Background: Sedum, with the largest number of species in the family Crassulaceae, is a taxonomically complex genus and an important group of horticultural plants within this family. Despite extensive historical research using diverse datasets, the branching patterns within this genus and the family remain debatable. Methods: In this study, we conducted sequencing and comparative analyses of plastomes from eight Sedum species, focusing on the diversities in nucleotide, microsatellite repeats, putative RNA editing, and gene content at IR junctions. The phylogenetic inferences were further conducted at the order level—Saxifragales. Results: Our IR junction analyses of the eight investigated Sedum species detected a unique 110 bp IR extension into rps19, a feature highly conserved across Crassulaceae species, indicating a remarkably family-specific pattern. Additionally, we obtained 79 PCGs from 148 Saxifragales species and constructed a phylogenetic tree using a larger set of plastomes than in previous studies. Our results confirm the polyphyly of Sedum and reveal that S. emarginatum is more closely related to S. makinoi than to S. alfredii, which is sister to S. plumbizincicola. Furthermore, we also performed analyses of codon usage, putative RNA editing sites, and microsatellite repeats. Conclusions: These findings and the generated sequence data will enrich plastid resources and improve understanding of the evolution of Sedum, Crassulaceae, and Saxifragales.

Mitochondrial codon usage and selective pressures drive adaptive evolution and translation efficiency. This study provides insights into the evolutionary constraints shaping 13 core mitochondrial proteins in Corvides, based on 117 species, including 51 newly assembled genomes. We present evidence linking codon-level sequence architecture, protein structure, and selective pressures. These protein-coding genes (PCGs) are under strong purifying selection, with dN/dS ratios ranging from 0.00779 (MT-CO1) to 0.16214 (MT-ATP8). This conservation is reflected in the 3D model of MT-CO1, where conserved residues cluster within 12 transmembrane helices forming the core of its proton-pumping function. At the sequence level, we identify signatures of selection for translational efficiency, which are critical for accurate synthesis and folding. These signatures include a significant preference for “optimal” codons that perfectly match tRNA anticodons (p < 0.001). We also find lineage-specific features such as codon aversion motifs (CAMs). The MT-ATP6 gene exhibits complete aversion of the CGA codon in Oriolus chinensis and of the ACT codon in O. kundoo. These sequence-level features resolve the deep phylogenetic relationships within the group, demonstrating the effectiveness of our multi-layered analytical framework. Overall, our results link codon-level sequence architecture with protein structural constraints, functional evolutionary signals, and mitochondrial genome evolution in Corvides.

Bioinformatics is an interdisciplinary field that combines biology with computational and mathematical sciences. In this course, phylogenetics is an important section, which focuses on evolutionary relationships of organisms on earth using computational methods. Furthermore, "Curriculum Ideological and Political Education" (CIPE) is an educational strategy that aims to integrate ideological and political elements into all subjects. In this study, we present our pedagogical framework for integrating CIPE into the teaching of phylogenetics. The three core components of this course are Evolutionary Theory, Computational Methods, and Practical Applications. These components support the development of three CIPE principles: Scientific Integrity, Critical Thinking, and Social Responsibility. We apply this pedagogical framework in practice through a case study approach, with examples covering biodiversity conservation, public health, and food security.

The order Testudines, one of the oldest monophyletic vertebrate lineages, offers an excellent opportunity to investigate mitogenome evolution and deep phylogenetic inference. However, comparative analyses across the order remain limited. To address this gap, we conducted a large-scale comparative mitogenomic analysis of 170 turtle species across 14 families, including 26 newly assembled mitogenomes. Using 13 protein-coding genes (PCGs) and 22 mitochondrial tRNAs, we characterized codon usage patterns, codon aversion motifs (CAMs), and tRNA secondary structures. Our analysis revealed a strong AT bias and significant inter-familial variation in codon usage bias. Multiple lines of evidence consistently indicated that natural selection was the primary force shaping codon usage patterns. We also identified species-specific CAMs and genus-associated tRNA secondary structure features as potential molecular indicators for evolutionary patterns and structural diversity. Phylogenetic analyses using Maximum Likelihood (ML) and Bayesian Inference (BI) recovered the two major suborders and provided insights into historically debated deep-node relationships, including the placement of Chelydridae and generic boundaries within Chelidae. Overall, this study provides a comprehensive perspective on mitogenome evolution in turtles and highlights the potential of codon aversion patterns and tRNA structural diversity as informative molecular evidence for comparative evolutionary genomics and mitochondrial diversity in Testudines.