Genomic resource development for shellfish of conservation concern

Molecular Ecology Resources

Volumn 13, Issue 2, 2013, Pages 295-305

  Timmins Schiffman, Emma B ^a   Friedman, Carolyn S ^a   Metzger, Dave C ^a   White, Samuel J ^a   Roberts, Steven B ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Gene expression; High throughput sequencing; Olympia oyster; Pinto abalone; Transcriptome

Indexed keywords

TRANSCRIPTOME;

ANIMAL; ARTICLE; CLASSIFICATION; ENDANGERED SPECIES; ENVIRONMENTAL PROTECTION; EVALUATION; EXPRESSED SEQUENCE TAG; GASTROPOD; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; OYSTER; PHYLOGENY; SHELLFISH; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CONSERVATION OF NATURAL RESOURCES; ENDANGERED SPECIES; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GASTROPODA; GENOMICS; OSTREIDAE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SHELLFISH; TRANSCRIPTOME;

HALIOTIDAE; HALIOTIS KAMTSCHATKANA; HALIOTIS KAMTSCHATKANA KAMTSCHATKANA; OSTREA CONCHAPHILA; OSTREA LURIDA; OSTREIDAE;

EID: 84873986749     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12052     Document Type: Article

References (66)

1. Altschul SF, Madden TL, Schäffer AA et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
2. Barton GM, Medzhitov R (2003) Toll-like receptor signaling pathways. Science, 300, 1524-1525.
3. Berlett BS, Stadtman ER (1997) Protein oxidation in aging, disease, and oxidative stress. Journal of Biological Chemistry, 272, 20313-20316.
4. Betti M, Ciacci C, Lorusso LC et al. (2006) Effects of tumor necrosis factor α (TNFα) on Mytilus haemocytes: role of stress-activated mitogen-activated protein kinases (MAPKs). Biology of the Cell, 98, 233-244.
5. Bouma JV, Rothaus DP, Straus KM, Vadopalas B, Friedman CS (2012) Low juvenile Pinto Abalone Haliotis kamtschatkana kamtschatkana abundance in the San Juan Archipelago, Washington State. Transactions of the American Fisheries Society, 141, 76-83.
6. Cahais V, Gayral P, Tsagkogeorga G et al. (2012) Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Molecular Ecology Resources, 12, 834-845.
7. Canesi L, Betti M, Ciacci C et al. (2002) Signaling pathways involved in the physiological response of mussel hemocytes to bacterial challenge: the role of stress-activated p38 MAP kinases. Developmental & Comparative Immunology, 26, 325-334.
8. Chapman RW, Mancia A, Beal M et al. (2011) The transcriptomic responses of the eastern oyster, Crassostrea virginica, to environmental conditions. Molecular Ecology, 20, 1431-1449.
9. Conus S, Simon H-U (2010) Cathepsins and their involvement in immune responses. Swiss Medical Weekly, 140, w13042.
10. David E, Tanguy A, Moraga D (2007) Peroxiredoxin 6: a new physiological and genetic indicator of multiple environmental stress response in Pacific oyster Crassostrea gigas. Aquatic Toxicology, 84, 389-398.
11. DeZoysa M, Jung S, Lee J (2009) First molluscan TNF- α homologue of the TNF superfamily in disk abalone: molecular characterization and expression analysis. Fish & Shellfish Immunology, 26, 625-631.
12. Dinnel PA, Peabody B, Peter-Contesse T (2009) Rebuilding olympia oysters, Ostrea lurida Carpenter 1864, in Fidalgo Bay, Washington. Journal of Shellfish Research, 28, 79-85.
13. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred II. error probabilities. Genome Research, 8, 186-194.
14. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred I. accuracy assessment. Genome Research, 8, 175-185.
15. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M (2011) Short read illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics, 12, 317-329.
16. Fleury E, Huvet A, Lelong C et al. (2009) Generation and analysis of 29, 745 unique expressed sequence tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database, the gigasdatabase. BMC Genomics, 10, 341-356.
17. Franchini P, van der Merwe M, Roodt-Wilding R (2011) Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis. BMC Research Notes, 4, 59-70.
18. Frankham R (2002) Relationship of genetic variation to population size in wildlife. Conservation Biology, 10, 1500-1508.
19. Friedman CS, Finley CA (2003) Anthropogenic introduction of the etiological agent of withering syndrome into northern California abalone populations via conservation efforts. Canadian Journal of Fisheries and Aquatic Sciences, 60, 1424-1431.
20. Fu D, Chen J, Zhang Y, Yu Z (2011) Cloning and expression of a heat shock protein (HSP) 90 gene in the haemocytes of Crassostrea hongkongensis under osmotic stress and bacterial challenge. Fish & Shellfish Immunology, 31, 118-125.
21. Gaitanaki C, Kefaloyianni E, Marmari A, Beis I (2004) Various stressors rapidly activate the p38-MAPK signaling pathway in Mytilus galloprovincialis (Lam.). Molecular and Cellular Biochemistry, 260, 119-127.
22. Genard B, Moraga D, Pernet F, David E, Boudry P, Tremblay R (2012) Expression of candidate genes related to metabolism, immunity and cellular stress during massive mortality in the American oyster Crassostrea virginica larvae in relation to biochemical and physiological parameters. Gene, 499, 70-75.
23. Gillespie GE (2009) Status of the olympia oyster, Ostrea lurida carpenter 1864, in British Columbia, Canada. Journal of Shellfish Research, 28, 59-68.
24. Griffitt RJ, Chandler GT, Greig TW, Quattro JM (2006) Cathepsin B and glutathione peroxidase show differing transcriptional responses in the grass shrimp, Palaemonetes pugio following exposure to three xenobiotics. Environmental Science and Technology, 40, 3640-3645.
25. Groth S, Rumrill S (2009) History of olympia oysters (Ostrea lurida Carpenter 1864) in oregon estuaries, and a description of recovering populations in Coos bay. Journal of Shellfish Research, 28, 51-58.
26. Hankewich S, Lessard J, Grebeldinger E (2008) Resurvey of Northern Abalone, haliotis kamtschatkana, populations in Southeast Queen Charlotte Islands, British Columbia, May 2007. Canadian Manuscript Report of Fisheries Aquatic Science, 2839, vii + 39 pp.
27. Hendrick JP, Hartl F (1993) Molecular chaperone functions of heat-shock proteins. Annual Review of Biochemistry, 62, 349-384.
28. Huang DW, Sherman BT, Lempicki RA (2009a) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4, 44-57.
29. Huang DW, Sherman BT, Lempicki RA (2009b) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37, 1-13.
30. IPCC (Intergovernmental Panel on Climate Change) (2007) Contribution of Working Groups I, II, and III to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Core Writing Team, Pachauri RK & Reisinger A (Eds) IPCC, Geneva, Switzerland, pp104.
31. Kawabe S, Yokoyama Y (2011) Novel isoforms of heat shock transcription factor 1 are induced by hypoxia in the Pacific oyster Crassostrea gigas. Journal of Experimental Zoology Part A: Ecological Genetics and Physiology, 315A, 394-407.
32. Kearse M, Moir R, Wilson A et al. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28, 1647-1649.
33. Livingstone DR, Nasci C, Solé M et al. (1997) Apparent induction of a cytochrom P450 with immunochemical similarities to CYP1A in digestive gland of the common mussel (Mytilus galloprovincialis L.) with exposure to 2, 2', 3, 4, 4', 5'-hexachlorobiphenyl and Arochlor 1254. Aquatic Toxicology, 38, 205-224.
34. Martin S, Richier S, Pedrotti M et al. (2011) Early development and molecular plasticity in the Mediterranean sea urchin Paracentrotus lividus exposed to CO2-driven acidification. Journal of Experimental Biology, 214, 1357-1368.
35. McGraw K (2009) The Olympia Oyster, Ostrea lurida Carpenter 1864 along the West Coast of North America. Journal of Shellfish Research, 28, 5-10.
36. Meistertzheim A, Tanguy A, Moraga D, Thébault M (2007) Identification of differentially expressed genes of the Pacific oyster Crassostrea gigas exposed to prolonged thermal stress. FEBS Journal, 274, 6392-6402.
37. Navarro A, Faria M, Barata C, Piña B (2011) Transcriptional response of stress genes to metal exposure in zebra mussel larvae and adults. Environmental Pollution, 159, 100-107.
38. NOAA (National Oceanographic and Atmospheric Administration) (2007) Species of Concern NOAA National Marine Fisheries Service, Pinto abalone Haliotis kamtschatkana. NOAA, Silver Spring, MD.
39. 2 alters response to thermal stress in sea urchin larvae. Marine Biology, 156, 439-446.
40. Parcellier A, Burbuxani S, Schmitt E, Solary E, Garrido C (2003) Heat shock proteins, cellular chaperones that modulate mitochondrial cell death pathways. Biochemical and Biophysical Research Communications, 304, 505-512.
41. Polson MP, Zacherl DC (2009) Geographic distribution and intertidal population status for the olympia oyster, Ostrea lurida carpenter 1864, from Alaska to Baja. Journal of Shellfish Research, 28, 68-77.
42. Qiu L, Song L, Xu W, Ni D, Yu Y (2007) Molecular cloning and expression of a toll receptor gene homologue from Zhikong Scallpo, Chlamys farreri. Fish & Shellfish Immunology, 22, 451-466.
43. Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conservation Biology, 17, 230-237.
44. Roberts SB, Hauser L, Seeb LW, Seeb JE (2012) Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing. PLoS ONE, 7, e30908. doi:10.1371/journal.pone.0030908.
45. Rogers-Bennett L (2007) Is climate change contributing to range reductions and localized extinctions in northern (Haliotis kamtschatkana) and flat (Haliotis walallensis) abalones? Bulletin of Marine Science, 81, 283-296.
46. Rothaus DP, Vadopalas B, Friedman CS (2008) Precipitous declines in pinto abalone (Haliotis kamtschatkana kamtschatkana) abundance in the San Juan Archipelago, Washington, USA, despite statewide fishery closure. Canadian Journal of Fisheries and Aquatic Sciences, 65, 2703-2711.
47. Sauvage C, Boudry P, deKoning DJ, Haley CS, Heurtebise S, Lapègue S (2010) QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas). Animal Genetics, 41, 390-399.
48. Seeb JE, Pascal CE, Grau ED et al. (2011) Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Molecular Ecology Resources, 11, 335-348.
49. Shen Y, Catchen J, Garcia T et al. (2012) Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 1, 102-108.
50. Stumpp M, Dupont S, Thorndyke MC, Melzner F (2011) CO2 induced seawater acidification impacts sea urchin larval development II: Gene expression patterns in pluteus larvae. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 160, 320-330.
51. Takeuchi T, Kawashima T, Koyanagi R et al. (2012) Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Research, 19, 117-130.
52. Tautz D, Domazet-Loso T (2011) The evolutionary origin of orphan genes. Nature Reviews, 12, 692-702.
53. Travers M, leBouffant R, Friedman CS et al. (2009) Pathogenic Vibrio harveyi, in contrast to non-pathogenic strains, intervenes with the p38 MAPK pathway to avoid an abalone haemoctye immune response. Journal of Cellular Biochemistry, 106, 152-160.
54. Trick M, Long Y, Meng J, Bancroft I (2009) Single nucleotide polymorphis (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnology Journal, 7, 334-346.
55. Vera JC, Wheat C, Fescemyer HW et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology, 17, 1636-1647.
56. Wallace SS (1999) Evaluating the effects of three forms of marine reserve on Northern Abalone populations in British Columbia, Canada. Conservation Biology, 13, 882-887.
57. Wang X, Martindale JL, Liu Y, Holbrook NJ (1998) The cellular response to oxidative stress: influences of mitogen-activated protein kinase signaling pathways on cell survival. Biochemical Journal, 15, 291-300.
58. Waterhouse RM, Adobnov EM, Tegenfeldt F, Li J, Kriventseva EV (2011) OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Research, 39, 930, doi:10.1093/nar/gk
59. Wheat CW, Fescemyer HW, Kvist J et al. (2011) Functional genomics of life history variation in a butterfly metapopulation. Molecular Ecology, 20, 1813-1828.
60. White J, Ruesink JL, Trimble AC (2009) The nearly forgotten oyster: Ostrea lurida carpenter 1864 (olympia oyster) history and management in Washington State. Journal of Shellfish Research, 28, 43-49.
61. Wikelski M, Cooke SJ (2006) Conservation physiology. Trends in Ecology & Evolution, 21, 28-46.
62. Wu C, Zhang W, Mai K, Xu W, Zhong X (2011) Effects of dietary zinc on gene expression of antioxidant enzymes and heat shock proteins in hepatopancreas of abalone Haliotis discus hannai. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 154, 1-6.
63. Zhang L, Li L, Zhang G (2011a) A Crassostrea gigas toll-like receptor and comparative analysis of TLR pathway in invertebrates. Fish & Shellfish Immunology, 30, 653-660.
64. Zhang W, Wu C, Mai K, Chen Q, Xu W (2011b) Molecular cloning, characterization and expression analysis of heat shock protein 90 from Pacific Abalone, Haliotis discus hannai Ino in response to dietary selenium. Fish & Shellfish Immunology, 30, 280-286.
65. Zhang Y, Fu D, Yu F, Liu Q, Yu Z (2011c) Two catalase homologs are involved in host protection against bacterial infection and oxidative stress in Crassostrea hongkongensis. Fish & Shellfish Immunology, 31, 894-903.
66. Zippay ML, Hofmann GE (2010) Effect of pH on gene expression and thermal tolerance of early life history stages of red Abalone (Haliotis rufescens). Journal of Shellfish Research, 29, 429-439.