Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae <i>s.l.</i> (Dipsacales) Plastomes
Caprifoliaceae <i>s.l</i>. 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, <...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-09-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/22/19/10485 |
| Summary: | Caprifoliaceae <i>s.l</i>. 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, <i>Fedia cornucopiae</i>, <i>Valeriana fauriei,</i> and <i>Valerianella locusta</i> from the subfamily Valerianoideae, as well as <i>Dipsacus japonicus</i> and <i>Scabiosa comosa</i> 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 <i>accD</i> 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 <i>Valeriana</i> <i>accD</i> gene harbors a large insertion of amino acid repeat (AAR) motifs, and intraspecific polymorphism with a variable number of AARs in the <i>Valeriana accD</i> gene was detected. We found a correlation between intron losses and increased ratios of nonsynonymous to synonymous substitution rates in the <i>clpP</i> gene with intensified positive selection. In addition, two Dipsacoideae plastomes revealed the loss of the plastid-encoded <i>rps15</i>, and a potential functional gene transfer to the nucleus was confirmed. |
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| ISSN: | 1661-6596 1422-0067 |