Efficient high-throughput sequencing of a laser microdissected chromosome arm

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Seifertova, Eva ^a   Zimmerman, Lyle B ^b   Gilchrist, Michael J ^b   Macha, Jaroslav ^a   Kubickova, Svatava ^c   Cernohorska, Halina ^c   Zarsky, Vojtech ^a   Owens, Nick D L ^b   Sesay, Abdul K ^b   Tlapakova, Tereza ^a   Krylov, Vladimir ^a  

^a CHARLES UNIVERSITY   (Czech Republic)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^c VETERINARY RESEARCH INSTITUTE   (Czech Republic)

Author keywords

Chromosomes; Genetic map; Next generation sequencing; Tropicalis; WGA; Xenopus

Indexed keywords

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CHROMOSOME 7; CHROMOSOME ANALYSIS; CHROMOSOME ARM; CHROMOSOME MAP; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; GENE LOCUS; GENE MAPPING; HIGH THROUGHPUT SEQUENCING; LASER MICRODISSECTION; MALE; NONHUMAN; SEQUENCE ANALYSIS; SRY GENE; XENOPUS TROPICALIS;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LASERS; MICRODISSECTION; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; SEQUENCE ANALYSIS, DNA; XENOPUS;

AMPHIBIA; TETRAPODA; XENOPUS TROPICALIS;

EID: 84878258738     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-357     Document Type: Article

References (30)

1. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012, 40:D571-D579. 10.1093/nar/gkr1100, 3245063, 22135293.
2. Barthelson R, McFarlin AJ, Rounsley SD, Young S. Plantagora: modeling whole genome sequencing and assembly of plant genomes. PLoS One 2011, 6:e28436. 10.1371/journal.pone.0028436, 3236183, 22174807.
3. Harland RM, Grainger RM. Xenopus research: metamorphosed by genetics and genomics. Trends Genet 2011, 27:507-515. 10.1016/j.tig.2011.08.003, 3601910, 21963197.
4. Kashiwagi K, Kashiwagi A, Kurabayashi A, Hanada H, Nakajima K, Okada M, Takase M, Yaoita Y. Xenopus tropicalis: an ideal experimental animal in amphibia. Exp Anim 2010, 59:395-405. 10.1538/expanim.59.395, 20660986.
5. Amaya E. Xenomics. Genome Res 2005, 15:1683-1691.
6. Carruthers S, Stemple DL. Genetic and genomic prospects for Xenopus tropicalis research. Semin Cell Dev Biol 2006, 17:146-153. 10.1016/j.semcdb.2005.11.009, 16427790.
7. Abu-Daya A, Khokha MK, Zimmerman LB. The hitchhiker's guide to Xenopus genetics. Genesis 2012, 50:164-175. 10.1002/dvg.22007, 3312310, 22344745.
8. Mácha J, Teichmanová R, Sater AK, Wells DE, Tlapáková T, Zimmerman LB, Krylov V. Deep ancestry of mammalian X chromosome revealed by comparison with the basal tetrapod Xenopus tropicalis. BMC Genomics 2012, 13:315. 10.1186/1471-2164-13-315, 3472169, 22800176.
9. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, et al. The genome of the Western clawed frog Xenopus tropicalis. Science 2010, 328:633-636. 10.1126/science.1183670, 2994648, 20431018.
10. Wells DE, Gutierrez L, Xu Z, Krylov V, Macha J, Blankenburg KP, Hitchens M, Bellot LJ, Spivey M, Stemple DL, et al. A genetic map of Xenopus tropicalis. Dev Biol 2011, 354:1-8. 10.1016/j.ydbio.2011.03.022, 3098391, 21458440.
11. Gilchrist MJ. From expression cloning to gene modeling: the development of Xenopus gene sequence resources. Genesis 2012, 50:143-154. 10.1002/dvg.22008, 3488295, 22344767.
12. Olmstead AW, Lindberg-Livingston A, Degitz SJ. Genotyping sex in the amphibian, Xenopus (Silurana) tropicalis, for endocrine disruptor bioassays. Aquat Toxicol 2010, 98:60-66. 10.1016/j.aquatox.2010.01.012, 20202696.
13. Bewick AJ, Chain FJ, Zimmerman LB, Sesay A, Gilchrist MJ, Owens ND, Seifertova E, Krylov V, Macha J, Tlapakova T, et al. A large pseudoautosomal region on the sex chromosomes of the frog Silurana tropicalis. Genome Biol Evol 2013, Epub ahead of print.
14. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010, 463:311-317. 10.1038/nature08696, 20010809.
15. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg LA, Bouffard P, Burt DW, Crasta O, Crooijmans RP, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 2010, 8:e1000475. 10.1371/journal.pbio.1000475, 2935454, 20838655.
16. Doležel J, Vrána J, Safář J, Bartoš J, Kubaláková M, Simková H. Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics 2012, 12:397-416. 10.1007/s10142-012-0293-0, 3431466, 22895700.
17. Ma L, Xiao Y, Huang H, Wang Q, Rao W, Feng Y, Zhang K, Song Q. Direct determination of molecular haplotypes by chromosome microdissection. Nat Methods 2010, 7:299-301. 10.1038/nmeth.1443, 2871314, 20305652.
18. Weise A, Timmermann B, Grabherr M, Werber M, Heyn P, Kosyakova N, Liehr T, Neitzel H, Konrat K, Bommer C, et al. High-throughput sequencing of microdissected chromosomal regions. Eur J Hum Genet 2010, 18:457-462. 10.1038/ejhg.2009.196, 2987241, 19888302.
19. Höckner M, Erdel M, Spreiz A, Utermann G, Kotzot D. Whole genome amplification from microdissected chromosomes. Cytogenet Genome Res 2009, 125:98-102. 10.1159/000227832, 19729911.
20. Khokha MK, Krylov V, Reilly MJ, Gall JG, Bhattacharya D, Cheung CY, Kaufman S, Lam DK, Macha J, Ngo C, et al. Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Dev Dyn 2009, 238:1398-1346. 10.1002/dvdy.21965, 2962985, 19441086.
21. Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, Jouve N, Šimková H, Valárik M, Doležel J, Mayer KF. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J 2012, 69:377-386. 10.1111/j.1365-313X.2011.04808.x, 21974774.
22. Yang H, Chen X, Wong WH. Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci U S A 2011, 108:12-17. 10.1073/pnas.1016725108, 3017199, 21169219.
23. Yoshimoto S, Okada E, Umemoto H, Tamura K, Uno Y, Nishida-Umehara C, Matsuda Y, Takamatsu N, Shiba T, Ito M. A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis. Proc Natl Acad Sci U S A 2008, 105:2469-2474. 10.1073/pnas.0712244105, 2268160, 18268317.
24. Schmid M, Steinlein C. Chromosome banding in Amphibia. XVI. High-resolution replication banding patterns in Xenopus laevis. Chromosoma 1991, 101:123-132. 10.1007/BF00357062, 1769277.
25. Kubickova S, Cernohorska H, Musilova P, Rubes J. The use of laser microdissection for the preparation of chromosome-specific painting probes in farm animals. Chromosome Res 2002, 10:571-577. 10.1023/A:1020914702767, 12498346.
26. Krylov V, Kubickova S, Rubes J, Macha J, Tlapakova T, Seifertova E, Sebkova N. Preparation of Xenopus tropicalis whole chromosome painting probes using laser microdissection and reconstruction of X. laevis tetraploid karyotype by Zoo-FISH. Chromosome Res 2010, 18:431-439. 10.1007/s10577-010-9127-x, 20390340.
27. Xenbase Xenopus laevis and Xenopus tropicalis biology and genomics resource [http://www.xenbase.org], Xenbase.
28. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
29. Bowtie an ultrafast, memory-efficient short read aligner http://bowtie-bio.sourceforge.net/, Bowtie.
30. Krylov V, Tlapakova T, Macha J. Localization of the single copy gene Mdh2 on Xenopus tropicalis chromosomes by FISH-TSA. Cytogenet Genome Res 2007, 116:110-112. 10.1159/000097427, 17268187.