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

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(22), P. 16273 - 16273

Published: Nov. 13, 2023

Cordia subcordata trees or shrubs, belonging to the Boraginaceae family, have strong resistance and adapted their habitat on a tropical coral island in China, but lack of genome information regarding its genetic background is unclear. In this study, was assembled using both short/long whole sequencing reads Hi-C reads. The 475.3 Mb, with 468.7 Mb (99.22%) sequences into 16 chromosomes. Repeat accounted for 54.41% genome. A total 26,615 genes were predicted, 25,730 functionally annotated different annotation databases. Based other 17 species, phylogenetic analysis 336 single-copy obtained from ortholog showed that C. sister Coffea eugenioides, divergence time estimated be 77 MYA between two species. Gene family evolution indicated significantly expanded gene families related chemical defenses against diseases. These results can provide reference deeper understanding helpful exploring adaptation mechanism islands future.

Language: Английский

Chloroplast Spacer DNA Analysis Revealed Insights into Phylogeographical Structure of Phoebe chekiangensis

Forests, Journal Year: 2024, Volume and Issue: 15(7), P. 1073 - 1073

Published: June 21, 2024

Research studies on the conservation genetics of endangered plants play a crucial role in establishing management plans for biodiversity conservation. Phoebe chekiangensis is precious and scarce tree species resource East China region. To comprehend origin, evolutionary history, geographical, historical factors that has contributed to current distribution pattern region, we conducted phylogeographic analysis utilized intergenic spacers chloroplast DNA (cpDNA). We amplified sequenced three spacer regions cpDNA (psbC-trnS, trnL-Intro, Ycf3) 306 individuals from 11 populations, encompassing majority its geographical range China. Our revealed total haplotypes. The research findings show genetic diversity was Hd = 0.423, nucleotide Pi × 10−3 0.400. At level, population differentiation index Fst 0.25610 (p < 0.05), gene flow Nm 0.73. variation between populations 29.14%, while within it 70.86%, with inter-population much lower than within-population variation. divergence time genera Machilus estimated be approximately 37.87 mya (PP 1; 95%HPD: 25.63–44.54 mya), crown group genus 21.30 9.76–34.94 mya). common ancestor haplotypes 7.85 mya, H7, H8, H10 (northern region) differentiated relatively late, 1.90 mya. Neutrality tests (NTs) mismatch (MDA) suggest frame expand southwestward along Wuyishan short adaptability environment low, thereby limiting formation new These results exhibited greater adaptation northern subtropics central subtropics, offering valuable insights utilization germplasm resources.

Language: Английский