Abstract
The chloroplast genome of Tetragonia tetragonioides (Aizoaceae; Caryophyllales) was sequenced to provide information for studies on phylogeny and evolution within Caryophyllales. The chloroplast genome of Tetragonia tetragonioides is 149,506 bp in length and includes a pair of inverted repeats (IRs) of 24,769 bp that separate a large single copy (LSC) region of 82,780 bp and a small single copy (SSC) region of 17,188 bp. Comparative analysis of the chloroplast genome showed that Caryphyllales species have lost many genes. In particular, the rpl2 intron and infA gene were not found in T. tetragonioides, and core Caryophyllales lack the rpl2 intron. Phylogenetic analyses were conducted using 55 genes in 16 complete chloroplast genomes. Caryophyllales was found to divide into two clades; core Caryophyllales and noncore Caryophyllales. The genus Tetragonia is closely related to Mesembryanthemum. Comparisons of the synonymous (Ks), nonsynonymous (Ka), and Ka/Ks substitution rates revealed that nonsynonymous substitution rates were lower than synonymous substitution rates and that Ka/Ks rates were less than 1. The findings of the present study suggest that most genes are a purified selection.
Highlights
Caryophyllales contains 37 families, 749 genera, and 11,600 species [1]
Comparative analyses of Caryophyllales species chloroplast genomes showed that many genes have been pseudogenized or lost and that some Caryophyllales species (Drosera and Carnegiea) have lost or exhibited expansion of inverted repeats (IRs) regions
Downie and Palmer [2] studied the chloroplast genome within Caryophyllales and observed some different gene orders
Summary
Caryophyllales contains 37 families, 749 genera, and 11,600 species [1]. This order is divided into two main clades: core Caryophyllales and noncore Caryophyllales. Previous studies have used molecular phylogenetic analyses based on restriction site data from nuclear and plastid markers [2–4]. DNA sequence data show that the nuclear maker is the ITS (internal transcribed spacer) and the plastid markers are atpB, matK, ndhF, psbB, rbcL, rpoC2, rps, rpl intron, rpoC1, IR (inverted repeat) region, and IR junction. Molecular data for Caryophyllales showed this order to be a monophyletic group. Several molecular studies have shown the phylogenetic position of the Aizoaceae (Tetragonioideae, Aizooideae and Sesuvioideae) within core Caryophyllales [3, 4], and some molecular studies have indicated that Aizoaceae was not included in the core Caryophyllales and was a paraphyletic group [2, 5]
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