Exploring the unmapped DNA and RNA reads in a songbird genome

Veronika N. Laine; Toni I. Gossmann; Kees van Oers; Marcel E. Visser; Martien A. M. Groenen

doi:10.1186/s12864-018-5378-2

journal article Open Access Jan 08, 2019

Exploring the unmapped DNA and RNA reads in a songbird genome

Veronika N. Laine

Toni I. Gossmann Kees van Oers Marcel E. Visser

Martien A. M. Groenen

BMC Genomics Vol. 20 No. 1 · Springer Science and Business Media LLC

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References

61

[1]

Isakov O, Modai S, Shomron N. Pathogen detection using short-RNA deep sequencing subtraction and assembly. Bioinformatics. 2011;27:2027–30. 10.1093/bioinformatics/btr349

[2]

Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, et al. Finding the lost treasures in exome sequencing data. Trends Genet. 2013;29:593–9. https://doi.org/10.1016/j.tig.2013.07.006 . 10.1016/j.tig.2013.07.006

[3]

Gouin A, Legeai F, Nouhaud P, Whibley A, Simon J-C, Lemaitre C. Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads. Heredity. 2015;114:494–501. https://doi.org/10.1038/hdy.2014.85 . 10.1038/hdy.2014.85

[4]

Whitacre LK, Tizioto PC, Kim J, Sonstegard TS, Schroeder SG, Alexander LJ, et al. What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual. BMC Genomics. 2015;16:1114. https://doi.org/10.1186/s12864-015-2313-7 . 10.1186/s12864-015-2313-7

[5]

Usman T, Hadlich F, Demasius W, Weikard R, Kühn C. Unmapped reads from cattle RNAseq data: a source for missing and misassembled sequences in the reference assemblies and for detection of pathogens in the host. Genomics. 2017;109:36–42. https://doi.org/10.1016/j.ygeno.2016.11.009 . 10.1016/j.ygeno.2016.11.009

[6]

Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RGW, Getz G, et al. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol. 2011;29:393–6. https://doi.org/10.1038/nbt.1868 . 10.1038/nbt.1868

[7]

Granata I, Sangiovanni M, Guarracino M. DecontaMiner: a pipeline for the detection and analysis of contaminating sequences in human NGS sequencing data. In: Dynamics of mathematical models in biology. Cham: Springer International Publishing; 2016. p. 137–48. https://doi.org/10.1007/978-3-319-45723-9_11 . 10.1007/978-3-319-45723-9_11

[8]

Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56–65. https://doi.org/10.1038/nature11632. 10.1038/nature11632.

[9]

Tae H, Karunasena E, Bavarva JH, McIver LJ, Garner HR. Large scale comparison of non-human sequences in human sequencing data. Genomics. 2014;104:453–8. https://doi.org/10.1016/j.ygeno.2014.08.009. 10.1016/j.ygeno.2014.08.009.

[10]

Comparative genomics reveals insights into avian genome evolution and adaptation

Guojie Zhang, Cai Li, Qiye Li et al.

Science 2014 10.1126/science.1251385

[11]

Whole-genome analyses resolve early branches in the tree of life of modern birds

Erich D. Jarvis, Siavash Mirarab, Andre J. Aberer et al.

Science 2014 10.1126/science.1253451

[12]

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

H Bradley Shaffer, Patrick Minx, Daniel E Warren et al.

Genome Biology 2013 10.1186/gb-2013-14-3-r28

[13]

Genome Size Reduction in the Chicken Has Involved Massive Loss of Ancestral Protein-Coding Genes

A. L. Hughes, R. Friedman

Molecular Biology and Evolution 2008 10.1093/molbev/msn207

[14]

Lovell PV, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, et al. Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol. 2014;15:565. https://doi.org/10.1186/s13059-014-0565-1 . 10.1186/s13059-014-0565-1

[15]

Hron T, Pajer P, Pačes J, Bartůněk P, Elleder D. Hidden genes in birds. Genome Biol. 2015;16:164. https://doi.org/10.1186/s13059-015-0724-z . 10.1186/s13059-015-0724-z

[16]

Denyer MP, Pinheiro DY, Garden OA, Shepherd AJ. Missed, not missing: Phylogenomic evidence for the existence of avian foxp3. PLoS One. 2016;11:1–13. 10.1371/journal.pone.0150988

[17]

Lovell PV, Wirthlin M, Carbone L, Warren WC, Mello CV. Response to Hron et al. Genome Biol. 2015;16:15–6. https://doi.org/10.1186/s13059-015-0725-y . 10.1186/s13059-015-0725-y

[18]

Bornelöv S, Seroussi E, Yosefi S, Pendavis K, Burgess SC, Grabherr M, et al. Correspondence on Lovell et al.: Identification of chicken genes previously assumed to be evolutionarily lost. Genome Biol. 2017;18:1–4. 10.1186/s13059-017-1231-1

[19]

Lovell PV, Mello CV. Correspondence on Lovell et al.: Response to Bornelöv et al. Genome Biol. 2017;18:17–9. 10.1186/s13059-017-1234-y

[20]

Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R, et al. Characterizing and measuring bias in sequence data. Genome Biol. 2013;14:R51. https://doi.org/10.1186/gb-2013-14-5-r51 . 10.1186/gb-2013-14-5-r51

[21]

Botero-Castro F, Figuet E, Tilak M, Nabholz B, Galtier N. Avian genomes revisited: hidden genes uncovered and the rates versus traits paradox in birds. Mol Biol Evol. 2017;34:3123–31. https://doi.org/10.1093/molbev/msx236 . 10.1093/molbev/msx236

[22]

Ellegren H. The evolutionary genomics of birds. Annu Rev Ecol Evol Syst. 2013;44:239–59. https://doi.org/10.1146/annurev-ecolsys-110411-160327 . 10.1146/annurev-ecolsys-110411-160327

[23]

Gosler A. The great tit. London: Hamlyn; 1994.

[24]

Richner H. Host-parasite interactions and life-history evolution. Zoology. 1998;101:333–44.

[25]

van Oers K, Santure AW, De Cauwer I, van Bers NEM, Crooijmans RPMA, Sheldon BC, et al. Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates. Heredity (Edinb). 2014;112:307–16. https://doi.org/10.1038/hdy.2013.107 . 10.1038/hdy.2013.107

[26]

Laine VN, Gossmann TI, Schachtschneider KM, Garroway CJ, Madsen O, Verhoeven KJF, et al. Evolutionary signals of selection on cognition from the great tit genome and methylome. Nat Commun. 2016;7:10474. https://doi.org/10.1038/ncomms10474 . 10.1038/ncomms10474

[27]

Kim J-M, Santure AW, Barton HJ, Quinn JL, Cole EF, Great Tit HapMap Consortium, et al. A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour. Mol Ecol Resour. 2018; December 2017:1–15. https://doi.org/10.1111/1755-0998.12778. 10.1111/1755-0998.12778.

[28]

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Wesley C Warren, LaDeana W Hillier, Chad Tomlinson et al.

G3 Genes|Genomes|Genetics 2017 10.1534/g3.116.035923

[29]

Miller MM, Taylor RL. Brief review of the chicken major histocompatibility complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance. Poult Sci. 2016;95:375–92. 10.3382/ps/pev379

[30]

Peona V, Weissensteiner MH, Suh A. How complete are ‘complete’ genome assemblies? - an avian perspective. Mol Ecol Resour. 2018; March:1188–95. https://doi.org/10.1111/1755-0998.12933 . 10.1111/1755-0998.12933

[31]

Santure AW, Gratten J, Mossman JA, Sheldon BC, Slate J. Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics. 2011;12:283. https://doi.org/10.1186/1471-2164-12-283 . 10.1186/1471-2164-12-283

[32]

Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China

Xiao-Yang Gao, Xiao-Yang Zhi, Hong-Wei Li et al.

Standards in Genomic Sciences 2015 10.1186/1944-3277-10-1

[33]

Isaksson C, Sepil I, Baramidze V, Sheldon BC. Explaining variance of avian malaria infection in the wild: the importance of host density, habitat, individual life-history and oxidative stress. BMC Ecol. 2013;13:15. 10.1186/1472-6785-13-15

[34]

Valkiunas G. Avian malaria parasites and other haemosporidia. Boca Raton. Florida: CRC Press; 2004. 10.1201/9780203643792

[35]

van Oers K, Drent PJ, de Goede P, van Noordwijk AJ. Realized heritability and repeatability of risk-taking behaviour in relation to avian personalities. Proc Biol Sci. 2004;271:65–73. https://doi.org/10.1098/rspb.2003.2518 . 10.1098/rspb.2003.2518

[36]

Stabler RM, Holt PA, Kitzmiller NJ. Trypanosoma avium in the Blood and bone marrow from 677 Colorado birds. J Parasitol. 1966;52:1141. https://doi.org/10.2307/3276358 . 10.2307/3276358

[37]

Dunn JC, Cole EF, Quinn JL. Personality and parasites: sex-dependent associations between avian malaria infection and multiple behavioural traits. Behav Ecol Sociobiol. 2011;65:1459–71. 10.1007/s00265-011-1156-8

[38]

Husnik F, McCutcheon JP. Functional horizontal gene transfer from bacteria to eukaryotes. Nat Rev Microbiol. 2017;16:67–79. https://doi.org/10.1038/nrmicro.2017.137 . 10.1038/nrmicro.2017.137

[39]

Danchin EGJ. Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube. BMC Biol. 2016;14:1–3. https://doi.org/10.1186/s12915-016-0330-x. 10.1186/s12915-016-0330-x.

[40]

Salzberg SL. Horizontal gene transfer is not a hallmark of the human genome. Genome Biol. 2017;18:1–5. 10.1186/s13059-017-1214-2

[41]

Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biol. 2015;16:1–13. 10.1186/s13059-015-0607-3

[42]

Gravina S, Sedivy JM, Vijg J. The dark side of circulating nucleic acids. Aging Cell. 2016;15:398–9. 10.1111/acel.12454

[43]

Mittra I, Khare NK, Raghuram GV, Chaubal R, Khambatti F, Gupta D, et al. Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes. J Biosci. 2015;40:91–111 http://www.ncbi.nlm.nih.gov/pubmed/25740145 . 10.1007/s12038-015-9508-6

[44]

Meng X-Y, Li D-H, Ti R-J, Song S. The complete mitochondrial genome of great tit Parus major (Aves, Passeriformes, Paridae). Mitochondrial DNA. 2015;00:1–2. https://doi.org/10.3109/19401736.2014.1003835 . 10.3109/19401736.2014.1003835

[45]

Derks MFL, Schachtschneider KM, Madsen O, Schijlen E, Verhoeven KJF, van Oers K. Gene and transposable element methylation in great tit (Parus major) brain and blood. BMC Genomics. 2016;17:332. https://doi.org/10.1186/s12864-016-2653-y . 10.1186/s12864-016-2653-y

[46]

Nakano K, Shiroma A, Shimoji M, Tamotsu H, Ashimine N, Ohki S, et al. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Hum Cell. 2017;30:149–61. https://doi.org/10.1007/s13577-017-0168-8 . 10.1007/s13577-017-0168-8

[47]

FastQC. https://www.bioinformatics.babraham.ac.uk/projects/fastqc /. Accessed 25 May 2018.

[48]

Trim Galore! https://www.bioinformatics.babraham.ac.uk/projects/trim_galore /. Accessed 25 May 2018.

[49]

Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin

Bioinformatics 2009 10.1093/bioinformatics/btp324

[50]

The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker et al.

Bioinformatics 2009 10.1093/bioinformatics/btp352

Showing 50 of 61 references

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References

Details

Published: Jan 08, 2019
Vol/Issue: 20(1)
License: View

Authors

Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands

M

Marcel E. Visser

Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen 6700 AB The Netherlands

M

Martien A. M. Groenen

Funding

European Research Council Award: 339092 – E-Response

Leverhulme Trust Award: ECF-2015-453

Natural Environment Research Council Award: NE/N013832/1

Cite This Article

Veronika N. Laine, Toni I. Gossmann, Kees van Oers, et al. (2019). Exploring the unmapped DNA and RNA reads in a songbird genome. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-018-5378-2

Exploring the unmapped DNA and RNA reads in a songbird genome

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