Abstract
Caprifoliaceae s.l. plastid genomes (plastomes) show that one inversion and two inverted repeat boundary shifts occurred in the common ancestor of this family, after which the plastomes are generally conserved. This study reports plastome sequences of five additional species, Fedia cornucopiae, Valeriana fauriei, and Valerianella locusta from the subfamily Valerianoideae, as well as Dipsacus japonicus and Scabiosa comosa from the subfamily Dipsacoideae. Combined with the published plastomes, these plastomes provide new insights into the structural evolution of plastomes within the family. Moreover, the three plastomes from the subfamily Valerianoideae exhibited accelerated nucleotide substitution rates, particularly at synonymous sites, across the family. The patterns of accD sequence divergence in the family are dynamic with structural changes, including interruption of the conserved domain and increases in nonsynonymous substitution rates. In particular, the Valeriana accD gene harbors a large insertion of amino acid repeat (AAR) motifs, and intraspecific polymorphism with a variable number of AARs in the Valeriana accD gene was detected. We found a correlation between intron losses and increased ratios of nonsynonymous to synonymous substitution rates in the clpP gene with intensified positive selection. In addition, two Dipsacoideae plastomes revealed the loss of the plastid-encoded rps15, and a potential functional gene transfer to the nucleus was confirmed.
Highlights
The plastid genome of angiosperms is generally conserved and has a quadripartite structure with a pair of inverted repeats (IR) separated by large and small single copy (LSC and SSC) regions [1]
Divergent accD and Clp protease proteolytic subunit (clpP) genes are likely caused by compensatory mutations in the interactions between nuclear-encoded plastid-targeted subunits [27,28]
Despite broader sampling and sequencing across the family, very little is known about the gene evolution, including structural changes and rate variation in the plastid-encoded accD and clpP genes
Summary
The plastid genome (plastome) of angiosperms is generally conserved and has a quadripartite structure with a pair of inverted repeats (IR) separated by large and small single copy (LSC and SSC) regions [1]. Divergent accD and clpP genes are likely caused by compensatory mutations in the interactions between nuclear-encoded plastid-targeted subunits [27,28]. This is because the function of the two genes depends on nuclear-encoded proteins that assemble plastid-localized subunits. Variations in inverted repeat (IR) boundary shifts and nucleotide substitution rates have been documented in the Caprifoliaceae s.l. plastomes [34,36]. Despite broader sampling and sequencing across the family, very little is known about the gene evolution, including structural changes and rate variation in the plastid-encoded accD and clpP genes. The correlation between structural evolution and nucleotide substitution rates in the plastid-encoded accD and clpP genes across this family was examined. We examined intra- and infraspecific length variations in the accD coding region of Valeriana fauriei Briq. and V. sambucifolia f. dageletiana (Nakai ex F.Maek.) Hara
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