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

Nicotiana species carry cellular T‐DNA sequences (cT‐DNAs), acquired by Agrobacterium‐mediated transformation. We characterized the cT‐DNA sequences of the ancestral Nicotiana tabacum species Nicotiana tomentosiformis by deep sequencing. N. tomentosiformis contains four cT‐DNA inserts derived from d...

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Bibliographic Details
Published in:The Plant journal : for cell and molecular biology 2014-11, Vol.80 (4), p.669-682
Main Authors: Chen, Ke, Dorlhac de Borne, François, Szegedi, Ernö, Otten, Léon
Format: Article
Language:English
Subjects:
Agrobacterium
Agrobacterium rhizogenes
Biochemistry, Molecular Biology
Biological Evolution
cT‐DNA
Deoxyribonucleic acid
DNA
DNA, Bacterial
Evolution
Gene Transfer, Horizontal
genes
Genes, Plant
High-Throughput Nucleotide Sequencing
horizontal gene transfer
Life Sciences
Molecular biology
natural transformation
Nicotiana - genetics
Nicotiana glauca
Nicotiana sylvestris
Nicotiana tabacum
Nicotiana tomentosiformis
octopine
Open Reading Frames
Plant biology
Rhizobium rhizogenes
Tobacco
transfer DNA
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Summary:Nicotiana species carry cellular T‐DNA sequences (cT‐DNAs), acquired by Agrobacterium‐mediated transformation. We characterized the cT‐DNA sequences of the ancestral Nicotiana tabacum species Nicotiana tomentosiformis by deep sequencing. N. tomentosiformis contains four cT‐DNA inserts derived from different Agrobacterium strains. Each has an incomplete inverted‐repeat structure. TA is similar to part of the Agrobacterium rhizogenes 1724 mikimopine‐type T‐DNA, but has unusual orf14 and mis genes. TB carries a 1724 mikimopine‐type orf14‐mis fragment and a mannopine‐agropine synthesis region (mas2‐mas1‐ags). The mas2′ gene codes for an active enzyme. TC is similar to the left part of the A. rhizogenes A4 T‐DNA, but also carries octopine synthase‐like (ocl) and c‐like genes normally found in A. tumefaciens. TD shows a complex rearrangement of T‐DNA fragments similar to the right end of the A4 TL‐DNA, and including an orf14‐like gene and a gene with unknown function, orf511. The TA, TB, TC and TD insertion sites were identified by alignment with N. tabacum and Nicotiana sylvestris sequences. The divergence values for the TA, TB, TC and TD repeats provide an estimate for their relative introduction times. A large deletion has occurred in the central part of the N. tabacum cv. Basma/Xanthi TA region, and another deletion removed the complete TC region in N. tabacum. Nicotiana otophora lacks TA, TB and TD, but contains TC and another cT‐DNA, TE. This analysis, together with that of Nicotiana glauca and other Nicotiana species, indicates multiple sequential insertions of cT‐DNAs during the evolution of the genus Nicotiana.
ISSN:0960-7412
1365-313X
DOI:10.1111/tpj.12661