What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae)

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Rasmussen, David A ^a   Noor, Mohamed A F ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; FLOW CYTOMETRY; FLY; GENE SEQUENCE; GENOME SIZE; INSECT GENETICS; INSECT GENOME; INTERSPERSED REPEAT; MEGASELIA SCALARIS; MICROSATELLITE MARKER; MITOCHONDRIAL GENOME; NONHUMAN; PYROSEQUENCING; SEQUENCE HOMOLOGY; TRANSPOSON; ANIMAL; BIOLOGY; DNA SEQUENCE; DROSOPHILA; FEMALE; GENETICS; GENOME; GENOMICS; MALE; METHODOLOGY;

MEGASELIA SCALARIS; PHORIDAE;

MICROSATELLITE DNA;

ANIMALS; COMPUTATIONAL BIOLOGY; DIPTERA; DROSOPHILA; FEMALE; GENOME, INSECT; GENOME, MITOCHONDRIAL; GENOMICS; INTERSPERSED REPETITIVE SEQUENCES; MALE; MICROSATELLITE REPEATS; SEQUENCE ANALYSIS, DNA;

EID: 69549112948     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-382     Document Type: Article

References (34)

1. Hudson ME Sequencing breakthroughs for genomic ecology and evolutionary biology Molecular Ecology Resources 2008, 8(1):3-17. 10.1111/ j.1471-8286.2007.02019.x
2. Abdelkrim J Robertson BC Stanton J-AL Gemmell NJ Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing BioTechniques 2009, 46(3):185-192. 10.2144/000113084 19317661
3. Allentoft ME Schuster SC Holdaway RN Hale ML McLay E Oskam C Gilbert MTP Spencer P Willerslev E Bunce M Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data BioTechniques 2009, 46(3):195-200. 10.2144/000113086 19317662
4. Green P 2× genomes Does depth matter? Genome Res 2007, 17(11):1547-1549. 10.1101/gr.7050807 17975171
5. Bouck J Miller W Gorrell JH Muzny D Gibbs RA Analysis of the quality and utility of random shotgun sequencing at low redundancies Genome Res 1998, 8(10):1074-1084. 310787 9799794
6. Kirkness EF Bafna V Halpern AL Levy S Remington K Rusch DB Delcher AL Pop M Wang W Fraser CM et al The dog genome: Survey sequencing and comparative analysis Science 2003, 301(5641):1898-1903. 10.1126/ science.1086432 14512627
7. Wernersson R Schierup MH Jorgensen FG Gorodkin J Panitz F Staerfeldt HH Christensen OF Mailund T Hornshoj H Klein A et al Pigs in sequence space: A 0.66× coverage pig genome survey based on shotgun sequencing BMC Genomics 2005, 6:70. 10.1186/1471-2164-6-70 1142312 15885146
8. Wicker T Narechania A Sabot F Stein J Vu GT Graner A Ware D Stein N Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats BMC Genomics 2008, 9:518. 10.1186/1471-2164-9-518 2584661 18976483
9. Disney RH Natural history of the scuttle fly, Megaselia scalaris Annual Review of Entomology 2008, 53:39-60. 10.1146/ annurev.ento.53.103106.093415 17622197
10. Biemont C Vieira C What transposable elements tell us about genome organization and evolution: The case of Drosophila Cytogenetic and Genome Research 2005, 110(14):25-34. 16093655
11. Kidwell MG Lisch DR Perspective: Transposable elements, parasitic DNA, and genome evolution Evolution 2001, 55(1):1-24. 11263730
12. Richards S Liu Y Bettencourt BR Hradecky P Letovsky S Nielsen R Thornton K Hubisz MJ Chen R Meisel RP et al Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution Genome Res 2005, 15(1):1-18. 10.1101/gr.3059305 540289 15632085
13. Traut W Willhoeft U A jumping sex determining factor in the fly Megaselia scalaris Chromosoma 1990, 99:407-412. 10.1007/BF01726692
14. Burt A Trivers R Genes in conflict: The biology of selfish genetic elements Cambridge, Mass.: Belknap Press 2006.
15. Garfield DA Noor MAF Characterization of novel repetitive element Leviathan in Drosophila pseudoobscura Drosophila Information Service 2007, 90:1-9.
16. Boore JL Animal mitochondrial genomes Nucleic Acids Res 1999, 27(8):1767-1780. 10.1093/nar/27.8.1767 148383 10101183
17. Hira PR Assad RM Okasha G Al-Ali FM Iqbal J Mutawali KE Disney RH Hall MJ Myiasis in Kuwait: Nosocomial infections caused by lucilia sericata and Megaselia scalaris Am J Trop Med Hyg 2004, 70(4):386-389. 15100451
18. Mazayad SA Rifaat MM Megaselia scalaris causing human intestinal myiasis in Egypt Journal of the Egyptian Society of Parasitology 2005, 35(1):331-340. 15881016
19. Wakid MH A laboratory-based study for first documented case of urinary myiasis caused by larvae of Megaselia scalaris (Diptera: Phoridae) in Saudi Arabia Korean Journal of Parasitology 2008, 46(1):33-36. 10.3347/ kjp.2008.46.1.33 2526290 18344675
20. Clark AG Eisen MB Smith DR Bergman CM Oliver B Markow TA Kaufman TC Kellis M Gelbart W Iyer VN et al Evolution of genes and genomes on the Drosophila phylogeny Nature 2007, 450(7167):203-218. 10.1038/nature06341 17994087
21. Holt RA Subramanian GM Halpern A Sutton GG Charlab R Nusskern DR Wincker P Clark AG Ribeiro JMC Wides R et al The genome sequence of the malaria mosquito Anopheles gambiae Science 2002, 298(5591):129-149. 10.1126/ science.1076181 12364791
22. Nene V Wortman JR Lawson D Haas B Kodira C Tu ZJ Loftus B Xi ZY Megy K Grabherr M et al Genome sequence of Aedes aegypti, a major arbovirus vector Science 2007, 316(5832):1718-1723. 10.1126/science.1138878 17510324
23. Peterson BK Hare EE Iyer VN Storage S Conner L Papaj DR Kurashima R Jang E Eisen MB Big genomes facilitate the comparative identification of regulatory elements PLoS ONE 2009, 4(3):e4688. 10.1371/ journal.pone.0004688 2650094 19259274
24. Malhi RS Sickler B Lin D Satkoski J Tito RY George D Kanthaswamy S Smith DG MamuSNP: A Resource for Rhesus Macaque (Macaca mulatta) Genomics PLoS ONE 2007, 2:e438. 10.1371/journal.pone.0000438 1859839 17487284
25. Altschul SF Madden TL Schäffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucl Acids Res 1997, 25:3389-3402. 10.1093/nar/ 25.17.3389 146917 9254694
26. Macas J Neumann P Navratilova A Repetitive DNA in the pea (Pisum sativum L.) genome: Comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula BMC Genomics 2007, 8:427. 10.1186/1471-2164-8-427 2206039 18031571
27. Swaminathan K Varala K Hudson ME Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey BMC Genomics 2007, 8:132. 10.1186/ 1471-2164-8-132 1894642 17524145
28. Li RQ Ye J Li SG Wang J Han YJ Ye C Wang J Yang HM Yu J Wong GKS et al ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun PLoS Computational Biology 2005, 1(4):313-321. 10.1371/journal.pcbi.0010043
29. Otto TD Gomes LHF Alves-Ferreira M deMiranda AB Degrave WM ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS) BMC Bioinformatics 2008, 9:366. 10.1186/1471-2105-9-366 2559850 18782453
30. Bosco G Campbell P Leiva-Neto JT Markow TA Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species Genetics 2007, 177(3):1277-1290. 10.1534/genetics.107.075069 2147996 18039867
31. Kofler R Schlötterer C Lelley T SciRoKo: A new tool for whole genome microsatellite search and investigation Bioinformatics 2007, 23(13):1683-1685. 10.1093/bioinformatics/btm157 17463017
32. Tweedie S Ashburner M Falls K Leyland P McQuilton P Marygold S Millburn G Osumi-Sutherland D Schroeder A Seal R et al FlyBase: Enhancing Drosophila Gene Ontology annotations Nucleic Acids Res 2009, 37:D555-D559. 10.1093/nar/gkn788 2686450 18948289
33. Lawson D Arensburger P Atkinson P Besansky NJ Bruggner RV Butler R Campbell KS Christley GKCS Dialynas E et al VectorBase: A data resource for invertebrate vector genomics Nucleic Acids Res 2009, 37:D583-D587. 10.1093/nar/gkn857 2686483 19028744
34. Jurka J Kapitonov VV Pavlicek A Klonowski P Kohany O Walichiewicz J Repbase Update, a database of eukaryotic repetitive elements Cytogenetic and Genome Research 2005, 110(14):462-467. 10.1159/000084979 16093699