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Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs.
Mol Biol Evol 2011; 28(10):2843-54MB

Abstract

We used next generation sequencing to characterize and compare the genomes of the recently derived allotetraploid, Nicotiana tabacum (<200,000 years old), with its diploid progenitors, Nicotiana sylvestris (maternal, S-genome donor), and Nicotiana tomentosiformis (paternal, T-genome donor). Analysis of 14,634 repetitive DNA sequences in the genomes of the progenitor species and N. tabacum reveal all major types of retroelements found in angiosperms (genome proportions range between 17-22.5% and 2.3-3.5% for Ty3-gypsy elements and Ty1-copia elements, respectively). The diploid N. sylvestris genome exhibits evidence of recent bursts of sequence amplification and/or homogenization, whereas the genome of N. tomentosiformis lacks this signature and has considerably fewer homogenous repeats. In the derived allotetraploid N. tabacum, there is evidence of genome downsizing and sequences loss across most repeat types. This is particularly evident amongst the Ty3-gypsy retroelements in which all families identified are underrepresented in N. tabacum, as is 35S ribosomal DNA. Analysis of all repetitive DNA sequences indicates the T-genome of N. tabacum has experienced greater sequence loss than the S-genome, revealing preferential loss of paternally derived repetitive DNAs at a genome-wide level. Thus, the three genomes of N. sylvestris, N. tomentosiformis, and N. tabacum have experienced different evolutionary trajectories, with genomes that are dynamic, stable, and downsized, respectively.

Authors+Show Affiliations

School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21512105

Citation

Renny-Byfield, Simon, et al. "Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana Tabacum, Predominantly Through the Elimination of Paternally Derived Repetitive DNAs." Molecular Biology and Evolution, vol. 28, no. 10, 2011, pp. 2843-54.
Renny-Byfield S, Chester M, Kovařík A, et al. Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Mol Biol Evol. 2011;28(10):2843-54.
Renny-Byfield, S., Chester, M., Kovařík, A., Le Comber, S. C., Grandbastien, M. A., Deloger, M., ... Leitch, A. R. (2011). Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Molecular Biology and Evolution, 28(10), pp. 2843-54. doi:10.1093/molbev/msr112.
Renny-Byfield S, et al. Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana Tabacum, Predominantly Through the Elimination of Paternally Derived Repetitive DNAs. Mol Biol Evol. 2011;28(10):2843-54. PubMed PMID: 21512105.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. AU - Renny-Byfield,Simon, AU - Chester,Michael, AU - Kovařík,Ales, AU - Le Comber,Steven C, AU - Grandbastien,Marie-Angèle, AU - Deloger,Marc, AU - Nichols,Richard A, AU - Macas,Jiri, AU - Novák,Petr, AU - Chase,Mark W, AU - Leitch,Andrew R, Y1 - 2011/04/21/ PY - 2011/4/23/entrez PY - 2011/4/23/pubmed PY - 2012/3/27/medline SP - 2843 EP - 54 JF - Molecular biology and evolution JO - Mol. Biol. Evol. VL - 28 IS - 10 N2 - We used next generation sequencing to characterize and compare the genomes of the recently derived allotetraploid, Nicotiana tabacum (<200,000 years old), with its diploid progenitors, Nicotiana sylvestris (maternal, S-genome donor), and Nicotiana tomentosiformis (paternal, T-genome donor). Analysis of 14,634 repetitive DNA sequences in the genomes of the progenitor species and N. tabacum reveal all major types of retroelements found in angiosperms (genome proportions range between 17-22.5% and 2.3-3.5% for Ty3-gypsy elements and Ty1-copia elements, respectively). The diploid N. sylvestris genome exhibits evidence of recent bursts of sequence amplification and/or homogenization, whereas the genome of N. tomentosiformis lacks this signature and has considerably fewer homogenous repeats. In the derived allotetraploid N. tabacum, there is evidence of genome downsizing and sequences loss across most repeat types. This is particularly evident amongst the Ty3-gypsy retroelements in which all families identified are underrepresented in N. tabacum, as is 35S ribosomal DNA. Analysis of all repetitive DNA sequences indicates the T-genome of N. tabacum has experienced greater sequence loss than the S-genome, revealing preferential loss of paternally derived repetitive DNAs at a genome-wide level. Thus, the three genomes of N. sylvestris, N. tomentosiformis, and N. tabacum have experienced different evolutionary trajectories, with genomes that are dynamic, stable, and downsized, respectively. SN - 1537-1719 UR - https://www.unboundmedicine.com/medline/citation/21512105/Next_generation_sequencing_reveals_genome_downsizing_in_allotetraploid_Nicotiana_tabacum_predominantly_through_the_elimination_of_paternally_derived_repetitive_DNAs_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msr112 DB - PRIME DP - Unbound Medicine ER -