Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective

Genes, Journal Year: 2024, Volume and Issue: 15(4), P. 444 - 444

Published: March 31, 2024

Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on between species, studies are scarce. Here, we sequenced from three species (Sedum alfredii, plumbizincicola, japonicum) to understand their evolutionary relationships plastome structural evolution. Our analyses revealed minimal size GC content variation across species. However, gene distribution at IR boundaries, repeat structures, codon usage patterns showed diversity both inter-specific intra-specific levels. Notably, an rps19 expansion a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving markers future studies. Phylogenetic confirmed non-monophyly divided Acre clade into two groups. Individuals same clustered together, with strong support S. tricarpum, plumbizincicola. Additionally, japonicum clearly affiliates clade. This study provides valuable insights intra-generic Sedum, well overall evolution within genus.

Language: Английский

Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics

Genes, Journal Year: 2024, Volume and Issue: 15(4), P. 441 - 441

Published: March 30, 2024

The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, conservation. As an important group horticultural ornamentals Crassulaceae family, Sempervivum plants are known their unique rosette-like structures reproduction through offsets. Despite popularity, classification status remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) widespread phenomenon unbalanced synonymous codons coding (CDS). However, due to limited available data, there has been no research that focused on CUB analysis among until now. To address these gaps, we sequenced released plastomes seven species one subspecies from Sempervivum, revealing several consistent patterns. These included shared 110 bp extension rps19 gene, 14 hypervariable regions (HVRs) distinct nucleotide diversity (π: 0.01173 0.02702), evidence selective pressures shaping usage. Notably, phylogenetic robustly divided monophyletic clade two sections: Jovibarba Sempervivum. In conclusion, this comprehensive resource provides valuable evolution offers potential molecular markers DNA barcoding.

Language: Английский

Novel Perspectives on Chloroplast tRNA Genomic and Structural Variations Imply the Evolution of Papilionoideae (Fabaceae)

Horticulturae, Journal Year: 2024, Volume and Issue: 10(9), P. 932 - 932

Published: Aug. 31, 2024

Papilionoideae is the most species-rich subfamily of third largest angiosperm family Fabaceae. One constituent large group, inverted-repeat-lacking clade (IRLC), well-known for broad loss one IR copy. Accumulating observations massive plastomic disparities have made IRLC a well-suited model exploring plastome evolution. However, there still amount left to explore. The present study focused on plastid tRNA (pttRNA) evolution within Papilionoideae, employing currently densest sampling strategies both (156) and non-IRLC (109) lineages. Strikingly, our results revealed abundant inter-lineage variabilities in sequences structures, including 3 nt difference average size trnS-UGA, consensus sequence across 29 tRNAs, distinct indels trnA-UGC, an impressive 248 intron trnI-GAU (potential markers). Additionally, was unequal stability atypical secondary structures trnS-GGA as well significantly diverse compositions substitution events all compared tRNAs (p < 0.05). Ultimately, these findings not only demonstrate significant differences unique markers pttRNAs other but also draw important conclusion that losses potentially promote highly evolutionary patterns IRLC, which could partly compensate potential IR-lacking impacts.

Language: Английский