Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Abstract Background Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. Results In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. Conclusions The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity

Additional file 2: of Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Table S1. Features of the mitogenomes of three Lycodon species. (DOCX 22 kb

Additional file 4: of Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Figure S3. Homology analysis of OL. The sequences of OL of Alethinophidians and four saurians are aligned. (PDF 574 kb

Additional file 3: of Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Figure S2. Bayesian phylogenetic inference tree based on the combined data set of RNA genes and Protein-coding genes. The numbers above the branches indicate the posterior probability. (PDF 256 kb

Additional file 7: of Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Table S4. Best-fit models and partitioning schemes selected by PartitionFinder for the dataset analyzed. (DOCX 22 kb

Additional file 6: of Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Table S3. Primers sequences used in this study. (DOC 66 kb

Additional file 1: of Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Figure S1. Gene organization of control regions and WANCY cluster in snake mitochondrial genomes. Circular mitogenomes are linearly depicted as an open bar divided into individual genes. Only relevant genes are shown, and in a way that does not reflect actual gene lengths. B, C, D, E came from Kumazawa et al. [16]; A, F from Yan et al. [18]; G from Chen and Zhao [19]. The H- and L- strand encoded genes are denoted above and below each gene box. Transfer RNAs are indicated by their single-letter abbreviations. Abbreviations: 12S, 16S, and P* stand for 12S rRNA, 16S rRNA, and a pseudogene for tRNAPro gene, respectively. Taxa for which have been reported to date are listed in Additional file 5: Table S2. (PDF 612 kb

Additional file 5: of Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Table S2. List of taxa used in this study. *: the species were used in Yan et al. [18]. #: the species were used in Chen and Zhao. [19]. (DOC 132 kb

Put Your Backbone into It: Excited-State Structural Relaxation of PffBT4T-2DT Conducting Polymer in Solution

Conformational and energetic disorder in organic semiconductors reduces charge and exciton transport because of the structural defects, thus reducing the efficiency in devices such as organic photovoltaics and organic light-emitting diodes. The main structural heterogeneity is because of the twisting of the polymer backbone that occurs even in polymers that are mostly crystalline. Here, we explore the relationship between polymer backbone twisting and exciton delocalization by means of transient absorption spectroscopy and density functional theory calculations. We study the PffBT4T-2DT polymer which has exhibited even higher device efficiency with nonfullerene acceptors than the current record breaking PCE11 polymer. We determine the driving force for planarization of a polymer chain caused by excitation. The methodology is generally applicable and demonstrates a higher penalty for nonplanar structures in the excited state than in the ground state. This study highlights the morphological and electronic changes in conjugated polymers that are brought about by excitation