Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

Molecular Ecology

Volumn 22, Issue 11, 2013, Pages 3112-3123

  Ogden, R ^a   Gharbi, K ^b   Mugue, N ^c   Martinsohn, J ^d   Senn, H ^e   Davey, J W ^b   Pourkazemi, M ^f   McEwing, R ^a   Eland, C ^b   Vidotto, M ^g   Sergeev, A ^c   Congiu, L ^g  

^a RZSS   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c RUSSIAN FEDERAL RESEARCH INSTITUTE OF FISHERIES AND OCEANOGRAPHY   (Russian Federation)

^d JOINT RESEARCH CENTRE   (Italy)

^e ROYAL ZOOLOGICAL SOCIETY OF SCOTLAND   (United Kingdom)

^f International Sturgeon Research Institute   (Iran)

^g UNIVERSITY OF PADOVA   (Italy)

Author keywords

Acipenser; caviar; DNA; fisheries; traceability; wildlife forensics

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; ENDANGERED SPECIES; FISH; GENETIC MARKER; GENETICS; GENOMICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; NUCLEOTIDE SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BASE SEQUENCE; ENDANGERED SPECIES; FISHES; GENETIC MARKERS; GENOMICS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

ACIPENSER; ACIPENSER BAERII; ACIPENSER PERSICUS; ACIPENSERIDAE;

EID: 84878453836     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12234     Document Type: Article

References (43)

1. Baird NA, Etter PD, Atwood TS, et al,. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3, e3376.
2. Birstein VJ, Doukakis P, Desalle R, (2000) Polyphyly of mtDNA lineages in the Russian sturgeon, Acipenser gueldenstaedtii: forensic and evolutionary implications. Conservation Genetics, 1, 81-88.
3. Boscari E, Barbisan F, Congiu L, (2011) Inheritance pattern of microsatellite loci in the polyploid Adriatic sturgeon (Acipenser naccarii). Aquaculture, 321, 223-229.
4. Bronzi P, Rosenthal H, Gessner J, (2011) Global sturgeon aquaculture production: an overview. Journal of Applied Ichthyology, 27, 169-175.
5. Catchen J, Amores A, Hohenlohe P, Cresko W, Postlethwait J, (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes. Genomes and Genetics, 1, 171-182.
6. CITES & UNEP (2012) Convention on international trade in endangered species of wild fauna and flora. Appenices I, II and III. Valid from 3 April 2012. http://www.cites.org/eng/app/appendices.php (accessed on 26 June 2012).
7. Congiu L, Pujolar JM, Forlani A, et al,. (2011) Managing polyploidy in ex situ conservation genetics: the case of the critically endangered adriatic sturgeon (Acipenser naccarii). PLoS ONE, 6, 1-10.
8. Davey JW, et al,. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews. Genetics, 12, 499-510.
9. Davey JW, Cezard T, Utrilla PF, Eland C, Gharbi K, Blaxter M, (This Issue) Special characters of RAD Sequencing data: implications for genotyping. Molecular Ecology.
10. DeSalle R, Birstein VJ, (1996) PCR identification of black caviar. Nature, 381, 197-198.
11. Doukakis P, (2009) Report on the Caspian Environment Program Regional Workshop on Sturgeon Genetics, 16-18 June 2009, Trabzon, Turkey. Available from the World Bank, full citation pending.
12. Drauch Schreier A, Gille DA, Mahardja B, May B, (2011) Neutral markers confirm the octoploid origin and reveal spontaneous polyploidy in white sturgeon, Acipenser transmontanus. Journal of Applied Ichthyology 27 (Suppl2), 24-33.
13. Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA, (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE, 6, e18561.
14. European Commission (2006a) COMMISSION REGULATION (EC) No 865/2006 of 4 May 2006 laying down detailed rules concerning the implementation of Council Regulation (EC) No 338/97 on the protection of species of wild fauna and flora by regulating trade therein.
15. European Commission (2006b) New rules to combat illegal caviar trade. Commission Press Release IP/06/611, Brussels 15/05/2006.
16. Fontana F, Congiu L, Mudrak VA, Quattro JM, Smith TIJ, Ware K, Doroshov SI, (2008) Evidence of hexaploid karyotype in shortnose sturgeon. Genome, 51, 113-119.
17. Garvin MR, Saitoh K, Gharrett AJ, (2010) Application of single nucleotide polymorphisms to non-model species: a technical review. Molecular Ecology Resources, 10, 915-934.
18. Hohenlohe P, Amish S, Catchen J, Allendorf FW, Luikart G, (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources 11 (Suppl 1), 117-122.
19. Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G, (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. Nature Genetics, 44, 226-232. Doi: 10.1038/ng.1028.
20. IUCN (2012) The IUCN Red List of Threatened Species. Version 2012.1. http://www.iucnredlist.org. (Accessed on 26 June 2012).
21. Ludwig A, (2008) Identification of Acipenseriformes species in trade. Journal of Applied Ichthyology, 24 (S1), 2-19.
22. Ludwig A, Belfiore NM, Pitra C, Svirsky V, Jenneckens I, (2001) Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus). Genetics, 158, 1203-1215.
23. Lunter G, Goodson M, (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Research, 21, 936-939.
24. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA, (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research, 17, 240-248.
25. Mugue NS, Barminsteva AE, Rastorguev SM, Mugue VN, Barminstev VA, (2008) Polymorphism of the mitochondrial DNA control region in eight sturgeon species and development of a system for DNA-based species identification. Russian Journal of Genetics, 44, 793-798.
26. Nielsen EE, Cariani A, MacAoidh E, et al,. (2012) Gene-associated markers provide tools for tackling IUU fishing and false eco-certification. Nature Communications, 3, 851.
27. Ogden R, (2008) Fisheries forensics: the use of DNA tools for improving compliance, traceability and enforcement in the fishing industry. Fish and Fisheries, 9, 462-472.
28. Ogden R, (2011) Unlocking the potential for genomic technologies for wildlife forensics. Molecular Ecology Resources, 11 (S1), 109-116.
29. Pikitch EK, Doukakis P, Lauck L, Chakrabarty P, Erickson DL, et al,. (2005) Status, trends and management of sturgeon and paddlefish fisheries. Fish and Fisheries, 6, 233-265.
30. Pourkazemi M, (2006) Caspian Sea sturgeon conservation and fisheries: past, presnt and future. Journal of Applied Ichthyology, 22 (S1), 12-16.
31. Pourkazemi M, (2009) Comprehensive study on assessment of sturgeons population genetic structure in the Caspian Sea. Iranian Fishery Research Organization. International Sturgeon Research Institute. Project final report. 315 pages.
32. Raymakers C, (2006) CITES, the Convention on International Trade in Endangered Species of Wild Fauna and Flora: its role in the conservation of Acipenseriformes. Journal of Applied Ichthyology, 22 (S1), 53-65.
33. Raymakers BC, Hoover C, (2002) Acipenseriformes: CITES implementation from Range States to consumer countries. Journal of Applied Ichthyology, 18, 629-638.
34. Rehbein H, Molkentin J, Schubring R, Lieckfeldt D, Ludwig A, (2008) Development of advanced analytical tools to determine the origin of caviar. Journal of Applied Ichthyology, 24 (Suppl.1), 65-70.
35. Robinson JT, Thorvaldsdõttir H, Winckler W, et al,. (2011) Integrative genomics viewer. Nature Biotechnology, 29, 24-26.
36. Rosenthal H, Wei Q, Chang J, Bronzi P, Gessner J, (2011) Conclusions and recommendations of the 6th International Symposium on Sturgeons (Wuhan, China, October 2009)*. Journal of Applied Ichthyology, 27, 157-161.
37. Ruban GI, Khodorevskaya RP, (2011) Caspian Sea sturgeon fishery: a historic overview. Journal of Applied Ichthyology, 27, 199-208.
38. Senn H, Ogden R, Cezard T, et al,. (This Issue) A simple pipeline for the generation of SNP genotyping assays from RAD paired-end data without a reference genome in the Eurasian Beaver. Molecular Ecology.
39. Serang O, Mollinari M, Garcia AAF, (2012) Efficient exact maximum a posteriori computation for Bayesian SNP genotyping in polyploids. PLoS ONE, 7, e30906.
40. Vasil'ev VP, (2009) Mechanisms of polyploid evolution in fish: polyploidy in sturgeons. In Biology, Conservation, and Sustainable Development of Sturgeons (eds, Carmona R, Domezain A, García-Gallego M, Hernando JA,), pp. 97-117. Springer, Berlin, Germany.
41. Waldman JR, Doukakis P, Wirgin I, (2008) Molecular analysis as a conservation tool for monitoring the trade of North American sturgeons and paddlefish. Journal of Applied Ichthyology, 24 (S1), 20-28.
42. Wei Y-L, Li C-X, Jia J, Hu L, Liu Y, (2012) Forensic identification using a multiplex assay of 47 SNPs. Journal of Forensic Sciences, 57, 1448-1456.
43. Willing E-M, Hoffmann M, Klein JD, Weigel D, Dreyer C, (2011) Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics (Oxford, England), 27, 2187-2193.