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2013) catalyzing in bacteria the formation of selenocysteinyl-t RNA starting from an UGA decoding t RNA(Sel C) charged with serine and selenophosphate, the product of the enzyme selenophosphate synthetase (Sel D).
Together with Sel B, a selenocysteinyl-t RNA-specific translation factor, Sel A, Sel C, and Sel D are components of the bacterial Sec-decoding trait, allowing the incorporation of Sec at specific UGA (opal) codons followed by Sec insertion sequence (SECIS) elements (Zinoni et al. As Sel A homologs can be found in organisms lacking the Sec-decoding trait (Romero et al. 2006), the presence of this gene does not imply that Sel A (Hp Sel A) is apparently orthologous to experimentally validated Sel A, other Sel components and selenoproteins were not identified in the genome, raising questions about the origin and role of the species (Flahou et al.
In contrast, the Li–Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records.
Combining estimates calibrated by two known fossil nodes and the Li–Tanimura method, we propose that monocots branched off from dicots 140–150 Myr ago (late Jurassic–early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100–115 Myr ago (Albian–Aptian of the Cretaceous).
The ORFs were searched for homology using t BLASTn in the same genome set, the results were parsed to count the occurrences of U: C, U: U, and U: X in sequence alignments.
7.7.8 (Stamatakis 2006) using the PROTCATGTR amino acid substitution model. Complete prokaryotic genomes were downloaded from the NCBI (National Center for Biotechnology Information) ftp site; ε-proteobacteria genomes considered for the analysis were selected from genome report files based on the availability of whole-genome phylogeny (Wang and Wu 2013) and clustered using a Genomic Similarity Score (GSSa) = 0.95 (Moreno-Hagelsieb et al. Proteins of the Sel machinery were identified by homology using annotated sequences from ).
The Sel A tree was compared with the species tree using the Ape “cophyplot” function. To discriminate between equivalent and nonequivalent homologs, known paralogous proteins (e.g., EF-Tu) were included in the search.
We estimated the dates of the monocot–dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset.
Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed.