Concerted evolution rapidly eliminates sequence variation in rDNA coding regions but not in intergenic spacers in Nicotiana tabacum allotetraploid
- 336 Downloads
Nicotiana tabacum (tobacco) is a natural allotetraploid that formed from two diploid progenitors (N. sylvestris—S-genome, N. tomentosiformis—T-genome) within past 0.2 million years. Previous classical studies have shown that its 35S rDNA has been largely homogenised towards T-genome-like homeologs. However, the degree of conversion at single nucleotide resolution remains unknown. Here, we analysed intragenomic variation of rDNA at high resolution in natural tobacco, synthetic tobacco and the progenitors employing genomic, molecular and cytogenetic methods. In synthetic tobacco, we identified 13 highly (≥10% units) polymorphic sites in the 18S-5.8S-26S coding region. In contrast, only a single polymorphic site was detected in natural tobacco, indicating that gene conversion has removed most of the polymorphisms over shallow evolutionary times. However, the non-coding 26S-18S intergenic spacer (IGS) was highly polymorphic in both natural (57 polymorphic sites) and synthetic tobacco (128 polymorphic sites). In natural tobacco, most (64%) IGS polymorphisms were inherited from the N. tomentosiformis progenitor, while 36% appeared de novo indicating rapid rates of sequence divergence of IGS. FISH revealed that the T-genome-like units (harbouring N. tomentosiformis-type IGS) occurred on all four loci in tobacco variety 095-55, including those loci derived from N. sylvestris progenitor, while the variety SR-1 retained 1–2 S-genome loci unconverted and transcriptionally silenced. We discuss potential caveats associated with experimental and in silico approaches used for determination of rDNA polymorphisms. We also hypothesise that polyploidy-associated gene conversion may eliminate mutated and non-functional genes that have accumulated in progenitor genomes, thereby contributing to success of polyploidy species.
KeywordsConcerted evolution Genetic variation Nicotiana tabacum Polyploidy rDNA
The research was funded by the Czech Science Foundation (P501/17/11642S and P506/16-02149J) and NERC.
Compliance with ethical standards
Conflicts of interest
The authors declare no conflicts of interest.
Human or animal participants
The present research does not involve human or animal participants. All authors have approved the manuscript.
- Bennett MD, Leitch I (2012) Angiosperm DNA C-values database (release 8.0, Dec. 2012). Available at http://data.kew.org/cvalues/. Accessed 2 Feb 2017
- Borowska-Zuchowska N, Kwasniewski M, Hasterok R (2016) Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid Brachypodium hybridum and its putative ancestors–dissecting complex repetitive structure of intergenic spacers. Front Pl Sci 7:1499. doi: 10.3389/fpls.2016.01499 Google Scholar
- Chelomina GN, Rozhkovan KV, Voronova AN, Burundukova OL, Muzarok TI, Zhuravlev YN (2016) Variation in the number of nucleoli and incomplete homogenization of 18S ribosomal DNA sequences in leaf cells of the cultivated Oriental ginseng (Panax ginseng Meyer). J Ginseng Res 40:176–184. doi: 10.1016/j.jgr.2015.07.005 CrossRefPubMedGoogle Scholar
- Chen K, de Borne FD, Szegedi E, Otten L (2014) Deep sequencing of the ancestral tobacco species Nicotiana tomentosiformis reveals multiple T-DNA inserts and a complex evolutionary history of natural transformation in the genus Nicotiana. Pl J 80:669–682. doi: 10.1111/tpj.12661 CrossRefGoogle Scholar
- Dadejova M, Lim KY, Souckova-Skalicka K, Matyasek R, Grandbastien MA, Leitch A, Kovarik A (2007) Transcription activity of rRNA genes correlates with a tendency towards intergenomic homogenization in Nicotiana allotetraploids. New Phytol 174:658–668. doi: 10.1111/j.1469-8137.2007.02034.x CrossRefPubMedGoogle Scholar
- Edwards KD, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans AD, Bombarely A, Allen F, Hurst R, White B, Kernodle SP, Bromley JR, Sanchez-Tamburrino JP, Lewis RS, Mueller LA (2017) A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genom 18:448. doi: 10.1186/s12864-017-3791-6 CrossRefGoogle Scholar
- Goodspeed TH (1954) The genus Nicotiana, Chronica Botanica. Waltham, MassachusettsGoogle Scholar
- Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
- Hemleben V, Ganal M, Gerstner J, Schiebel K, Torres RA (1988) Organization and length heterogeneity of plant ribosomal RNA genes. In: Kahl G (ed) The architecture of eukaryotic gene. Wiley, Weinheim, pp 371–384Google Scholar
- Ksiazczyk T, Kovarik A, Eber F, Huteau V, Khaitova L, Tesarikova Z, Coriton O, Chevre AM (2011) Immediate unidirectional epigenetic reprogramming of NORs occurs independently of rDNA rearrangements in synthetic and natural forms of a polyploid species Brassica napus. Chromosoma 120:557–571. doi: 10.1007/s00412-011-0331-z CrossRefPubMedGoogle Scholar
- Ksiazczyk T, Zwierzykowska E, Molik K, Taciak M, Krajewski P, Zwierzykowski Z (2015) Genome-dependent chromosome dynamics in three successive generations of the allotetraploid Festuca pratensis × Lolium perenne hybrid. Protoplasma 252:985–996. doi: 10.1007/s00709-014-0734-9 CrossRefPubMedGoogle Scholar
- Lim KY, Skalicka K, Koukalova B, Volkov RA, Matyasek R, Hemleben V, Leitch AR, Kovarik A (2004) Dynamic changes in the distribution of a satellite homologous to intergenic 26-18S rDNA spacer in the evolution of Nicotiana. Genetics 166:1935–1946. doi: 10.1534/genetics.166.4.1935 CrossRefPubMedPubMedCentralGoogle Scholar
- Malinska H, Tate JA, Matyasek R, Leitch AR, Soltis DE, Soltis PS, Kovarik A (2010) Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploids. BMC Evol Biol 10:291. doi: 10.1186/1471-2148-10-291 CrossRefPubMedPubMedCentralGoogle Scholar
- Matyasek R, Renny-Byfield S, Fulnecek J, Macas J, Grandbastien MA, Nichols R, Leitch A, Kovarik A (2012) Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genom 13:722. doi: 10.1186/1471-2164-13-722 CrossRefGoogle Scholar
- Pontes O, Neves N, Silva M, Lewis MS, Madlung A, Comai L, Viegas W, Pikaard CS (2004) Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc Natl Acad Sci USA 101:18240–18245. doi: 10.1073/pnas.0407258102 CrossRefPubMedPubMedCentralGoogle Scholar
- Renny-Byfield S, Chester M, Kovařík A, Le Comber SC, Grandbastien MA, Deloger M, Nichols RA, Macas J, Novák P, Leitch AR (2011) Next generation sequencing reveals evidence of genome downsizing and elimination of paternally derived repetitive DNA sequences in tobacco. Molec Biol Evol 28:2843–2854. doi: 10.1093/molbev/msr112 CrossRefPubMedGoogle Scholar
- Renny-Byfield S, Kovarik A, Chester M, Nichols RA, Macas J, Novak P, Leitch AR (2012) Independent, rapid and targeted loss of highly repetitive DNA in natural and synthetic allopolyploids of Nicotiana tabacum. PLoS ONE 7:e36963. doi: 10.1371/journal.pone.0036963 CrossRefPubMedPubMedCentralGoogle Scholar
- Sano Y, Sano R (1990) Variation of the intergenic spacer region of ribosomal DNA in cultivated and wild rice species. Genome 33:209–218Google Scholar
- Skalicka K, Lim KY, Matyasek R, Matzke M, Leitch AR, Kovarik A (2005) Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. New Phytol 166:291–303. doi: 10.1111/j.1469-8137.2004.01297.x CrossRefPubMedGoogle Scholar