elifesciences.org De novo synthesis of a sunscreen compound in vertebrates Andrew R Osborn1†, Khaled H Almabruk1†, Garrett Holzwarth2,3†, Shumpei Asamizu1‡, Jane LaDu4, Kelsey M Kean5, P Andrew Karplus5, Robert L Tanguay4, Alan T Bakalinsky2, Taifo Mahmud1* 1Department of Pharmaceutical Sciences, Oregon State University, Corvallis, United States; 2Department of Food Science and Technology, Oregon State University, Corvallis, United States; 3Department of Microbiology, Oregon State University, Corvallis, United States; 4Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, United States; 5Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States Abstract Ultraviolet-protective compounds, such as mycosporine-like amino acids (MAAs) and related gadusols produced by some bacteria, fungi, algae, and marine invertebrates, are critical for the survival of reef-building corals and other marine organisms exposed to high-solar irradiance. These compounds have also been found in marine fish, where their accumulation is thought to be of *For correspondence: taifo. dietary or symbiont origin. In this study, we report the unexpected discovery that fish can synthesize [email protected] gadusol de novo and that the analogous pathways are also present in amphibians, reptiles, and birds. †These authors contributed Furthermore, we demonstrate that engineered yeast containing the fish genes can produce and equally to this work secrete gadusol. -
Comparative Analysis of Repetitive Elements in Fish Genomes by Zihao
Comparative analysis of repetitive elements in fish genomes by Zihao Yuan A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama May 5, 2018 Keywords: Fish, Repetitive elements, Genome, Expression, Evolution Copyright 2018 by Zihao Yuan Approved by Zhanjiang Liu, Chair, Professor of School of Fisheries, Aquaculture and Aquatic Sciences Rex Dunham, Co-chair, Professor of School of Fisheries, Aquaculture and Aquatic Sciences Charles Y. Chen, Professor of Department of Crop, Soil and Environmental Sciences Bill Daniels, Associate Professor of School of Fisheries, Aquaculture and Aquatic Sciences Abstract Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, this dissertation work focused on comparative analysis of repetitive elements presented in three chapters: general overview and literature review (Chapter 1), analysis and annotation of the repetitive elements in the channel catfish genome (Chapter 2), and comparative analysis of repetitive elements from a large number (52) of the fish genomes (Chapter 3) Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for the industry. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. -
Understanding Explosive Diversification Through Cichlid Fish Genomics
REVIEWS Understanding explosive diversification through cichlid fish genomics Walter Salzburger Abstract | Owing to their taxonomic, phenotypic, ecological and behavioural diversity and propensity for explosive diversification, the assemblages of cichlid fish in the East African Great Lakes Victoria, Malawi and Tanganyika are important role models in evolutionary biology. With the release of five reference genomes and many additional genomic resources, as well as the establishment of functional genomic tools, the cichlid system has fully entered the genomic era. The in-depth genomic exploration of the East African cichlid fauna — in combination with the examination of their ecology , morphology and behaviour — permits novel insights into the way organisms diversify. Model organisms Why is species richness so unequally distributed across and morphological diversity as a consequence of adap- Non- human species studied in the tree of life? Why did some organismal lineages diver- tation to novel or hitherto underutilized ecological detail in the context of a sify into new forms in a seemingly explosive manner, niches14,15 — combine the advantages of laboratory and particular research question whereas others have lingered phenotypically unvaried natural model species in the context of the genesis of with the motivation to be able to make more general over millions of years? These questions have puzzled biodiversity. Therefore, iconic examples of adaptive radi- statements about the generations of biologists ever since Darwin and Wallace ation, such as Darwin’s finches on the Galapagos archi- functioning of organisms. jointly introduced their theory of evolution by natural pelago, anole lizards on the islands of the Caribbean, selection1. 160 years of scholarly study later, there is a rea- threespine stickleback fish in post- glacial rivers and Clades sonable understanding of how and under which circum- lakes, and cichlid fish in East Africa (BOx 1), have long Branches on an evolutionary 2–7 tree, consisting of a common stances new species can originate . -
A Taxonomically-Restricted Uric Acid Transporter Provides Insight Into Antioxidant Equilibrium
bioRxiv preprint doi: https://doi.org/10.1101/287870; this version posted March 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 A taxonomically-restricted Uric Acid transporter provides insight into antioxidant 2 equilibrium 3 Diogo Oliveira*,1, André Machado*,1, Tiago Cardoso1, Mónica Lopes-Marques1, L. 4 Filipe C. Castro1,2● and Raquel Ruivo1 ● 5 1CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, U. 6 Porto – University of Porto, Porto, Portugal 7 2Department of Biology, Faculty of Sciences, U. Porto - University of Porto, 8 Portugal 9 *Equal contribution 10 ●Corresponding authors at: CIIMAR, Terminal de Cruzeiros do Porto de Leixões, 11 Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal. Tel.: +351 223 12 401 831 13 14 Running head: Novel uric acid transporter in fish and amphibians 15 16 17 bioRxiv preprint doi: https://doi.org/10.1101/287870; this version posted March 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 18 Abstract 19 Nucleobase-Ascorbate Transporter (NAT) family includes ascorbic acid, 20 nucleobases and uric acid transporters, with a broad evolutionary distribution. In 21 vertebrates, four members have been previously recognized, the ascorbate transporters 22 Slc23a1 and Slc3a2, the nucleobase transporter Slc23a4 and an orphan transporter 23 SLC23A3. Here we identify a fifth member of the vertebrate slc23 complement (slc23a5), 24 expressed in neopterygians (gars and teleosts) and amphibians, and clarify the 25 evolutionary relationships between the novel gene and known slc23 genes. -
The Rises and Falls of Opsin Genes in 59 Ray-Finned Fish Genomes And
www.nature.com/scientificreports OPEN The rises and falls of opsin genes in 59 ray-fnned fsh genomes and their implications for Received: 20 October 2016 Accepted: 3 November 2017 environmental adaptation Published: xx xx xxxx Jinn-Jy Lin1,2,3, Feng-Yu Wang4, Wen-Hsiung Li1,3,5 & Tzi-Yuan Wang3 We studied the evolution of opsin genes in 59 ray-fnned fsh genomes. We identifed the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, frst emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specifc whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fshes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under diferent living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-fnned fsh evolution. Visual perception is important for an animal because it conveys the color, shape, size and movement of its surround- ing objects. -
Supporting Information
Supporting Information Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity Between the Spike Receptor-Binding Domain and Host ACE2 Xiaoqiang Huang1, Chengxin Zhang1, Robin Pearce1, Gilbert S. Omenn1, and Yang Zhang1,2* 1Department of Computational Medicine and Bioinformatics, 2Department of Biological Chemistry, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA * To whom correspondence should be addressed. Tel: +1 734 647 1549; Fax: +1 734 615 6443; Email: [email protected] Table of Contents Supporting Tables Table S1. 30 ACE2 proteins that were excluded from analysis due to inaccurate annotations (shown as ‘X’) in their sequences. Table S2. Six ACE2 proteins with five or more missing interface residues. Table S3. 285 ACE2 proteins used for detailed analysis in this work. Table S4. Binding energy and the three kinds of sequence identity for the 285 selected species. Table S5. Comparison of experimental and predicted N-glycosylation sites on hACE2. Table S6. Potential N-glycosylation sites in the 285 selected ACE2 proteins. Table S7. Comparison of the interface residues in the 285 ACE2 proteins. Supporting Figures Figure S1. The distribution of protein length, and sequence identity for all, interface, and the five key residues for 285 ACE2 orthologs. Figure S2. Matthews correlation coefficient for classifying experimentally determined effective ACE2 receptors from the less effective ones by the binding energy calculated from 500 models. Figure S3. Matthews correlation coefficient for classifying experimentally determined effective ACE2 receptors from the less effective ones by sequence identity in terms of all (a), interface (b), and key (c) residues. Figure S3.