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Open Access Highly Accessed Research article

Expansion and diversification of the SET domain gene family following whole-genome duplications in Populus trichocarpa

Li Lei13, Shi-Liang Zhou1, Hong Ma2* and Liang-Sheng Zhang2*

Author Affiliations

1 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China

2 State Key Laboratory of Genetic Engineering, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China

3 Graduate University of the Chinese Academy of Sciences, Beijing 100039, China

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BMC Evolutionary Biology 2012, 12:51  doi:10.1186/1471-2148-12-51

Published: 12 April 2012

Additional files

Additional file 1:

Unrooted phylogenetic trees constructed using (A) ML and (B) BI methods based on SET amino acid sequences from Populus and Arabidopsis SET proteins.

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Additional file 2:

Detailed locations of all duplicated pairs of SET genes in Populus from recent and ancient polyploidy events in the syntenic region.

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Additional file 3:

Table-S1 Ks of SET gene pairs in Suv, Ash, Atxr5, E(z) and Trx subfamilies. Table-S2 Raw data from microarray expression analyses for Populus SET genes. Sample abbreviations are defined in Figure 6 and Additional file 4. Table-S3 Raw data from ESTs for Arabidopsis SET genes. Table-S4 Raw data from transcriptome data for soybean SET genes.

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Additional file 4:

Transcript abundance in different subgroups across different tissues, organs, and treatments in Populus based on the genome-wide microarray data. Sample abbreviations are defined in Figure 6

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Additional file 5:

Structure of duplicated gene pairs within the Populus SET gene family. Exons, green filled boxes; introns, black single lines. UTRs are indicated by thick blue lines at both ends. Intron phases 0, 1 and 2 are indicated by numbers 0, 1 and 2 in the figure.

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Additional file 6:

Examples of five scenarios for terminus diversity in duplicated gene pairs of the SET family in Populus. This number corresponds to the one in Figure 6, and the red box represents the location of the mutations causing the patterns.

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