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1 Exon Probe Sets and Bioinformatics Pipelines for All Levels of Fish Phylogenomics
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics 2 3 Lily C. Hughes1,2,3,*, Guillermo Ortí1,3, Hadeel Saad1, Chenhong Li4, William T. White5, Carole 4 C. Baldwin3, Keith A. Crandall1,2, Dahiana Arcila3,6,7, and Ricardo Betancur-R.7 5 6 1 Department of Biological Sciences, George Washington University, Washington, D.C., U.S.A. 7 2 Computational Biology Institute, Milken Institute of Public Health, George Washington 8 University, Washington, D.C., U.S.A. 9 3 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian 10 Institution, Washington, D.C., U.S.A. 11 4 College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China 12 5 CSIRO Australian National Fish Collection, National Research Collections of Australia, 13 Hobart, TAS, Australia 14 6 Sam Noble Oklahoma Museum of Natural History, Norman, O.K., U.S.A. 15 7 Department of Biology, University of Oklahoma, Norman, O.K., U.S.A. 16 17 *Corresponding author: Lily C. Hughes, [email protected]. 18 Current address: Department of Organismal Biology and Anatomy, University of Chicago, 19 Chicago, IL. 20 21 Keywords: Actinopterygii, Protein coding, Systematics, Phylogenetics, Evolution, Target 22 capture 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. -
참서대과 (Pisces: Cynoglossidae) 자어 2종의 미토콘드리아 DNA에 의한 형태동정의 타당성
Kor J Fish Aquat Sci 43(5), 482-488 한수지, 43(5), 482-488, 2010 참서대과 (Pisces: Cynoglossidae) 자어 2종의 미토콘드리아 DNA에 의한 형태동정의 타당성 권혁준・김진구✽ 부경대학교 자원생물학과 Validation of Morphology-based Identification of Two Cynoglossidae Larvae using Mitochondrial DNA Hyuck Joon Kwun and Jin Koo Kim* Department of Marine Biology, Pukyong National University, Busan 608-737, Korea Three specimens of Cynoglossidae larvae were collected from the southern Korean Sea in May and August of 2009, and were identified using morphological and molecular analysis. Specimens were divided into two groups based on the number of elongated dorsal fin rays on the top of the head: Cynoglossidae sp. A was defined as having two elongated dorsal fin rays, while Cynoglossidae sp. B possessed a single elongated dorsal fin ray. One specimen of Cynoglossidae sp. A, a post-larva with a notochord length (NL) of 5.8 mm was thought to be a Cynoglossus joyneri larva based on the presence of 115 dorsal pterogiophores, 85 anal pterogiophores, and 50 myomeres. Two specimens of Cynoglossidae sp. B, a 4.1 mm NL larva and a 11.3 mm NL juvenile, were thought to be Cynoglossus abbreviatus based on the presence of yolk in the former and 133 dorsal fin rays, 105 anal fin rays, and 63 myomeres in the latter. To test this morphology-based identification, molecular analysis was conducted using 419-422 bp of mitochondrial DNA 16S rRNA. Cynoglossidae sp. A was clearly matched to a Cynoglossus joyneri adult (d=0.000) and Cynoglossidae sp. B clustered closely with Cynoglossus abbreviatus adults (d=0.002). -
Belgian Register of Marine Species
BELGIAN REGISTER OF MARINE SPECIES September 2010 Belgian Register of Marine Species – September 2010 BELGIAN REGISTER OF MARINE SPECIES, COMPILED AND VALIDATED BY THE VLIZ BELGIAN MARINE SPECIES CONSORTIUM VLIZ SPECIAL PUBLICATION 46 SUGGESTED CITATION Leen Vandepitte, Wim Decock & Jan Mees (eds) (2010). Belgian Register of Marine Species, compiled and validated by the VLIZ Belgian Marine Species Consortium. VLIZ Special Publication, 46. Vlaams Instituut voor de Zee (VLIZ): Oostende, Belgium. 78 pp. ISBN 978‐90‐812900‐8‐1. CONTACT INFORMATION Flanders Marine Institute – VLIZ InnovOcean site Wandelaarkaai 7 8400 Oostende Belgium Phone: ++32‐(0)59‐34 21 30 Fax: ++32‐(0)59‐34 21 31 E‐mail: [email protected] or [email protected] ‐ 2 ‐ Belgian Register of Marine Species – September 2010 Content Introduction ......................................................................................................................................... ‐ 5 ‐ Used terminology and definitions ....................................................................................................... ‐ 7 ‐ Belgian Register of Marine Species in numbers .................................................................................. ‐ 9 ‐ Belgian Register of Marine Species ................................................................................................... ‐ 12 ‐ BACTERIA ............................................................................................................................................. ‐ 12 ‐ PROTOZOA ........................................................................................................................................... -
Co-Occurrence of Tetrodotoxin and Saxitoxins and Their Intra-Body Distribution in the Pufferfish Canthigaster Valentini
toxins Article Co-Occurrence of Tetrodotoxin and Saxitoxins and Their Intra-Body Distribution in the Pufferfish Canthigaster valentini Hongchen Zhu 1, Takayuki Sonoyama 2, Misako Yamada 1, Wei Gao 1, Ryohei Tatsuno 3, Tomohiro Takatani 1 and Osamu Arakawa 1,* 1 Graduate School of Fisheries and Environmental Sciences, Nagasaki University. 1-14, Bunkyo-machi, Nagasaki, Nagasaki 852-8521, Japan; [email protected] (H.Z.); [email protected] (M.Y.); [email protected] (W.G.); [email protected] (T.T.) 2 Shimonoseki Marine Science Museum. 6-1, Arcaport, Shimonoseki, Yamaguchi 750-0036, Japan; [email protected] 3 Department of Food Science and Technology, National Fisheries University, Japan Fisheries Research and Education Agency. 2-7-1, Nagatahonmachi, Shimonoseki, Yamaguchi 759-6595, Japan; tatsuno@fish-u.ac.jp * Correspondence: [email protected]; Tel.: +81-95-819-2844 Received: 9 June 2020; Accepted: 2 July 2020; Published: 3 July 2020 Abstract: Pufferfish of the family Tetraodontidae possess tetrodotoxin (TTX) and/or saxitoxins (STXs), but the toxin ratio differs, depending on the genus or species. In the present study, to clarify the distribution profile of TTX and STXs in Tetraodontidae, we investigated the composition and intra-body distribution of the toxins in Canthigaster valentini. C. valentini specimens (four male and six female) were collected from Amami-Oshima Island, Kagoshima Prefecture, Japan, and the toxins were extracted from the muscle, liver, intestine, gallbladder, gonads, and skin. Analysis of the extracts for TTX by liquid chromatography tandem mass spectrometry and of STXs by high-performance liquid chromatography with post-column fluorescence derivatization revealed TTX, as well as a large amount of STXs, with neoSTX as the main component and dicarbamoylSTX and STX itself as minor components, in the skin and ovary. -
The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes
G C A T T A C G G C A T genes Article The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes Dong In Kim y, Wataru Kai y, Sho Hosoya y, Mana Sato, Aoi Nozawa, Miwa Kuroyanagi, Yuka Jo, Satoshi Tasumi, Hiroaki Suetake, Yuzuru Suzuki and Kiyoshi Kikuchi * Fisheries Laboratory, University of Tokyo, Maisaka, Shizuoka 431-0214, Japan; [email protected] (D.I.K.); Wataru.Kai@fluidigm.com (W.K.); [email protected] (S.H.); [email protected] (M.S.); [email protected] (A.N.); [email protected] (M.K.); [email protected] (Y.J.); tasumi@fish.kagoshima-u.ac.jp (S.T.); [email protected] (H.S.); [email protected] (Y.S.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 16 October 2019; Accepted: 3 December 2019; Published: 10 December 2019 Abstract: Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. -
ASFIS ISSCAAP Fish List February 2007 Sorted on Scientific Name
ASFIS ISSCAAP Fish List Sorted on Scientific Name February 2007 Scientific name English Name French name Spanish Name Code Abalistes stellaris (Bloch & Schneider 1801) Starry triggerfish AJS Abbottina rivularis (Basilewsky 1855) Chinese false gudgeon ABB Ablabys binotatus (Peters 1855) Redskinfish ABW Ablennes hians (Valenciennes 1846) Flat needlefish Orphie plate Agujón sable BAF Aborichthys elongatus Hora 1921 ABE Abralia andamanika Goodrich 1898 BLK Abralia veranyi (Rüppell 1844) Verany's enope squid Encornet de Verany Enoploluria de Verany BLJ Abraliopsis pfefferi (Verany 1837) Pfeffer's enope squid Encornet de Pfeffer Enoploluria de Pfeffer BJF Abramis brama (Linnaeus 1758) Freshwater bream Brème d'eau douce Brema común FBM Abramis spp Freshwater breams nei Brèmes d'eau douce nca Bremas nep FBR Abramites eques (Steindachner 1878) ABQ Abudefduf luridus (Cuvier 1830) Canary damsel AUU Abudefduf saxatilis (Linnaeus 1758) Sergeant-major ABU Abyssobrotula galatheae Nielsen 1977 OAG Abyssocottus elochini Taliev 1955 AEZ Abythites lepidogenys (Smith & Radcliffe 1913) AHD Acanella spp Branched bamboo coral KQL Acanthacaris caeca (A. Milne Edwards 1881) Atlantic deep-sea lobster Langoustine arganelle Cigala de fondo NTK Acanthacaris tenuimana Bate 1888 Prickly deep-sea lobster Langoustine spinuleuse Cigala raspa NHI Acanthalburnus microlepis (De Filippi 1861) Blackbrow bleak AHL Acanthaphritis barbata (Okamura & Kishida 1963) NHT Acantharchus pomotis (Baird 1855) Mud sunfish AKP Acanthaxius caespitosa (Squires 1979) Deepwater mud lobster Langouste -
Complete Mitochondrial Genome Sequences of Three Rhombosoleid
Wang et al. Zoological Studies 2014, 53:80 http://www.zoologicalstudies.com/content/53/1/80 RESEARCH Open Access Complete mitochondrial genome sequences of three rhombosoleid fishes and comparative analyses with other flatfishes (Pleuronectiformes) Shu-Ying Wang, Wei Shi, Xian-Guang Miao and Xiao-Yu Kong* Abstract Background: Peltorhamphus novaezeelandiae, Colistium nudipinnis, and Pelotretis flavilatus belong to the family Rhombosoleidae of Pleuronectiformes. Their high phenotypic similarity has provoked great differences in the number and nomenclature of the taxa that depend primarily on morphological features. These facts have made it necessary to develop molecular markers for taxonomy and phylogenetic studies. In this study, the complete mitogenomes (mtDNA) of the three rhombosoleid fishes were determined for the comparative studies and potential development of molecular markers in the future. Results: The lengths of the complete mitogenome of the three flatfishes are 16,889, 16,588, and 16,937 bp in the order mentioned above. The difference of lengths mainly results from the presence of tandem repeats at the 3′-end with variations of motif length and copy number in the control regions (CR). The gene content and arrangement is identical to that of the typical teleostean mtDNA. Two large intergenic spacers of 28 and 18 bp were found in P. flavilatus mtDNA. The genes are highly conserved except for the sizes of ND1 (which is 28 bp shorter than the two others), ND5 (13 bp longer), and tRNAGlu (5 bp longer) in P. flavilatus mtDNA. The symbolic structures of the CRs are observed as in other fishes, including ETAS, CSB-F, E, D, C, B, A, G-BOX, pyrimidine tract, and CSB2, 3. -
Neoteleostei Stenopterygii Bristle Mouth Cyclothone Sp. Viperfish
27.4.2012 „modern fishes“ - enhanced Neoteleostei cods tetraodonts • More then 15.000 species • Incredible diversity • Not established systematics Deep sea fishes perches Stenopterygii Bristle mouth Cyclothone sp. • Stomiiformes, Ateleopodiformes • Long independent evolution • Tropical – temperate deep sea fishes • Photophores, large mouth, (adipose fin) • Black (silvery) Viperfish Chauliodus sp. Dragonfish Idiacanthus sp. 1 27.4.2012 Scopelomorpha Daggertooth Anotopterus pharao • Aulopiformes, Myctophiformes, Lamprioformes, Polymixiiformes • Similar to salmoniform fishes • Adipose fin • 14 families 600 species • Deep sea Lancetfish Alepisaurus sp. Lanternfish Myctophum sp. Percopsiformes Sandroller Percopsis sp. • 3 familes 9 species • small fish 5 –20 cm • freshwater habitats in North America 2 27.4.2012 Ophidiiformes Pearlfish Carapus sp. • 3 families, 200 species • Seawater, freshwater and brakishwater, Deep‐ sea • Also in caves (blin d) • Eel‐like fishes Cod fish-Gadus morhua Gadiformes Ordo: Gadiformes • 4 families, 500 species Family: Gadidae • Bottom‐oriented fish • Mainly marine, deep sea, continental shelf, fhfreshwaters Burbot-Lota lota Ordo:Gadiformes Merlucius merlucius Family:Gadidae 3 27.4.2012 Batrachoidiformes Lophiiformes • tma • zima Ceratias holboelli • ohromný prostor Ordo: Lophiiphormes Family: Ceratiidae ilici um males Mugiliformes Atheriniformes 4 27.4.2012 Beloniformes Belone belone ordo Beloniformes Cyprinodontiformes Poecilia sp. Poecilidae Cyprinidontiformes Stephanoberyciloformes Beryciloformes 5 27.4.2012 -
Novel Gene Rearrangement and the Complete Mitochondrial Genome of Cynoglossus Monopus: Insights Into the Envolution of the Family Cynoglossidae (Pleuronectiformes)
International Journal of Molecular Sciences Article Novel Gene Rearrangement and the Complete Mitochondrial Genome of Cynoglossus monopus: Insights into the Envolution of the Family Cynoglossidae (Pleuronectiformes) Chen Wang 1, Hao Chen 2, Silin Tian 1, Cheng Yang 1 and Xiao Chen 1,3,* 1 College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; [email protected] (C.W.); [email protected] (S.T.); [email protected] (C.Y.) 2 Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA; [email protected] 3 Guangdong Laboratory for Lingnan Modern Agriculture, South China Agriculture University, Guangzhou 510642, China * Correspondence: [email protected]; Tel.: +86-139-2210-4624; Fax: +86-20-8528-0547 Received: 12 August 2020; Accepted: 16 September 2020; Published: 20 September 2020 Abstract: Cynoglossus monopus, a small benthic fish, belongs to the Cynoglossidae, Pleuronectiformes. It was rarely studied due to its low abundance and cryptical lifestyle. In order to understand the mitochondrial genome and the phylogeny in Cynoglossidae, the complete mitogenome of C. monopus has been sequenced and analyzed for the first time. The total length is 16,425 bp, typically containing 37 genes with novel gene rearrangements. The tRNA-Gln gene is inverted from the light to the heavy strand and translocated from the downstream of tRNA-Ile gene to its upstream. The control region (CR) translocated downstream to the 3’-end of ND1 gene adjoining to inverted to tRNA-Gln and left a 24 bp trace fragment in the original position. The phylogenetic trees were reconstructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 32 tonguefish species and two outgroups. -
Sea Slug Pleurobranchaea Maculata and Coincidence of Dog Deaths Along Auckland Beaches September 2009 TR 2009/108
Review of Tetrodotoxins in the Sea Slug Pleurobranchaea maculata and Coincidence of Dog Deaths along Auckland Beaches September 2009 TR 2009/108 Auckland Regional Council Technical Report No.108 September 2009 ISSN 1179-0504 (Print) ISSN 1179-0512 (Online) ISBN 978-1-877540-23-3 Approved for ARC Publication by: Name: Grant Barnes Position: Group Manager Monitoring & Research Organisation: Auckland Regional Council Date: 18 September 2009 Recommended Citation: McNabb, P.; Mackenzie, L.; Selwood, A.; Rhodes, L.; Taylor, D.; Cornelison C. (2009). Review of tetrodotoxins in the sea slug Pleurobranchaea maculata and coincidence of dog deaths along Auckland Beaches. Prepared by Cawthron Institute for the Auckland Regional Council. Auckland Regional Council Technical Report 2009/ 108. © 2009 Auckland Regional Council This publication is provided strictly subject to Auckland Regional Council's (ARC) copyright and other intellectual property rights (if any) in the publication. Users of the publication may only access, reproduce and use the publication, in a secure digital medium or hard copy, for responsible genuine non-commercial purposes relating to personal, public service or educational purposes, provided that the publication is only ever accurately reproduced and proper attribution of its source, publication date and authorship is attached to any use or reproduction. This publication must not be used in any way for any commercial purpose without the prior written consent of ARC. ARC does not give any warranty whatsoever, including without limitation, as to the availability, accuracy, completeness, currency or reliability of the information or data (including third party data) made available via the publication and expressly disclaim (to the maximum extent permitted in law) all liability for any damage or loss resulting from your use of, or reliance on the publication or the information and data provided via the publication. -
4 Alat Tangkap Dan Ikan
4.5 Jenis-Jenis Ikan 4.5.1. Ikan Bersirip (Finfish) (1.1) Ikan Sebelah, Indian Halibuts, Spiny Turbot - Psettodidae Karakteristik: bentuk badan pipih (lateral), mulut lebar posisi terminal dan kedua mata berada pada satu sisi tubuh bagian atas. Ikan ini berenang di atas dasar, kadang menyembunyikan diri di dasar pasir atau pasir berlumpur – termasuk ikan predator, jenis makanan ikan kecil dan Benthos. Warna umumnya coklat kemerahan. Umumnya ditangkap pada ukuran 50 cm, namun bisa mencapai panjang 64 cm. Sebutan ikan sebelah berasal dari tiga famili, ialah: Bothidae, Psettodidae, dan Paralichthydae. Spesies yang paling umum adalah Psettodes erumei. Nama lokal yang banyak digunakan ialah: Beteh, Grobiat, Lewe, kalankan, Pila-Pila, Sisa Nabo, Tipo, Togok. Habitat: ikan sebelah termasuk ikan demersal, berenang di atas dasar atau menyembunyikan diri di dasar. Tipe substrat yang digemari terutama pasir dan berlumpur – ikan sebelah paling banyak ditemukan di wilayah perairan Utara Jawa, Selatan Kalimantan, Sumatera sampai Papua. Alat tangkap: alat tangkap paling dominan menangkap ikan sebelah ialah Trawl dasar (pukat harimau). Juga, dia sering ditangkap dengan Pukat Pantai, Dogol dan Payang. Kadang-kadang dia juga tertangkap dengan alat Gill Net Dasar. Gambar 4.15 Morfologi umum ikan Sebelah yang ditangkap di perairan Utara Jawa (Foto: diambil dari Gelondong Gede Tuban, oleh Setyohadi). Deskripsi spesies yang diduga ditemukan di Indonesia: No Nama Latin Nama lokal Keterangan 1 Arnoglossus macrolophus Sebelah, Large- Kategori:Tidak komersial, tidak disukai oleh konsumen (Alcock, 1889) crested left eye karena sisiknya kasar; di tangkap dengan alat tangkap flounder Hook & lines ukuran > 13 cm dan ukurannya terlalu kecil (13 cm), termasuk famili Bothidae; habitat: hidup pada 84 Karakteristik perikanan laut Indonesia: jenis ikan dasar perairan berpasir, lumpur dan kerikil; tercatat pernah ditemukan Padang Sumatera, Kalimantan, Jawa dan Flores. -
Comments on Puffers of the Genus Takifugu from Russian Waters with the First Record of Yellowfin Puffer, Takifugu Xanthopterus (
Bull. Natl. Mus. Nat. Sci., Ser. A, 42(3), pp. 133–141, August 22, 2016 Comments on Puffers of the Genus Takifugu from Russian Waters with the First Record of Yellowfin Puffer, Takifugu xanthopterus (Tetraodontiformes, Tetraodontidae) from Sakhalin Island Yury V. Dyldin1, Keiichi Matsuura2 and Sergey S. Makeev3 1 Tomsk State University, Lenin Avenue 36, Tomsk, 634050, Russia E-mail: [email protected] 2 National Museum of Nature and Science, 4–1–1 Amakubo, Tsukuba, Ibaraki 305–0005, Japan E-mail: [email protected] 3 FGBI Sakhalinrybvod, ul. Emelyanova, 43A, 693000 Yuzhno-Sakhalinsk, Russia E-mail: [email protected] (Received 31 March 2016; accepted 22 June 2016) Abstract In August 2015 a single specimen of Takifugu xanthopterus was collected at the mouth of the Lyutoga River in Aniva Bay, southern Sakhalin Island in the southern Sea of Okhotsk. This is the first discovery of this species from Sakhalin Island, and represents the northernmost record for the species. Also we report eight species of Takifugu from Russia based on newly collected specimens, our survey of literature and the fish collection of the Zoological Institute, Russian Academy of Sciences. Key words : Puffers, Takifugu, taxonomy, Sakhalin, new record Introduction phyreus (Temminck and Schlegel, 1850) and T. rubripes (Temminck and Schlegel, 1850) have Sakhalin Island is the largest island of the Rus- been collected in this area (see Schmidt, 1904; sian Federation and surrounded by the Seas of Lindberg et al., 1997; Sokolovsky et al., 2011). Japan and Okhotsk (Fig. 1). The west coast of During the course of study on the fish fauna of Sakhalin is washed by the warm Tsushima Cur- Sakhalin Island by the first author, specimens of rent and the east coast by the cold East Sakhalin the genus Takifugu have become available for Current.