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Open Access Highly Accessed Research article

The SLEEPER genes: a transposase-derived angiosperm-specific gene family

Marijn Knip, Sylvia de Pater and Paul JJ Hooykaas*

Author Affiliations

Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

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BMC Plant Biology 2012, 12:192  doi:10.1186/1471-2229-12-192

Published: 16 October 2012

Additional files

Additional file 1:

Table S1. Sequences found using TBLASTN queries in EST databases of Amborella trichopoda (AAGP) and mixed conifer libraries (TIGR) [18] and BLASTN in the Phytozome [19]Selaginella genomic database. This table was created using the DAYSLEEPER amino acid sequence as a query (TBLASTN) and the DNA coding sequence of DAYSLEEPER (BLASTN). The top three of Amborella hits, the three conifer hits and three top Selaginella hits are displayed, including the sequence identifier, species name (conifers) and the BLAST-scores and E-values. Standard BLAST parameters were used for TBLASTN queries, for BLASTN queries the expect threshold was increased to 100.

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Additional file 2:

Figure S1. Synteny between the pericentromeric region of chromosome 3 of Arabidopsis thaliana and chromosome 11 of Vitis vinifera. The genes (1–5) depicted were also used in a comparison between Brassicaceae species by Hall et al. [22]. Gene 3 of the grapevine genome represents VINESLEEPER2. “CEN” is the centromere.

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Additional file 3:

Table S2. Primerlist. Primer names, descriptions and sequences are shown.

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Additional file 4:

Figure S2. Phylogenetic tree of Arabidopsis thaliana and Capsella rubella SLEEPERS. We estimated the non-synonymous substitution rate (Ka), synonymous substitution rate (Ks) and Ka/Ks values between DAYSLEEPER and CYTOSLEEPER and their respective homologs in Capsella rubella. We used the coding sequences of the genes that we found using BLASTN with the DAYLEEPER and CYTOSLEEPER coding sequences in the Phytozome [19]Capsella rubella genomic database. We found hits for both queries with scores of 2786 and 1891 respectively both with an E-value of 0. A FASTA file containing the unaligned coding sequences were used in the online “Ka/Ks Calculation tool” of the Bergen Center for Computational Science (http://services.cbu.uib.no/tools/kaks) [41,42]. The values in the phylogenetic tree represent the calculated Ka/Ks ratio’s.

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Additional file 5:

Figure S3. Model of the domestication of a hAT transposase by a retrocopy process. This figure is based on a figure by Vaknin et al. [43]. An active hAT transposase gene is transcribed into mRNA. A promiscuous reverse-transcriptase reverse-transcribes the spliced mRNA into cDNA, which subsequently becomes inserted in the genome. This process results in a retrocopy that is devoid of any introns and regulatory sequences. Promoter and UTR sequences can be obtained by the retrocopy from its neighboring sequences, or by a nearby secondary integration event of another transposable element. Acquisition of UTR’s or coding material is a process called exonisation and can eventually yield a functional and actively transcribed gene: a retrogene. Overlapping ellipses represent hAT transposon associated host duplications and the adjacent arrows represent terminal inverted repeats. UTR’s are depicted as light grey boxes, coding sequences as dark grey boxes and promoter boxes as white boxes. Exons are indicated with lines. Start of transcription is marked by an arrow.

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Additional file 6:

Table S3. Plasmids used for localization of SLEEPER fusion proteins in protoplasts and complementation of the daysleeper phenotype in Arabidopsis thaliana. Collection number and brief description and purpose in this work are shown.

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