Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences

Piece and parcel of gymnosperm organellar genomes

MAIN CONCLUSION

Significant past, present, and potential future research into the organellar (plastid and mitochondrial) genomes of gymnosperms that can provide insight into the unknown origin and evolution of plants is highlighted. Gymnosperms are vascular seed plants that predominated the ancient world before their sister clade, angiosperms, took over during the Late Cretaceous. The divergence of gymnosperms and angiosperms took place around 300 Mya, with the latter evolving into the diverse group of flowering plants that dominate the plant kingdom today. Although gymnosperms have reportedly made some evolutionary innovations, the literature on their genome advances, particularly their organellar (plastid and mitochondrial) genomes, is relatively scattered and fragmented. While organellar genomes can shed light on plant origin and evolution, they are frequently overlooked, due in part to their limited contribution to gene expression and lack of evolutionary dynamics when compared to nuclear genomes. A better understanding of gymnosperm organellar genomes is critical because they reveal genetic changes that have contributed to their unique adaptations and ecological success, potentially aiding in plant survival, enhancement, and biodiversity conservation in the face of climate change. This review reveals significant information and gaps in the existing knowledge base of organellar genomes in gymnosperms, as well as the challenges and research needed to unravel their complexity.

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

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

The complete chloroplast genome of Meconopsis bella Prain 1894 (Papaveraceae), a high-altitude plant distributed on the Qinghai-Tibet plateau

Meconopsis bella Prain 1894 (M. bella) is a rare herb within the family Papaveraceae of which unique and gorgeous purple flowers are blooming in the flowering phase. In this study, we reported the complete chloroplast (cp) genome of M. bella, which was mainly distributed on the Qinghai-Tibet plateau. The complete chloroplast genome sequence of M. bella was 153,073 bp in size and was characterized by a typical quadripartite structure consisting of a large single-copy (LSC) region of 83,562 bp, a small single-copy (SSC) region of 178,33 bp and two identical inverted repeats (IR) regions of 25,839 bp. The genome contained 133 genes, including 88 protein-encoding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis based on the maximum-likelihood (ML) method showed that M. bella was closely related to M. paniculate and M. pinnatifolia within the genus Meconopsis.