Cấu trúc nhiễm sắc thể của các họ lặp lại chính trên khoai tây (Solanum tuberosum) và khám phá thêm trong bộ gen đã giải mã của nó

Springer Science and Business Media LLC - Tập 289 - Trang 1307-1319 - 2014
Xiaomin Tang1,2, Erwin Datema3, Myriam Olortegui Guzman4, Jan M. de Boer1, Herman J. van Eck1,5, Christian W. B. Bachem1, Richard G. F. Visser1,5, Hans de Jong4
1Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
2Department of Biology, Colorado State University, Fort Collins, USA
3Keygene N.V., Wageningen, The Netherlands
4Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
5Center for BioSystems Genomics (CBSG), Wageningen, The Netherlands

Tóm tắt

Một trong những công nghệ mạnh mẽ nhất trong việc giải mã tổ chức của bộ gen thực vật nhân thực là phương pháp lai huỳnh quang độ phân giải cao đối với các trình tự DNA lặp lại và đơn sao trên các nhiễm sắc thể pachytene. Công nghệ này cho phép tích hợp thông tin lập bản đồ vật lý với vị trí nhiễm sắc thể, bao gồm tâm động, đầu mút nhiễm sắc thể, vùng tổ chức nucleolus, cũng như euchromatin và heterochromatin. Trong báo cáo này, chúng tôi đã xác định vị trí nhiễm sắc thể của các phân số lặp lại khác nhau của DNA bộ gen khoai tây (Cot100, Cot500 và Cot1000) trên các nhiễm sắc thể. Chúng tôi cũng đã phân tích các yếu tố lặp lại khác nhau đặc trưng cho khoai tây bao gồm các yếu tố lặp lại P5 và REP2, trong đó REP2 là một phần của retrotransposon LTR kiểu Gypsy lớn hơn và bao phủ hầu hết các vùng nhiễm sắc thể, với một số điểm sáng huỳnh quang rõ rệt trong heterochromatin. Lặp lại chuỗi tandem phong phú nhất là lặp lại của khoai tây genomic 1, bao phủ các vùng tiểu đầu mút của hầu hết các nhánh nhiễm sắc thể. Việc căn chỉnh nhiều lần dữ liệu của các trình tự lặp lại này trong các BAC khoai tây RH89-039-16 đã được lắp ráp và bản lắp ráp thí điểm của bộ gen DM1-3 516 R44 đã làm sáng tỏ sự bảo tồn của các lặp lại này trong bộ gen khoai tây. Các trình tự đồng thuận thu được do đó đã tiết lộ các yếu tố di truyền hoàn chỉnh tự nhiên từ đó chúng được phát sinh.

Từ khóa

#Khoai tây #di truyền học #nhiễm sắc thể #lai huỳnh quang #DNA lặp lại #retrotransposon

Tài liệu tham khảo

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 Anzai T, Takahashi H, Fujiwara H (2001) Elimination of active Tad elements during the sexual phase of the Neurospora crassa life cycle. Fungal Genet Biol 33:49–57 Baur JA, Zou Y, Shay JW, Wright WE (2001) Telomere position effect in human cells. Science 292:2075–2077 Belyayev A, Raskina O, Nevo E (2001) Chromosomal distribution of reverse transcriptase containing retroelements in two Triticeae species. Chromosome Res 9:129–136 Bender J (2004) Chromatin-based silencing mechanisms. Curr Opin Plant Biol 7:521–526 Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580 Brandes A, Heslop-Harrison JS, Kamm A, Kubis S, Doudrick RL, Schmidt T (1997) Comparative analy-sis of the chromosomal and genomic organization of Ty1-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol Biol 33:11–21 Brown TA (2007) Genomes 3, Garland Science. Taylor & Francis Group, New York and London Chang SB, Yang TJ, Datema E, van Vugt J, Vosman B, Kuipers A, Meznikova M, Szinay D, Lankhorst RK, Jacobsen E, de Jong H (2008) FISH mapping and molecular organization of the major repetitive sequences of tomato. Chromosome Res 16:919–933 Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215–220 D’Agostino N, Traini A, Frusciante L, Chiusano ML (2009) SolEST database: a “one-stop shop” approach to the study of Solanaceae transcriptomes. BMC Plant Biol 9:142 Datema E, Mueller LA, Buels R, Giovannoni JJ, Visser RGF, Stiekema WJ, van Ham RCHJ (2008) Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. BMC Plant Biol 8:34 Dong F, Song J, Naess SK, Helgeson JP, Gebhardt C, Jiang J (2000) Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato. Theor Appl Genet 101:1001–1007 Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8:186–194 Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185 Ganal MW, Lapitan NLV, Tanksley SD (1988) A molecular and cytogenetic survey of major repeated DNA sequences in tomato (Lycopersicon esculentum). Mol Gen Genet 213:262–268 Ganal MW, Lapitan NLV, Tanksley SD (1991) Macrostructure of the tomato telomeres. Plant Cell 3:87–94 Gebhardt C, Eberle B, Leonards-Schippers C, Walkemeier B, Salamini F (1995) Isolation, characterization and RFLP linkage mapping of a DNA repeat family of Solanum spegazzinii by which chromosome ends can be localized on the genetic map of potato. Genet Res Camb 65:1–10 Gong Z, Wu Y, Koblizkova A, Torres GA, Wang K, Iovene M, Neumann P, Zhang W, Novak P, Buell CR, Macas J, Jiang J (2012) Repeatless and repeat-based centromeresn in potato: implications for centromere evolution. Plant Cell 24:3559–3574 Gottschling DE, Aparicio OM, Billington BL, Zakian VA (1990) Position effect at S cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63:751–762 Hall IM, Shankaranarayana GD, Noma KI, Ayoub N, Cohen A, Grewal SI (2002) Establishment and maintenance of a heterochromatin domain. Science 297:2232–2237 Hemleben V, Kovarik A, Torres-Ruiz RA, Volkov RA, Beridze T (2007) Plant highly repeated satellite DNA: molecular evolution, distribution and use for identification of hybrids. Syst Biodivers 5(3):277–289 Hermsen JGT, Taylor LM, van Breukelen EWM, Lipski A (1978) Inheritance of genetic markers from two potato dihaploids and their respective parent cultivars. Euphytica 27:681–688 Heslop-Harrison JS, Brandes A, Taketa S, Schmidt T, Vershinin AV, Alkhimova EG, Kamm A, Doudrick RL, Schwarzacher T, Katsiotis A, Kubis S, Kumar A, Pearce SR, Flavell AJ, Harrison GE (1997) The chromosomal distributions of Ty1-copia group rerotransposable elements in higher plants and their implications for genome evolution. Genetica 100:197–204 Jurka J, Bao W, Kojima K, Kapitonov VV (2011) Repetitive elements: bioinformatic identification, classification and analysis. In: Encyclopedia of life sciences (ELS). Wiley, Chichester. doi:10.1002/9780470015902.a0005270.pub2 Koukalová B, Reich J, Matyásek R, Kuhrová V, Bezdek M (1989) A BamHI family of highly repeated DNA sequences of Nicotiana tabacum. Theor Appl Genet 78:77–80 Lamb JC, Meyer JM, Corcoran B, Kato A, Han F, Birchler JA (2007) Distinct chromosomal distributions of highly repetitive sequences in maize. Chromosome Res 15:33–49 Lapitan NLV (1992) Organization and evolution of higher plant nuclear genomes. Genome 35:171–181 Lapitan NLV, Ganal MW, Tanksley SD (1989) Somatic chromosome karyotype of tomato based on in situ hybridization of the TGRI satellite repeat. Genome 32:992–998 Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948 Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–476 Lisch D (2013) How important are transposons for plant evolution? Nat Rev Genet 14(1):49–61 Malkamaki U, Clark MS, Rita H, Valkonen JPT, Pehu E (1996) Analyses of solanaceous species using repetitive genomic DNA sequences isolated from Solanum brevidens. Plant Sci 117:121–129 Mroczek RJ, Dawe RK (2003) Distribution of retroelements in centromeres and neocentromeres of maize. Genetics 165:809–819 Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst EV, Keyder ER, Menda N, Zamir D, Tanksley SD (2005) The SOL genomics network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 138(3):1310–1317 Nagaki K, Talbert PB, Zhong CX, Dawe RK, Henikoff S, Jiang J (2003) Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163(3):1221–1225 Nagaki K, Shibata F, Suzuki G, Kanatani A, Ozaki S, Hironaka A, Kashihara K, Murata M (2011) Coexistence of NtCENH3 and two retrotransposons in tobacco centromeres. Chromosome Res 19(5):591–605 Pearce SR, Harrison G, Li D, Heslop-Harrison JS, Kumar A, Flavell AJ (1996) The Ty1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation. Mol Gen Genet 250:305–315 Pearce SR, Harrison G, Heslop-Harrison JS, Flavell AJ, Kumar A (1997) Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale). Genome 40:617–625 Pehu E, Thomas M, Poutala T, Karp A, Jones MGK (1990) Species-specific sequences in the genus Solanum: identification, characterization, and application to study somatic hybrids of S. brevidens and S. tuberosum. Theor Appl Genet 80:693–698 Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH (2002) Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 12:795–807 Pich U, Schubert I (1998) Terminal heterochromatin and alternative telomeric sequences in Allium cepa. Chromosome Res 6:315–321 Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–197 Preiszner J, Takacs I, Bilgin M, Gyorgyey J, Dudits D, Feher A (1994) Organization of a Solanum brevidens repetitive sequence related to the TGRI subtelomeric repeats of Lycopersicon esculentum. Theor Appl Genet 89:1–8 Presting GG, Malysheva L, Fuchs J, Schubert I (1998) A TY3/GYPSY retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J 16:721–728 Rogers SO, Bendich AJ (1988) Extraction of DNA from plant tissues. Plant Mol Biol Man A6:1–10 Rokka VM, Clark MS, Knudson DL, Pehu E, Lapitan NLV (1998) Cytological and molecular characterization of repetitive DNA sequences of Solanum brevidens and Solanum tuberosum. Genome 41:487–494 Rouppe van der Voort JN, van Zandvoort P, van Eck HJ, Folkertsma RT, Hutten RC, Draaistra J, Gommers FJ, Jacobsen E, Helder J, Bakker J (1997) Use of allele specificity of comigrating AFLP markers to align genetic maps from different potato genotypes. Mol Gen Genet 255:438–447 Schweizer G, Ganal M, Ninnemann H, Hemleben V (1988) Species-specific DNA sequences for identification of somatic hybrids between Lycopersicon esculentum and Solanum acaule. Theor Appl Genet 75:679–684 Schweizer G, Borisjuk N, Borisjuk L, Stadler M, Stelzer T, Schilde L, Hemleben V (1993) Molecular analysis of highly repeated genome fractions in Solanum and their use as markers for the characterization of species and cultivars. Theor Appl Genet 85:801–808 Stadler M, Stelzer T, Borisjuk N, Zanke C, Schilde-Rentschler L, Hemleben V (1995) Distribution of novel and known repeated elements of Solanum and application for the identification of somatic hybrids among Solanum species. Theor Appl Genet 91:1271–1278 Stupar RM, Song J, Tek AL, Cheng Z, Dong F, Jiang J (2002) Highly condensed potato pericentromeric heterochromatin contains rDNA-related tandem repeats. Genetics 162:1435–1444 Szinay D, Bai Y, Visser R, de Jong H (2010) FISH applications for genomics and plant breeding strategies in tomato and other solanaceous crops. Cytogenet Genome Res 129:199–210 Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T et al (2000) Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature 408(6814):823–826 Tang X, de Boer JM, van Eck HJ, Bachem C, Visser RGF, de Jong H (2009) Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology. Chromosome Res 17:899–915 Tek AL, Jiang J (2004) The centromeric regions of potato chromosomes contain megabase-sized tandem arrays of telomere-similar sequence. Chromosoma 113:77–83 Tek AL, Song J, Macas J, Jiang J (2005) Sobo, a recently amplified satellite repeat of potato, and its implications for the origin of tandemly repeated sequences. Genetics 170:1231–1238 Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641 Torres GA, Gong Z, Iovene M, Hirsch CD, Buell CR, Bryan GJ, Novak P, Macas J, Jiang J (2011) Organization and evolution of subtelomeric satellite repeats in the potato genome. G3 Genes∣Genomes∣Genetics 1:85–92 Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13:36–46 Visser RGF, Hoekstra R, van der Leij FR, Pijnacker LP, Witholt B, Feenstra WJ (1988) In situ hybridization to somatic metaphase chromosomes of potato. Theor Appl Genet 76:420–424 Visser RGF, Bachem CWB, de Boer JM, Bryan GJ, Chakrabati SK, Feingold S, Gromadka R, van Ham RCHJ, Huang S, Jacobs JME, Kuznetsov B, de Melo PE, Milbourne D, Orjeda G, Sagredo B, Tang X (2009) Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world’s third most important food crop. Am J Potato Res 86:417–429 Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837 Wenke T, Dobel T, Sorensen TR, Junghans H, Weisshaar B, Schmidt T (2011) Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes. Plant Cell 23:3117–3128 Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8(12):973–982 Zanke C, Hemleben V (1997) A new Solanum satellite DNA containing species-specific sequences which can be used for identification of genome parts in somatic hybrids of potato. Plant Sci 126:185–191 Zhong XB, de Jong JH, Zabel P (1996a) Preparation of tomato meiotic pachytene and mitotic metaphase chromosomes suitable for fluorescence in situ hybridization (FISH). Chromosome Res 4:24–28 Zhong XB, Fransz PF, van Eden JW, Zabel P, van Kammen A, de Jong JH (1996b) High resolution mapping by fluorescence in situ hybridisation to pachytene chromosomes and extended DNA fibers. Plant Mol Biol Rep 14:232–242 Zhong XB, Fransz PF, van Eden JW, Ramanna MS, van Kammen A, Zabel P, de Jong H (1998) FISH studies reveal the molecular and chromosomal organization of individual telomere domains in tomato. Plant J 13:507–517 Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, Nagaki K, Birchler JA, Jiang J, Dawe RK (2002) Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14:2825–2836 Zhu W, Ouyang S, Iovene M, O’Brien K, Vuong H, Jiang J, Buell CR (2008) Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genom 9:286 Zwick MS, Hanson RE, McKnight TD, Islam-Faridi MH, Stelly DM, Wing RA, Price HJ (1997) A rapid procedure for the isolation of Cot-1 DNA from plants. Genome 40:138–142