Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Ekblom, Robert ^a   Smeds, Linnéa ^a   Ellegren, Hans ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Error rate; mtDNA; Next generation sequencing; Sequencing bias; SSE

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL TISSUE; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; COPY NUMBER VARIATION; CORRELATIONAL STUDY; DNA SEQUENCE; FEMALE; FLYCATCHER; GENE MAPPING; GENETIC PARAMETERS; GENOMIC FRAGMENT; GULO GULO; HIGH THROUGHPUT SEQUENCING; MALE; MITOCHONDRIAL GENOME; MITOCHONDRION; MUSTELIDAE; NONHUMAN; NUCLEOTIDE MOTIF; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; SEQUENCING COVERAGE; SEQUENCING ERROR; VERTEBRATE; ANIMAL; CLASSIFICATION; DNA BASE COMPOSITION; GENETICS; MOLECULAR GENETICS; PROCEDURES; SONGBIRD;

FICEDULA ALBICOLLIS; GULO GULO; VERTEBRATA;

ANIMALS; BASE COMPOSITION; DNA COPY NUMBER VARIATIONS; DNA, MITOCHONDRIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; MUSTELIDAE; SEQUENCE ANALYSIS, DNA; SONGBIRDS;

EID: 84904736781     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-467     Document Type: Article

References (50)

1. Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6(11s):S22-S32. 10.1038/nmeth.1371, 19844228.
2. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 7(3):562-578. 10.1038/nprot.2012.016, 3334321, 22383036.
3. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 2009, 19(9):1586-1592. 10.1101/gr.092981.109, 2752127, 19657104.
4. Yandell M, Ence D. A beginner's guide to eukaryotic genome annotation. Nat Rev Genet 2012, 13(5):329-342. 10.1038/nrg3174, 22510764.
5. Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing. Genome Res 2010, 20(9):1165-1173. 10.1101/gr.101360.109, 2928494, 20508146.
6. Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 2011, 13(1):36-46. 3324860, 22124482.
7. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105. 10.1093/nar/gkn425, 2532726, 18660515.
8. Aird D, Ross M, Chen W-S, Danielsson M, Fennell T, Russ C, Jaffe D, Nusbaum C, Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 2011, 12(2):R18. 10.1186/gb-2011-12-2-r18, 3188800, 21338519.
9. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 2014, 15(2):121-132. 10.1038/nrg3642, 24434847.
10. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 2011, 39(13):e90. 10.1093/nar/gkr344, 3141275, 21576222.
11. Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 2012, 40(10):e72. 10.1093/nar/gks001, 3378858, 22323520.
12. van Heesch S, Mokry M, Boskova V, Junker W, Mehon R, Toonen P, de Bruijn E, Shull J, Aitman T, Cuppen E, Guryev V. Systematic biases in DNA copy number originate from isolation procedures. Genome Biol 2013, 14(4):R33. 10.1186/gb-2013-14-4-r33, 4054094, 23618369.
13. Cheung M-S, Down TA, Latorre I, Ahringer J. Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res 2011, 39(15):e103. 10.1093/nar/gkr425, 3159482, 21646344.
14. Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML. Special features of RAD Sequencing data: implications for genotyping. Mol Ecol 2012, 22(11):3151-3164. 3712469, 23110438.
15. Wolf J, Bryk J. General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq. BMC Genomics 2011, 12(1):91. 10.1186/1471-2164-12-91, 3040151, 21284834.
16. Szatkiewicz JP, Wang W, Sullivan PF, Wang W, Sun W. Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation. Nucleic Acids Res 2013, 41(3):1519-1532. 10.1093/nar/gks1363, 3561969, 23275535.
17. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes. Nat Methods 2009, 6(4):291-295. 10.1038/nmeth.1311, 2664327, 19287394.
18. Meacham F, Boffelli D, Dhahbi J, Martin D, Singer M, Pachter L. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 2011, 12(1):451. 10.1186/1471-2105-12-451, 3295828, 22099972.
19. Allhoff M, Schonhuth A, Martin M, Costa I, Rahmann S, Marschall T. Discovering motifs that induce sequencing errors. BMC Bioinformatics 2013, 14(Suppl 5):S1.
20. Ross M, Russ C, Costello M, Hollinger A, Lennon N, Hegarty R, Nusbaum C, Jaffe D. Characterizing and measuring bias in sequence data. Genome Biol 2013, 14(5):R51. 10.1186/gb-2013-14-5-r51, 4053816, 23718773.
21. Minoche A, Dohm J, Himmelbauer H. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems. Genome Biol 2011, 12(11):R112. 10.1186/gb-2011-12-11-r112, 3334598, 22067484.
22. Rasmussen DA, Noor MAF. What can you do with 0.1 x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). BMC Genomics 2009, 10(1):382. 10.1186/1471-2164-10-382, 2735751, 19689807.
23. Feldmeyer B, Hoffmeier K, Pfenninger M. The complete mitochondrial genome of Radix balthica (Pulmonata, Basommatophora), obtained by low coverage shot gun next generation sequencing. Mol Phylogenet Evol 2010, 57(3):1329-1333. 10.1016/j.ympev.2010.09.012, 20875865.
24. Nabholz B, Jarvis ED, Ellegren H. Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny. Mol Phylogenet Evol 2010, 57(1):466-470. 10.1016/j.ympev.2010.06.009, 20601014.
25. Iorizzo M, Senalik D, Szklarczyk M, Grzebelus D, Spooner D, Simon P. De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome. BMC Plant Biol 2012, 12(1):61. 10.1186/1471-2229-12-61, 3413510, 22548759.
26. Miller JM, Malenfant RM, Moore SS, Coltman DW. Short reads, circular genome: skimming SOLiD sequence to construct the bighorn sheep mitochondrial genome. J Hered 2012, 103(1):140-146. 10.1093/jhered/esr104, 21948953.
27. Blower DC, Hereward JP, Ovenden JR. The complete mitochondrial genome of the dusky shark Carcharhinus obscurus. Mitochondrial DNA 2013, 24(6):619-621. Early Online, 10.3109/19401736.2013.772154, 23551174.
28. Hung C-M, Lin R-C, Chu J-H, Yeh C-F, Yao C-J, Li S-H. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One 2013, 8(2):e56301. 10.1371/journal.pone.0056301, 3577829, 23437111.
29. Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y. Finding the lost treasures in exome sequencing data. Trends Genet 2013, 29(10):593-599. 10.1016/j.tig.2013.07.006, 3926691, 23972387.
30. Miller FJ, Rosenfeldt FL, Zhang C, Linnane AW, Nagley P. Precise determination of mitochondrial DNA copy number in human skeletal and cardiac muscle by a PCR-based assay: lack of change of copy number with age. Nucleic Acids Res 2003, 31(11):e61. 10.1093/nar/gng060, 156738, 12771225.
31. Robin ED, Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J Cell Physiol 1988, 136(3):507-513. 10.1002/jcp.1041360316, 3170646.
32. Arnason U, Gullberg A, Janke A, Kullberg M. Mitogenomic analyses of caniform relationships. Mol Phylogenet Evol 2007, 45(3):863-874. 10.1016/j.ympev.2007.06.019, 17919938.
33. Walker CW, Vilà C, Landa A, Lindén M, Ellegren H. Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations. Mol Ecol 2001, 10(1):53-63. 10.1046/j.1365-294X.2001.01184.x, 11251787.
34. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010, 463(7279):311-317. 10.1038/nature08696, 3951497, 20010809.
35. Ellegren H, Smeds L, Burri R, Olason PI, Backstrom N, Kawakami T, Kunstner A, Makinen H, Nadachowska-Brzyska K, Qvarnstrom A, Uebbing S, Wolf JBW. The genomic landscape of species divergence in Ficedula flycatchers. Nature 2012, 491(7426):756-760.
36. Sequence assembly with MIRA3, The Definitive Guide [http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html], Sequence assembly with MIRA3, The Definitive Guide.
37. Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 2009, 6(11s):S13-S20. 10.1038/nmeth.1374, 19844226.
38. Wilhelm BT, Landry J-R. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 2009, 48(3):249-257. 10.1016/j.ymeth.2009.03.016, 19336255.
39. Chinnery PF, Thorburn DR, Samuels DC, White SL, Dahl H-HM, Turnbull DM, Lightowlers RN, Howell N. The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both?. Trends Genet 2000, 16(11):500-505. 10.1016/S0168-9525(00)02120-X, 11074292.
40. Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011, 333(6040):348-353. 10.1126/science.1205822, 21764749.
41. Oyola S, Otto T, Gu Y, Maslen G, Manske M, Campino S, Turner D, MacInnis B, Kwiatkowski D, Swerdlow H, Quail M. Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes. BMC Genomics 2012, 13(1):1. 10.1186/1471-2164-13-1, 3312816, 22214261.
42. Smeds L, Künstner A. ConDeTri - A content dependent read trimmer for Illumina data. PLoS One 2011, 6(10):e26314. 10.1371/journal.pone.0026314, 3198461, 22039460.
43. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
44. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . Genome Project Data Processing S The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, Genome Project Data Processing S.
45. Richly E, Leister D. NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 2004, 21(6):1081-1084. 10.1093/molbev/msh110, 15014143.
46. Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 2011, 27(6):764-770. 10.1093/bioinformatics/btr011, 3051319, 21217122.
47. Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 2012, In Press Available online.
48. Grant JR, Stothard P. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008, 36(suppl 2):W181-W184. 2447734, 18411202.
49. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9(4):286-298. 10.1093/bib/bbn013, 18372315.
50. R Core Team R: A Language and Environment for Statistical Computing 2013, Vienna: R Foundation for Statistical Computing, R Core Team.