Complete Plastid Genome Sequences of Three Rosids (Castanea, Prunus, Theobroma): Evidence for At Least Two Independent Transfers of rpl22 to the Nucleus

Molecular Biology and Evolution, Jan 2011

Functional gene transfer from the plastid to the nucleus is rare among land plants despite evidence that DNA transfer to the nucleus is relatively frequent. During the course of sequencing plastid genomes from representative species from three rosid genera (Castanea, Prunus, Theobroma) and ongoing projects focusing on the Fagaceae and Passifloraceae, we identified putative losses of rpl22 in these two angiosperm families. We further characterized rpl22 from three species of Passiflora and one species of Quercus and identified sequences that likely represent pseudogenes. In Castanea and Quercus, both members of the Fagaceae, we identified a nuclear copy of rpl22, which consisted of two exons separated by an intron. Exon 1 encodes a transit peptide that likely targets the protein product back to the plastid and exon 2 encodes rpl22. We performed phylogenetic analyses of 97 taxa, including 93 angiosperms and four gymnosperm outgroups using alignments of 81 plastid genes to examine the phylogenetic distribution of rpl22 loss and transfer to the nucleus. Our results indicate that within rosids there have been independent transfers of rpl22 to the nucleus in Fabaceae and Fagaceae and a putative third transfer in Passiflora. The high level of sequence divergence between the transit peptides in Fabaceae and Fagaceae strongly suggest that these represent independent transfers. Furthermore, Blast searches did not identify the “donor” genes of the transit peptides, suggesting a de novo origin. We also performed phylogenetic analyses of rpl22 for 87 angiosperms and four gymnosperms, including nuclear-encoded copies for five species of Fabaceae and Fagaceae. The resulting trees indicated that the transfer of rpl22 to the nucleus does not predate the origin of angiosperms as suggested in an earlier study. Using previously published angiosperm divergence time estimates, we suggest that these transfers occurred approximately 56–58, 34–37, and 26–27 Ma for the Fabaceae, Fagaceae, and Passifloraceae, respectively.

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Complete Plastid Genome Sequences of Three Rosids (Castanea, Prunus, Theobroma): Evidence for At Least Two Independent Transfers of rpl22 to the Nucleus

Robert K. Jansen 2 Christopher Saski 1 Seung-Bum Lee 0 Anne K. Hansen 2 Henry Daniell 0 0 Department of Molecular Biology and Microbiology, University of Central Florida 1 Clemson University, Genomics Institute 2 Section of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin Functional gene transfer from the plastid to the nucleus is rare among land plants despite evidence that DNA transfer to the nucleus is relatively frequent. During the course of sequencing plastid genomes from representative species from three rosid genera (Castanea, Prunus, Theobroma) and ongoing projects focusing on the Fagaceae and Passifloraceae, we identified putative losses of rpl22 in these two angiosperm families. We further characterized rpl22 from three species of Passiflora and one species of Quercus and identified sequences that likely represent pseudogenes. In Castanea and Quercus, both members of the Fagaceae, we identified a nuclear copy of rpl22, which consisted of two exons separated by an intron. Exon 1 encodes a transit peptide that likely targets the protein product back to the plastid and exon 2 encodes rpl22. We performed phylogenetic analyses of 97 taxa, including 93 angiosperms and four gymnosperm outgroups using alignments of 81 plastid genes to examine the phylogenetic distribution of rpl22 loss and transfer to the nucleus. Our results indicate that within rosids there have been independent transfers of rpl22 to the nucleus in Fabaceae and Fagaceae and a putative third transfer in Passiflora. The high level of sequence divergence between the transit peptides in Fabaceae and Fagaceae strongly suggest that these represent independent transfers. Furthermore, Blast searches did not identify the ''donor'' genes of the transit peptides, suggesting a de novo origin. We also performed phylogenetic analyses of rpl22 for 87 angiosperms and four gymnosperms, including nuclear-encoded copies for five species of Fabaceae and Fagaceae. The resulting trees indicated that the transfer of rpl22 to the nucleus does not predate the origin of angiosperms as suggested in an earlier study. Using previously published angiosperm divergence time estimates, we suggest that these transfers occurred approximately 56-58, 34-37, and 26-27 Ma for the Fabaceae, Fagaceae, and Passifloraceae, respectively. - Introduction Subsequent to the endosymbiotic origin of plastids from a cyanobacterial ancestor, there was a massive transfer of genes to the nucleus (reviewed in Timmis et al. 2004). Cyanobacteria encode 5,0007,000 genes, and only 20200 of these have been retained in plastid genomes. This early mass transfer of genes suggests that a large proportion of nuclear genes originated in the plastid; estimates in Arabidopsis indicate that 18% of its nuclear genes originate from the ancestral plastid genome (Martin et al. 2002). The streamlining of the ancestral plastid genome has resulted in a very compact genome, highly conserved with respect to organization, gene content, and gene order. Examination of the 125 land plant plastid genomes currently on GenBank shows that genome size, gene content, and gene order are for the most part highly conserved, with substantial variation in intergenic spacer regions (Daniell et al. 2006; Saski et al. 2007) and regulatory sequences (Ruhlman et al. 2010). Most genomes have a quadripartite structure with two copies of a large inverted repeat separating two unequally sized single-copy regions termed the large and small single-copy regions. Land plant plastid genomes are 108217 kb, with the vast majority in the 150170 kb range. Most plastid genomes contain 110 130 distinct genes; the majority of these genes (about 80) code for proteins and are mostly involved in photosynthesis or gene expression with the remainder being transfer RNA (about 30) or ribosomal RNA (4) genes (Raubeson and Jansen 2005; Bock 2007). Although most functional gene transfers to the nucleus occurred during early stages of plastid evolution, nonfunctional DNA transfers to the nucleus continue at a high rate (Martin et al. 2002; Timmis et al. 2004; Matsuo et al. 2005; Noutsos et al. 2005). Recent examinations of plant nuclear genomes demonstrated the presence of a large number of nuclear-localized plastid DNA fragments (nupDNAs). An extensive analysis of rice (Matsuo et al. 2005) estimated that there were 701 insertions of plastid DNA into the nucleus, for a total of 0.9 mb of nupDNAs representing 0.12% of the nuclear genome. The inserted fragment sizes varied in length from 38 bp to 131 kb, and the largest one included almost the entire plastid genome. Two studies examined the rate of plastid DNA transfer to the nucleus in tobacco The Author 2010. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: using plastid transformation. Using transgenic tobacco plants, Huang et al. (2003) found (...truncated)


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Robert K. Jansen, Christopher Saski, Seung-Bum Lee, Anne K. Hansen, Henry Daniell. Complete Plastid Genome Sequences of Three Rosids (Castanea, Prunus, Theobroma): Evidence for At Least Two Independent Transfers of rpl22 to the Nucleus, Molecular Biology and Evolution, 2011, pp. 835-847, 28/1, DOI: 10.1093/molbev/msq261