A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i>
<i>Chrysosplenium</i>, a perennial herb in the family Saxifragaceae, prefers to grow in low light and moist environments and is divided into two sections of <i>Alternifolia</i> and <i>Oppositifolia</i> based on phyllotaxy. Although there has been some progress in...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-09-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/24/19/14735 |
| Summary: | <i>Chrysosplenium</i>, a perennial herb in the family Saxifragaceae, prefers to grow in low light and moist environments and is divided into two sections of <i>Alternifolia</i> and <i>Oppositifolia</i> based on phyllotaxy. Although there has been some progress in the phylogeny of <i>Chrysosplenium</i> over the years, the phylogenetic position of some species is still controversial. In this study, we assembled chloroplast genomes (cp genomes) of 34 <i>Chrysosplenium</i> species and performed comparative genomic and phylogenetic analyses in combination with other cp genomes of previously known <i>Chrysosplenium</i> species, for a total of 44 <i>Chrysosplenium</i> species. The comparative analyses revealed that cp genomes of <i>Chrysosplenium</i> species were more conserved in terms of genome structure, gene content and arrangement, SSRs, and codon preference, but differ in genome size and SC/IR boundaries. Phylogenetic analysis showed that cp genomes effectively improved the phylogenetic support and resolution of <i>Chrysosplenium</i> species and strongly supported <i>Chrysosplenium</i> species as a monophyletic taxon and divided into three branches. The results also showed that the sections of <i>Alternifolia</i> and <i>Oppositifolia</i> were not monophyletic with each other, and that <i>C. microspermum</i> was not clustered with other <i>Chrysosplenium</i> species with alternate leaves, but with <i>C. sedakowii</i> into separate branches. In addition, we identified 10 mutational hotspot regions that could serve as potential DNA barcodes for <i>Chrysosplenium</i> species identification. In contrast to <i>Peltoboykinia</i>, the <i>clp</i>P and <i>ycf</i>2 genes of <i>Chrysosplenium</i> were subjected to positive selection and had multiple significant positive selection sites. We further detected a significant positive selection site on the <i>pet</i>G gene between the two sections of <i>Chrysosplenium</i>. These evolutionary characteristics may be related to the growth environment of <i>Chrysosplenium</i> species. This study enriches the cp genomes of <i>Chrysosplenium</i> species and provides a reference for future studies on its evolution and origin. |
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| ISSN: | 1661-6596 1422-0067 |