De novo assembly and annotation of the Asian tiger mosquito (Aedesalbopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti)

Genome Biology and Evolution

Volumn 7, Issue 4, 2015, Pages 1192-1205

  Goubert, Clément ^a,b,c   Modolo, Laurent ^a,b,c   Vieira, Cristina ^a,b,c   Moro, Claire Valiente ^b,c,d   Mavingui, Patrick ^b,c,d,e   Boulesteix, Matthieu ^a,b,c  

^a LABORATOIRE DE BIOMÉTRIE ET BIOLOGIE EVOLUTIVE   (France)

^b UNIVERSITÉ LYON 1   (France)

^c UNIVERSITÉ DE LYON   (France)

^d CNRS   (France)

^e UNIVERSITÉ DE LA RÉUNION   (France)

Author keywords

Aedes albopictus; Bioinformatic pipeline; Repeated DNA; TE analysis; Transposable elements; Trinity

Indexed keywords

DNA; TRANSPOSON;

AEDES; ANIMAL; CHEMISTRY; COMPARATIVE STUDY; GENETICS; GENOMICS; INSECT GENOME; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; PROCEDURES; SOFTWARE; TRANSPOSON;

AEDES; ANIMALS; DNA; DNA TRANSPOSABLE ELEMENTS; GENOME, INSECT; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; REPETITIVE SEQUENCES, NUCLEIC ACID; SOFTWARE;

EID: 84942239872     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv050     Document Type: Article

References (48)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
2. Arensburger P, Hice RH, Wright JA, Craig NL, Atkinson PW. 2011. The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs. BMC Genomics 12:606.
3. Beck CR, Garcia-Perez JL, Badge RM, Moran JV. 2011. LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet. 12:187-215.
4. Bellini R, et al. 2010. Dispersal and survival of Aedes albopictus (Diptera: Culicidae) males in Italian urban areas and significance for sterile insect technique application. J Med Entomol. 47:1082-1091.
5. Biedler J, Tu Z. 2003. Non-LTR retrotransposons in the African malaria mosquito, Anopheles gambiae: unprecedented diversity and evidence of recent activity. Mol Biol Evol. 20:1811-1825.
6. Biémont C, Vieira C. 2004. [The influence of transposable elements on genome size]. J Soc Biol. 198:413-417.
7. Black WC, Ferrari JA, Sprengert D. 1988. Breeding structure of a colonising species: Aedes albopictus (Skuse) in the United States. Heredity (Edinb) 60(Pt 2):173-181.
8. Black WC, Rai KS. 1988. Genome evolution in mosquitoes: intraspecific and interspecific variation in repetitive DNA amounts and organization. Genet Res. 51:185-196.
9. Bonizzoni M, Gasperi G, Chen X, James AA. 2013. The invasive mosquito species Aedes albopictus: current knowledge and future perspectives. Trends Parasitol. 29:460-468.
10. Boulesteix M, Biémont C. 2005. Transposable elements in mosquitoes. Cytogenet Genome Res. 110:500-509.
11. Brown JE, et al. 2014. Human impacts have shaped historical and recent evolution in Aedes aegypti, the dengue and yellow fever mosquito. Evolution 68:514-525.
12. Casacuberta E, González J. 2013. The impact of transposable elements in environmental adaptation. Mol Ecol. 22:1503-1517.
13. Chénais B, Caruso A, Hiard S, Casse N. 2012. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene 509:7-15.
14. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 38:1767-1771.
15. Goodier JL, Kazazian HH. 2008. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135:23-35.
16. Grabherr MG, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29:644-652.
17. Hawley WA. 1988. The biology of Aedes albopictus. J Am Mosq Control Assoc Suppl. 1:1-39.
18. Holt RA, et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:129-149.
19. Huang X. 1999. CAP3: a DNA sequence assembly program. Genome Res. 9:868-877.
20. Jurka J, Bao W, Kojima KK. 2011. Families of transposable elements, population structure and the origin of species. Biol Direct. 6:44.
21. Jurka J, et al. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110:462-467.
22. Kapitonov VV, Jurka J. 2003. Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A. 100:6569-6574.
23. Koch P, Platzer M, Downie BR. 2014. RepARK-de novo creation of repeat libraries from whole-genome NGS reads. Nucleic Acids Res. 42:e80.
24. Kumar A, Rai KS. 1990. Intraspecific variation in nuclear DNA content among world populations of a mosquito, Aedes albopictus (Skuse). Theor Appl Genet. 79:748-752.
25. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9:357-359.
26. Lerat E, Burlet N, Biémont C, Vieira C. 2011. Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes. Gene 473:100-109.
27. Li W, Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
28. Linquist S, et al. 2013. Distinguishing ecological from evolutionary approaches to transposable elements. Biol Rev Camb Philos Soc. 88:573-584.
29. Marinotti O, et al. 2013. The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Res. 41:7387-7400.
30. McLain DK, Rai KS, Fraser MJ. 1987. Intraspecific and interspecific variation in the sequence and abundance of highly repeated DNA among mosquitoes of the Aedes albopictus subgroup. Heredity (Edinb) 58:373-381.
31. Medley KA, Jenkins DG, Hoffman EA. 2015. Human-aided and natural dispersal drive gene flow across the range of an invasive mosquito. Mol Ecol. 24:284-295.
32. Modolo L, Lerat E. 2014. Identification and analysis of transposable elements in genomic sequences. In: Poptsova MS, editor. Genome analysis: current procedures and application. Norfolk (UK): Caister Academic Press. p. 165-181.
33. Mousson L, et al. 2005. Phylogeography of Aedes (Stegomyia) aegypti (L.) and Aedes (Stegomyia) albopictus (Skuse) (Diptera: Culicidae) based on mitochondrial DNA variations. Genet Res. 86:1-11.
34. Nene V, et al. 2007. Genome sequence of Aedes aegypti, a major arbovirus vector. Science 316:1718-1723.
35. Novák P, Neumann P, Macas J. 2010. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11:378.
36. Pashley DP, Rai KS. 1983. Comparison of allozyme and morphological relationships in some Aedes (Stegomyia) mosquitoes (Diptera: Culicidae). Ann Entomol Soc Am. 76:388-394.
37. Rao PN, Rai KS. 1987. Inter and intraspecific variation in nuclear DNA content in Aedes mosquitoes. Heredity (Edinb) 59:253-258.
38. Rebollo R, Horard B, Hubert B, Vieira C. 2010. Jumping genes and epigenetics: towards new species. Gene 454:1-7.
39. Reiter P. 1996. [Oviposition and dispersion of Aedes aegypti in an urban environment]. Bull Soc Pathol Exot. 89:120-122.
40. Staton SE, et al. 2012. The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements. Plant J. 72:142-153.
41. Tange O. 2011. GNU parallel: the command-line power tool.; login USENIX Mag. 3:42-47.
42. Tu Z, Isoe J, Guzova JA. 1998. Structural, genomic, and phylogenetic analysis of Lian, a novel family of non-LTR retrotransposons in the yellow fever mosquito, Aedes aegypti. Mol Biol Evol. 15:837-853.
43. Vela D, Fontdevila A, Vieira C, García Guerreiro MP. 2014. A genome-wide survey of genetic instability by transposition in Drosophila hybrids. PLoS One 9:e88992.
44. Venner S, Feschotte C, Biémont C. 2009. Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet. 25:317-323.
45. Wicker T, et al. 2007. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 8:973-982.
46. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.
47. Zhou D, et al. 2014. Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites. BMC Genomics 15:42.
48. Zytnicki M, Akhunov E, Quesneville H. 2014. Tedna: a transposable element de novo assembler. Bioinformatics 30:2656-2658.