Whole Genome Duplication of Intra- and Inter-chromosomes in the Tomato Genome

Chi Song; Juan Guo; Wei Sun; Ying Wang

doi:10.1016/j.jgg.2012.06.002

Volume 39 Issue 7

Jul. 2012

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Article Navigation > Journal of Genetics and Genomics > 2012 > 39(7): 361-368

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Whole Genome Duplication of Intra- and Inter-chromosomes in the Tomato Genome

doi: 10.1016/j.jgg.2012.06.002

Chi Song^{a, b},
Juan Guo^{a, b},
Wei Sun^{b, c},
Ying Wang^a

a
Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
b
Graduate University of Chinese Academy of Sciences, Beijing 100049, China
c
South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China

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Corresponding author: E-mail address: yingwang@wbgcas.cn (Ying Wang)
Received Date: 2012-06-13
Accepted Date: 2012-06-17
Rev Recd Date: 2012-06-17

Available Online: 2012-06-22

Publish Date: 2012-07-20

Abstract

Abstract

Whole genome duplication (WGD) events have been proven to occur in the evolutionary history of most angiosperms. Tomato is considered a model species of the Solanaceae family. In this study, we describe the details of the evolutionary process of the tomato genome by detecting collinearity blocks and dating the WGD events on the tree of life by combining two different methods: synonymous substitution rates (Ks) and phylogenetic trees. In total, 593 collinearity blocks were discovered out of 12 pseudo-chromosomes constructed. It was evident that chromosome 2 had experienced an intra-chromosomal duplication event. Major inter-chromosomal duplication occurred among all the pseudo-chromosome. We calculated the Ks value of these collinearity blocks. Two peaks of Ks distribution were found, corresponding to two WGD events occurring approximately 36–82 million years ago (MYA) and 148–205 MYA. Additionally, the results of phylogenetic trees suggested that the more recent WGD event may have occurred after the divergence of the rosid-asterid clade, but before the major diversification in Solanaceae. The older WGD event was shown to have occurred before the divergence of the rosid-asterid clade and after the divergence of rice-Arabidopsis (monocot-dicot).
- Whole genome duplication,
- Collinearity block,
- Phylogenetic tree

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References(37)

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