A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs

Chromosoma

Volumn 124, Issue 2, 2015, Pages 263-275

  Camacho, J P M ^a   Ruiz Ruano, F J ^a   Martin Blazquez R ^a   Lopez Leon M D ^a   Cabrero, J ^a   Lorite, P ^b   Cabral de Mello, D C ^c   Bakkali, M ^a  

^a UNIVERSITY OF GRANADA   (Spain)

^b UNIVERSITY OF JAÉN   (Spain)

^c SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; REPETITIVE DNA; RESTRICTION ENDONUCLEASE; SATELLITE DNA; HETEROCHROMATIN; HISTONE; RIBOSOME DNA;

ANIMAL EXPERIMENT; ARTICLE; C BANDING; CHROMOSOME MAP; CHROMOSOME MARKER; CHROMOSOME SIZE; CONTROLLED STUDY; DENSITOMETRY; EMBRYO; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE SEQUENCE; GENETIC LINKAGE; GENOME; HETEROCHROMATIN; LOCUSTA MIGRATORIA; MALE; MULTIGENE FAMILY; NEXT GENERATION SEQUENCING; NONHUMAN; PEST ORGANISM; SCHISTOCERCA GREGARIA; SEX CHROMOSOME; TANDEM REPEAT; ANIMAL; CAELIFERA; CHROMOSOMAL MAPPING; CHROMOSOME; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; INSECT GENOME; METABOLISM; NUCLEOTIDE REPEAT;

ANIMALIA; LOCUSTA MIGRATORIA; SCHISTOCERCA GREGARIA;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES; DNA, RIBOSOMAL; DNA, SATELLITE; FEMALE; GENOME, INSECT; GRASSHOPPERS; HETEROCHROMATIN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONES; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

EID: 84929943558     PISSN: 00095915     EISSN: 14320886     Source Type: Journal    
DOI: 10.1007/s00412-014-0499-0     Document Type: Article

References (82)

1. Anders S, Pyl PT, Huber W (2014) HTSeq—a Python framework to work with high-throughput sequencing data. bioRxiv preprint doi:10.1101/002824
2. Badisco L, Huybrechts J, Simonet G, Verlinden H, Marchal E, Huybrechts R, Schoofs L, De Loof A, Vanden Broeck J (2011) Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database. PLoS One 6:e17274
3. Bakkali M (2011) Microevolution of cis-regulatory elements: an example from the pair-rule segmentation gene fushi tarazu in the Drosophila melanogaster subgroup. PLoS One 6:e27376
4. Bakkali M (2013) A bird’s-eye view on the modern genetics workflow and its potential applicability to the locust problem. C R Biol 336:375–383
5. Belova T, Zhan B, Wright J, Caccamo M, Asp T, Simkova H, Kent M, Bendixen C, Panitz F, Lien S, Dolezel J, Olsen OA, Sandve SR (2013) Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat. BMC Genomics 14:222
6. Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15:621–627
7. Bensasson D, Zhang DX, Hewitt GM (2000) Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. Mol Biol Evol 17:406–415
8. Brown AK, Wilmore PJ (1974) Location of repetitious DNA in the chromosomes of the desert locust (Schistocerca gregaria). Chromosoma 47:379–383
9. Bueno D, Palacios-Gimenez OM, Cabral-de-Mello DC (2013) Chromosomal mapping of repetitive DNAs in the grasshopper reveal possible ancestry of the B chromosome and H3 histone spreading. PLoS One 8:e66532
10. Cabral-de-Mello DC, Valente GT, Nakajima RT, Martins C (2012) Genomic organization and comparative chromosome mapping of the U1 snRNA gene in cichlid fish, with an emphasis in Oreochromis niloticus. Chromosome Res 20:279–292
11. Cabrero J, Camacho JP (2008) Location and expression of ribosomal RNA genes in grasshoppers: abundance of silent and cryptic loci. Chromosome Res 16:595–607
12. Cabrero J, Bakkali M, Bugrov A, Warchalowska-Sliwa E, Lopez-Leon MD, Perfectti F, Camacho JP (2003) Multiregional origin of B chromosomes in the grasshopper Eyprepocnemis plorans. Chromosoma 112:207–211
13. Cabrero J, Lopez-Leon MD, Teruel M, Camacho JP (2009) Chromosome mapping of H3 and H4 histone gene clusters in 35 species of acridid grasshoppers. Chromosome Res 17:397–404
14. Camacho JPM, Viseras E, Navas-Castillo J, Cabrero J (1984) C-heterochromatin content of supernumerary chromosome segments of grasshoppers: detection of an euchromatic extra segment. Heredity 53:167–175
15. Camacho JPM, Cabrero J, Viseras E, Lopez-Leon MD, Navas-Castillo J, Alche JD (1991) G-banding in two species of grasshoppers and its relationship to C, N and fluorescence banding techniques. Genome 34:638–643
16. Craig-Cameron TA (1970) Actinomycin-D and chiasma frequency in Schistocerca gregaria (Forskal). Chromosoma 30:169–179
17. Craig-Cameron T, Jones GH (1970) The analysis of exchanges in tritium-labelled meiotic chromosomes. 1. Heredity (Edinb) 25:223–232
18. Csik L, Koller PC (1939) Relational coiling and chiasma frequency. Zeitschr Zellforsch Microsk Anat Abt B Chromosoma 1:191–196
19. Diaz MO, Barsacchi-Pilone G, Mahon KA, Gall JG (1981) Transcripts from both strands of a satellite DNA occur on lampbrush chromosome loops of the newt Notophthalmus. Cell 24:649–659
20. Dolezel J, Bartos J, Voglmayr H, Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry A 51:127–128, author reply 129
21. Drummond AJ, Ashton B, Cheung M, Heled J, Kearse M (2009) Geneious 4.8. Biomatters Auckland, New Zealand
22. Dutt K (1966) Karyotype study of a fresh water snake Cerberus rhynohops. (Abstr). In: Proc Int Symp Animal Venoms Inst. Butantan, Sao Paulo, pp 15–16
23. Epstein LM, Mahon KA, Gall JG (1986) Transcription of a satellite DNA in the newt. J Cell Biol 103:1137–1144
24. Ferrier DE, Akam M (1996) Organization of the Hox gene cluster in the grasshopper, Schistocerca gregaria. Proc Natl Acad Sci U S A 93:13024–13029
25. Fox DP (1966a) The effect of X-rays on the chromosomes of locust embryos: II Chromatid interchanges and the organization of the interphase nucleus. Chromosoma 20:173–194
26. Fox DP (1966b) The effects of X-rays on the chromosomes of locust embryos. I. The early responses. Chromosoma 19:300–316
27. Fox DP (1967a) The effects of X-rays on the chromosomes of locust embryos. 3. The chromatid aberration types. Chromosoma 20:386–412
28. Fox DP (1967b) The effects of X-rays on the chromosomes of locust embryos. IV. Dose–response and variation in sensitivity of the cell cycle for the induction of chromatid aberrations. Chromosoma 20:413–441
29. Fox DP (1970) A non-doubling DNA series in somatic tissues of the locusts Schistocerca gregaria (Forskal) and Locusta migratoria (Linn.). Chromosoma 29:446–461
30. Fox DP (1973) The control of chiasma distribution in the locust, Schistocerca gregaria (Forskal). Chromosoma 43:289–328
31. Fox DP, Santos JL (1985) N-bands and nucleolus expression in Schistocerca gregaria and Locusta migratoria. Heredity 54:333–341
32. Fox DP, Carter KC, Hewitt GM (1973) Giemsa banding and chiasma distribution in the desert locust. Heredity (Edinb) 31:272–276
33. Gaubatz JW, Cutler RG (1990) Mouse satellite DNA is transcribed in senescent cardiac muscle. J Biol Chem 265:17753–17758
34. Gordon A, Hannon GJ (2010) Fastx-toolkit. FASTQ/A short-reads pre-processing tools. Unpublished http://hannonlab.cshl.edu/fastx_toolkit
35. Gregory TR (2005) Synergy between sequence and size in large-scale genomics. Nat Rev Genet 6:699–708
36. Hagele K (1979) Characterization of heterochromatin in Schistocerca gregaria by C- and N-banding methods. Chromosoma 70:239–250
37. Hardie DC, Gregory TR, Hebert PD (2002) From pixels to picograms: a beginners’ guide to genome quantification by Feulgen image analysis densitometry. J Histochem Cytochem 50:735–749
38. Henderson SA (1962) Temperature and chiasma formation in Schistocerca gregaria. Chromosoma 13:437–463
39. Henderson SA (1963) Chiasma distribution at diplotene in a locust. Heredity 18:173
40. Henderson SA (1964) RNA synthesis during male meiosis and spermiogenesis. Chromosoma 15:345–366
41. Henderson SA (1988) Four effects of elevated temperature on chiasma formation in the locust Schistocerca gregaria. Heredity 60:387–401
42. Hori T, Suzuki Y, Solovei I, Saitoh Y, Hutchison N, Ikeda JE, Macgregor H, Mizuno S (1996) Characterization of DNA sequences constituting the terminal heterochromatin of the chicken Z chromosome. Chromosome Res 4:411–426
43. Jain HK, Singh U (1967) Actinomycin D induced chromosome breakage and suppression of meiosis in the locust, Schistocerca gregaria. Chromosoma 21:463–471
44. Jamrich M, Warrior R, Steele R, Gall JG (1983) Transcription of repetitive sequences on Xenopus lampbrush chromosomes. Proc Natl Acad Sci U S A 80:3364–3367
45. John B, Henderson SA (1962) Asynapsis and polyploidy in Schistocerca paranensis. Chromosoma 13:111–147
46. John B, Hewitt GM (1966) Karyotype stability and DNA variability in the Acrididae. Chromosoma 20:155–172
47. John B, Naylor B (1961) Anomalous chromosome behaviour in germ line of Schistocerca gregaria. Heredity 16:187–198
48. Jones GH (1977) A test for early termination of chiasmata in diplotene spermatocytes of Schistocerca gregaria. Chromosoma 63:287–294
49. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760
50. Lorite P, Renault S, Rouleux-Bonnin F, Bigot S, Periquet G, Palomeque T (2002) Genomic organization and transcription of satellite DNA in the ant Aphaenogaster subterranea (Hymenoptera, Formicidae). Genome 45:609–616
51. Lorite P, Torres MI, Palomeque T (2013) Characterization of two unrelated satellite DNA families in the Colorado potato beetle Leptinotarsa decemlineata (Coleoptera, Chrysomelidae). Bull Entomol Res 103:538–546
52. McClintock B (1934) The relationship of a particular chromosomal element to the development of nucleoli in Zea mays. Z Zellforsch 21:294–328
53. Meyne J, Hirai H, Imai HT (1995) FISH analysis of the telomere sequences of bulldog ants (Myrmecia: Formicidae). Chromosoma 104:14–18
54. Munoz-Pajares AJ, Martinez-Rodriguez L, Teruel M, Cabrero J, Camacho JP, Perfectti F (2011) A single, recent origin of the accessory B chromosome of the grasshopper Eyprepocnemis plorans. Genetics 187:853–863
55. Novak P, Neumann P, Macas J (2010) Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11:378
56. Novak P, Neumann P, Pech J, Steinhaisl J, Macas J (2013) RepeatExplorer: a galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792–793
57. Oliver MJ, Petrov D, Ackerly D, Falkowski P, Schofield OM (2007) The mode and tempo of genome size evolution in eukaryotes. Genome Res 17:594–601
58. Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34:401–437
59. Palomeque T, Lorite P (2008) Satellite DNA in insects: a review. Heredity (Edinb) 100:564–573
60. Pezer Z, Ugarkovic D (2012) Satellite DNA-associated siRNAs as mediators of heat shock response in insects. RNA Biol 9:587–595
61. Rasch EM, Rasch RW (1981) Cytophotometric determination of genome size for two species of cave crickets (Orthoptera, Rhaphidophoridae). J Histochem Cytochem 29:885
62. Renault S, Rouleux-Bonnin F, Periquet G, Bigot Y (1999) Satellite DNA transcription in Diadromus pulchellus (Hymenoptera). Insect Biochem Mol Biol 29:103–111
63. Rouleux-Bonnin F, Renault S, Bigot Y, Periquet G (1996) Transcription of four satellite DNA subfamilies in Diprion pini (Hymenoptera, Symphyta, Diprionidae). Eur J Biochem 238:752–759
64. Rozen S, Skaletsky H (1999) Primer3 on the WWW for general users and for biologist progremmers. In: Bioinformatics methods and protocols. Humana Press, pp 365–386
65. Rufas JS, Gosalvez J (1982) Development of silver stained structures during spermatogenesis of Schistocerca gregaria (Forsk.) (Orthoptera:Acrididae). Caryologia 35:261–267
66. Ruiz-Ruano FJ, Ruiz-Estevez M, Rodriguez-Perez J, Lopez-Pino JL, Cabrero J, Camacho JP (2011) DNA amount of X and B chromosomes in the grasshoppers Eyprepocnemis plorans and Locusta migratoria. Cytogenet Genome Res 134:120–126
67. Solovei IV, Joffe BI, Gaginskaya ER, Macgregor HC (1996) Transcription of lampbrush chromosomes of a centromerically localized highly repeated DNA in pigeon (Columba) relates to sequence arrangement. Chromosome Res 4:588–603
68. Timothy D, Littlewood J, Olson P (2000) Small subunit rDNA and the platyhelminthes: signal, noise, conflict and compromise. In: Littlewood DTJ, Bray RA (eds) Interrelationships of the platyhelminthes. CRC Press, UK, pp 381–330, 380
69. Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: computational chalenges and solutions. Nat Rev Genet 13:36–46
70. Varadaraj K, Skinner DM (1994) Cytoplasmic localization of transcripts of a complex G + C-rich crab satellite DNA. Chromosoma 103:423–431
71. Varley JM, Macgregor HC, Nardi I, Andrews C, Erba HP (1980) Cytological evidence of transcription of highly repeated DNA sequences during the lampbrush stage in Triturus cristatus carnifex. Chromosoma 80:289–307
72. Vaughan HE, Heslop-Harrison JS, Hewitt GM (1999) The localization of mitochondrial sequences to chromosomal DNA in orthopterans. Genome 42:874–880
73. Wang S, Lorenzen MD, Beeman RW, Brown SJ (2008) Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome. Genome Biol 9:R61
74. Wang X, Fang X, Yang P, Jiang X, Jiang F, Zhao D, Li B, Cui F, Wei J, Ma C, Wang Y, He J, Luo Y, Wang Z, Guo X, Guo W, Zhang Y, Yang M, Hao S, Chen B, Ma Z, Yu D, Xiong Z, Zhu Y, Fan D, Han L, Wang B, Chen Y, Wang J, Yang L, Zhao W, Feng Y, Chen G, Lian J, Li Q, Huang Z, Yao X, Lv N, Zhang G, Li Y, Zhu B, Kang L (2014) The locust genome provides insight into swarm formation and long-distance flight. Nat Commun 5:2957
75. Westerman M (1967) The effect of X-irradiation on male meiosis in Schistocerca gregaria (Forskal). Chromosoma 22:401–416
76. Westerman M (1968) The effect of x-irradiation on male meiosis in Schistocerca gregaria (Forskal). II. The induction of chromosome mutations. Chromosoma 24:17–36
77. Westerman M, Barton NH, Hewitt GM (1987) Differences in DNA content between two chromosomal races of the grasshopper Podisma pedestris. Heredity 58:221–228
78. White MJD (1934) The influence of temperature on chiasma frequency. J Genet 29:203–216
79. Wilmore PJ, Brown AK (1975) Molecular properties of orthopteran DNA. Chromosoma 51:337–345
80. Wolf KW (1996) The structure of condensed chromosomes in mitosis and meiosis of insects. Int J Insect Morphol Embryol 25:37–62
81. Wolf KW, Sumner AT (1996) Scanning electron microscopy of heterochromatin in chromosome spreads of male germ cells in Schistocerca gregaria (Acrididae, Orthoptera) after trypsinization. Biotech Histochem 71:237–244
82. Wolf KW, Turner BM (1996) The pattern of histone H4 acetylation on the X chromosome during spermatogenesis of the desert locust Schistocerca gregaria. Genome 39:854–865