De novo assembly of the transcriptome of an invasive snail and its multiple ecological applications

Molecular Ecology Resources

Volumn 12, Issue 6, 2012, Pages 1133-1144

  Sun, J ^a   Wang, M ^a   Wang, H ^b   Zhang, H ^a   Zhang, X ^c   Thiyagarajan, V ^d   Qian, P Y ^b   Qiu, J W ^a  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

^b HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

^c Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^d UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Apple snail; Microsatellite; Pomacea; Proteome; Single nucleotide polymorphism; Transcriptome

Indexed keywords

GASTROPODA; MALUS X DOMESTICA; POMACEA; POMACEA CANALICULATA;

EID: 84867541892     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12014     Document Type: Article

References (64)

1. Albrecht EA, Carreño NB, Castro-Vazquez A (1996) A quantitative study of copulation and spawning in the South American apple-snail, Pomacea canaliculata (Prosobranchia: Ampullariidae). Veliger, 39, 142-147.
2. Angeloni F, Wagemaker CA, Jetten MS et al. (2011) De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques. Molecular Ecology Resources, 11, 662-674.
3. Blumenthal D (2006) Interactions between resource availability and enemy release in plant invasion. Ecology Letters, 9, 887-895.
4. Bock DG, Zhan A, Lejeusne C, MacIsaac HJ, Cristescu ME (2011) Looking at both sides of the invasion: patterns of colonization in the violet tunicate Botrylloides violaceus. Molecular Ecology, 20, 503-516.
5. Broz AK, Broeckling CD, He J, Dai X, Zhao PX, Vivanco JM (2007) A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa. BMC Plant Biology, 7, 25.
6. Capy P, Gasperi G, Biémont C, Bazin C (2000) Stress and transposable elements: co-evolution or useful parasites? Heredity, 85, 101-106.
7. Carlsson NOL, Brönmark C, Hansson LA (2004) Invading herbivory: the golden apple snail alters ecosystem functioning in Asian wetlands. Ecology, 85, 1575-1580.
8. Chuong TT, Hayes KA, Cowie RH (2008) Lack of mitochondrial DNA diversity in invasive apple snails (Ampullariidae) in Hawaii. Malacologia, 50, 351-357.
9. Clark MS, Thorne MA, Toullec JY et al. (2011) Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome. PLoS ONE, 6, e15919.
10. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
11. Cowie RH (2002) Apple snails as agricultural pests: their biology, impacts, and management. In: Molluscs as Crop Pests (ed. Barker GM), pp. 145-192. CABI Publishing, Wallingford, New Zealand.
12. Dreon M, Lavarias S, Garin CF, Heras H, Pollero RJ (2002) Synthesis, distribution, and levels of an egg lipoprotein from the apple snail Pomacea canaliculata (Mollusca: Gastropoda). Journal of Experimental Zoology, 292, 323-330.
13. Dreon MS, Ituarte S, Heras H (2010) The role of the proteinase inhibitor ovorubin in apple snail eggs resembles plant embryo defense against predation. PLoS ONE, 5, e15059.
14. Ellegren H (2008) Comparative genomics and the study of evolution by natural selection. Molecular Ecology, 17, 4586-4596.
15. Fang L, Wong PK, Lin L, Lan C, Qiu J-W (2010) Impact of invasive apple snails in Hong Kong on wetland macrophytes, nutrients, phytoplankton and filamentous algae. Freshwater Biology, 55, 1191-1204.
16. 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.
17. Hayes KA, Joshi RC, Thiengo SC, Cowie RH (2008) Out of South America: multiple origins of non-native apple snails in Asia. Diversity and Distributions, 14, 701-712.
18. Hayes KA, Cowie RH, Jørgensen A, Schultheiß R, Albrecht C, Thiengo SC (2009a) Molluscan models in evolutionary biology: apple snails (Gastropoda: Ampullariidae) as a system for addressing fundamental questions. American Malacological Bulletin, 27, 47-58.
19. Hayes KA, Cowie RH, Thiengo SC (2009b) A global phylogeny of apple snails: Gondwanan origin, generic relationships, and the influence of outgroup choice (Caenogastropoda: Ampullariidae). Biological Journal of the Linnean Society, 98, 61-76.
20. Henkel SK, Hofmann GE (2008) Differing patterns of hsp70 gene expression in invasive and native kelp species: evidence for acclimation-induced variation. Journal of Applied Phycology, 20, 1915-1924.
21. Herborg LM, Weetman D, Van Oosterhout C, Hänfling B (2007) Genetic population structure and contemporary dispersal patterns of a recent European invader, the Chinese mitten crab, Eriocheir sinensis. Molecular Ecology, 16, 231-242.
22. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proceedings International Conference on Intelligent Systems for Molecular Biology, 13, 8-148.
23. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research, 110, 462-467.
24. Kimura Y, Tosa Y, Shimada S et al. (2001) OARE-1, a Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses. Plant and Cell Physiology, 42, 1345-1354.
25. Kolar CS, Lodge DM (2001) Progress in invasion biology: predicting invaders. Trends in Ecology & Evolution, 16, 199-204.
26. Kwong KL, Wong PK, Lau SSS, Qiu J-W (2008) Determinants of the distribution of apple snails in Hong Kong two decades after their initial invasion. Malacologia, 50, 293-302.
27. Li R, Zhu H, Ruan J et al. (2009) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research, 20, 265-272.
28. Lockwood BL, Somero GN (2010) Transcriptomic responses to salinity stress in invasive and native blue mussels (genus Mytilus). Molecular Ecology, 20, 517-529.
29. Loreto EL, Carareto CM, Capy P (2008) Revisiting horizontal transfer of transposable elements in Drosophila. Heredity, 100, 545-554.
30. Lu P, Vogel C, Wang R, Yao X, Marcotte EM (2006) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnology, 25, 117-124.
31. Martín PR, Estebenet AL, Cazzaniga NJ (2001) Factors affecting the distribution of Pomacea canaliculata (Gastropoda: Ampullariidae) along its southernmost natural limit. Malacologia, 43, 13-23.
32. McClintock B (1984) The significance of response of the genome to challenge. Science, 226, 792-801.
33. Meyer E, Aglyamova GV, Wang S et al. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics, 10, 219.
34. Moseley PL (1997) Heat shock proteins and heat adaptation of the whole organism. Journal of Applied Physiology, 83, 1413-1417.
35. Moyle PB, Light T (1996) Biological invasions of fresh water: empirical rules and assembly theory. Biological Conservation, 78, 149-161.
36. Nardon C, Deceliere G, Loevenbruck C, Weiss M, Vieira C, Biémont C (2005) Is genome size influenced by colonization of new environments in dipteran species? Molecular Ecology, 14, 869-878.
37. Naylor R (1996) Invasions in agriculture: assessing the cost of the golden apple snail in Asia. Ambio, 25, 443-448.
38. Pimental D, Zuniga R, Morrison D (2005) Update on the environmental and economic costs associated with alien-invasive species in the United States. Ecological Economics, 52, 273-288.
39. Ramakrishnan V (2007) Salinity, pH, temperature, desiccation and hypoxia tolerance in the invasive freshwater apple snail Pomacea insularum. PhD thesis, The University of Texas at Arlington.
40. Rawlings TA, Hayes KA, Cowie RH, Collins TM (2007) The identity, distribution, and impacts of non-native apple snails in the continental United States. BMC Evolutionary Biology, 7, 97.
41. Renaut S, Nolte AW, Bernatchez L (2010) Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Ecology, 19(Suppl. 1), 115-131.
42. Santos CAZ, Penteado CHS, Mendes EG (1987) The respiratory responses of an amphibious snail Pomacea lineata (Spix, 1827), to temperature and oxygen tension variations. Comparative Biochemistry and Physiology Part A: Physiology, 86, 409-415.
43. Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11(Suppl. 1), 1-8.
44. Seuffert ME, Burela S, Martín PR (2010) Influence of water temperature on the activity of the freshwater snail Pomacea canaliculata (Caenogastropoda: Ampullariidae) at its southernmost limit (Southern Pampas, Argentina). Journal of Thermal Biology, 35, 77-84.
45. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) ABySS: a parallel assembler for short read sequence data. Genome Research, 19, 1117-1123.
46. Sun J, Zhang Y, Thiyagarajan V, Qian P-Y, Qiu J-W (2010) Protein expression during the embryonic development of a gastropod. Proteomics, 10, 2701-2711.
47. Sun J, Zhang H, Wang H et al. (2012) First proteome of the egg perivitelline fluid of a freshwater gastropod with aerial oviposition. Journal of Proteome Research, 11, 4240-4248.
48. Thumma BR, Sharma N, Southerton SG (2012) Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection. BMC Genomics, 13, 364.
49. Tomanek L, Zuzow MJ (2010) The proteomic response of the mussel congeners Mytilus galloprovincialis and M. trossulus to acute heat stress: implications for thermal tolerance limits and metabolic costs of thermal stress. Journal of Experimental Biology, 213, 3559-3574.
50. Vidal O, Sanz N, Araguas R-M, Fernández-Cebrian R, Diez-del-Molino D, García-Marín J-L (2012) SNP diversity in introduced populations of the invasive Gambusia holbrooki. Ecology of Freshwater Fish, 21, 100-108.
51. Voisin M, Engel CR, Viard F (2006) Differential shuffling of native genetic diversity across introduced regions in a brown alga: aquaculture vs. maritime traffic effects. Proceedings of the National Academy of Sciences, 102, 5432-5437.
52. Voolstra CR, Sunagawa S, Matz MV et al. (2011) Rapid evolution of coral proteins responsible for interaction with the environment. PLoS ONE, 6, e20392.
53. Wang S, Zhang L, Matz M (2009) Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (cnidaria, anthozoa, scleractinia). Journal of Heredity, 100, 329-337.
54. Wang H, Zhang H, Wong YH et al. (2010a) Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina. Proteomics, 10, 2972-2981.
55. Wang S, Zhang L, Meyer E, Bao Z (2010b) Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome. Biology Direct, 5, 18.
56. Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS (2010c) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics, 11, 400.
57. Wong PK, Kwong KL, Qiu J-W (2009) Complex interactions among fish, snails and macrophytes: implications for biological control of an invasive snail. Biological Invasions, 11, 2223-2232.
58. Wong PK, Liang Y, Liu NY, Qiu JW (2010) Palatability of macrophytes to the invasive freshwater snail Pomacea canaliculata: differential effects of multiple plant traits. Freshwater Biology, 55, 2023-2031.
59. Wu J-Y, Wu Y-T, Li M-C, Chiu Y-W, Liu M-Y, Liu L-L (2011) Reproduction and juvenile growth of the invasive apple snails Pomacea canaliculata and P. scalaris (Gastropoda: Ampullariidae) in Taiwan. Zoological Studies, 50, 61-68.
60. Zerebecki RA, Sorte CJB (2011) Temperature tolerance and stress proteins as mechanisms of invasive species success. PLoS ONE, 6, e14806.
61. Zhan A, Bao Z, Lu W et al. (2007) Development and characterization of 45 novel microsatellite markers for sea cucumber (Apostichopus japonicus). Molecular Ecology Notes, 7, 1345-1348.
62. Zhan A, Perepelizin PV, Ghabooli S et al. (2012) Scale-dependent post-establishment spread and genetic diversity in an invading mollusc in South America. Diversity and Distributions. DOI: 10.1111/j.1472-4642.2012.00894.x.
63. Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563-584.
64. Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J (2006) KaKs_Calculator: Calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics, 4, 259-263.