Inaugural Article: Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution -- Data Supplement - Supporting Information -- Proceedings of the National Academy of Sciences

Supporting information for Adams et al. (2002) Proc. Natl. Acad. Sci. USA, 10.1073/pnas.042694899

Supporting Material and Methods
Cox1
sequences from Lachnocaulon, Goodenia, and Phlox were isolated by PCR amplification using the primers (5'-TTTCATCTTCGGTGCC-3' and 5'-TATGAAAAGCTGGAGG-3'). PCR conditions were as in Adams et al. (1). PCR products were sequenced directly using the above primers and two additional primers (5'-GGAGCAGTTGATTTAGC-3' and 5'-GAGCAATGTCTAGCCC-3') on an Applied Biosystems 3700 DNA sequencer. The cox1 sequences determined in this study have been assigned GenBank numbers AY053574–AY053576. The soybean rps19 genomic locus was PCR-amplified by using primers located in the untranslated regions (5'-CACTCTGCCTTTCCTTTCCCTTCATAGC-3' and 5'-GTGATATTTATCTTCTGTACTTTTGGAC-3'), followed by sequencing the entire coding sequence and a portion of the intron from both ends. GenBank accession numbers for nuclear rps19 ESTs used in this study are: Gossypium arboreum (AW729551, BG444724, BG446776), Medicago trunculata (AL380000, AL379999), and soybean (AI441037, AI900351, AI900154, AW424213). GenBank accession numbers for rps1 ESTs used in this study are: tomato (BF096359), Medicago (AL374656, AW695859, BE318248, BE318248), Lotus japonicus (AU088861), Lupinus luteus (BG153957). Supporting Results

Evidence that the rps19 and rps1 sequences of maize, cotton, legumes, and tomato (present in EST databases) are indeed located in the nucleus in these plants and were derived by gene transfer from the mitochondrion and encode mitochondrial proteins includes the following: (i) These sequences are highly divergent relative to homologs in the mitochondrial genome, as expected for genes transferred to the nucleus, given the much higher mutation rate in the nucleus than the mitochondrion in plants (2, 3). (ii) Because the most closely related sequences to the rps19 and rps1 genes in question are angiosperm mitochondrial rps19 or rps1 sequences, the genes were almost certainly derived by gene transfer to the nucleus. (iii) Their products are predicted to be targeted to the mitochondrion by the programs Mitoprot (4), TargetP (5), and Predotar version 0.5 (www.inra.fr/Internet/Produits/Predotar). (iv) In the case of soybean rps19, we determined the genomic sequence and identified a spliceosomal intron in the 5' untranslated region near the start codon (spliceosomal introns have been found only in the nucleus and never in mitochondrial genomes).

References:

1. Adams, K. L., Rosenblueth, M., Qiu, Y.-L. & Palmer, J. D. (2001) Genetics 158, 1289–1300.

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