ArticleScientific reports2020
Patterns and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic Context using Plastomic Data of Ferns.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 48 citations in OpenAlex.
- The Complete Chloroplast Genome of Tree Fern Cyathea delgadii and Its Comparison to Other Cyatheales.Biochemical genetics · 2026Article
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- The complete chloroplast genome and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2026Article
- Plastomic insights into the genetic variation and phylogenetic relationships of Macadamia.Scientific reports · 2025Article
- The complete chloroplast genome sequence ofMitochondrial DNA. Part B, Resources · 2025Article
- Mitochondrial genome ofFrontiers in plant science · 2025Article
- Comparative chloroplast genomics, phylogenetic relationships and molecular markers development of Aglaonema commutatum and seven green cultivars of Aglaonema.Scientific reports · 2024Article
- Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships.BMC genomics · 2024Article
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- The complete chloroplast genome sequence and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2024Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2024Article
- Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae).BMC plant biology · 2023Article
- Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily.Scientific reports · 2023Article
- Plastomes ofPlants (Basel, Switzerland) · 2023Article
- The complete chloroplast genome and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2023Article
- The complete chloroplast genome and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2023Article
- Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns.Frontiers in plant science · 2022Article
- Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae).BMC plant biology · 2021Article
- Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae.Ecology and evolution · 2021Article
- Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts.Frontiers in plant science · 2021Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The trans-splicing rps12 gene of fern plastomes (plastid genomes) exhibits a unique structure owing to its variations in intragenic exon location and intron content, and thus, it provides an excellent model system for examining the effect of plastid gene structure on rates and patterns of molecular evolution. In this study, 16 complete fern plastome sequences were newly generated via the Illumina HiSeq sequencing platform. We reconstructed the phylogeny of ferns and inferred the patterns and rates of plastid rps12 gene evolution in a phylogenetic context by combining these plastome data with those of previously published fern species. We uncovered the diversity of fern plastome evolution by characterizing the structures of these genomes and obtained a highly supported phylogenetic framework for ferns. Furthermore, our results revealed molecular evolutionary patterns that were completely different from the patterns revealed in previous studies. There were significant differences in the patterns and rates of nucleotide substitutions in both intron-containing and intron-less rps12 alleles. Rate heterogeneity between single-copy (SC) and inverted repeat (IR) exons was evident. Unexpectedly, however, IR exons exhibited significantly higher synonymous substitution rates (dS) than SC exons, a pattern that contrasts the regional effect responsible for decreased rates of nucleotide substitutions in IRs. Our results reveal that structural changes in plastid genes have important effects on evolutionary rates, and we propose possible mechanisms to explain the variations in the nucleotide substitution rates of this unusual gene.
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