Project description:Understanding the genomic toolkit that enabled animal terrestrialization, the shift from aquatic to terrestrial habitats, is key to uncovering the evolutionary origins of land biodiversity. Yet, the genomic basis of the physiological and metabolic adaptations required for life on land remains poorly understood across most terrestrial animal phyla. Planarians (Platyhelminthes) offer a powerful model, as only one terrestrial lineage, the Geoplanidae (order Tricladida), is known. Here, we integrated genomics, transcriptomics, and proteomics to explore the genetic changes potentially supporting terrestrial adaptation. We identified a major burst of gene gain in the lineage leading to Tricladida, preceding the radiation of terrestrial planarians. Upon abiotic stress exposure, terrestrial and freshwater species exhibited distinct responses: most differentially expressed genes belonged to orthogroups gained in Tricladida, with over half under strong directional selection in terrestrial flatworms, suggesting their adaptive relevance. Transcriptomic profiles revealed divergent strategies: terrestrial species upregulated ancient genes, while freshwater species downregulated a separate set of ancestral genes. Across all datasets, the abiotic stress response toolkit in terrestrial planarians was markedly different from freshwater relatives, with significant regulatory divergence. Our results highlight gene gain and co-option, rather than lineage-specific innovations, as key drivers of terrestrial flatworm evolution, emphasizing genomic exaptation and regulatory shifts as central to terrestrialization in Platyhelminthes. This study provides the first genome-wide view of the genetic basis of flatworm terrestrialization and sheds light on broader patterns of animal terrestrial adaptation.
Project description:Cytoplasmic male sterility (CMS) represents a crucial biological tool for the effective utilization of heterosis in plant breeding. Despite its importance, the molecular mechanisms underlying cytoplasmic male sterility in M. sativa have not yet been fully elucidated. In this study, the mitochondrial genomes of the cytoplasmic male-sterile line MS-JN1A and the maintainer line MS-JN1B of M. sativa were assembled and sequenced. Comparative analysis of the mitochondrial genomes revealed that the mitochondrial genome of the sterile line has undergone pronounced structural rearrangements. Moreover, the differentially expressed mitochondrial gene atp8, together with its associated open reading frames (ORFs), was identified as a key candidate underlying CMS. In the anthers of MS-JN1A, ATP levels and reactive oxygen species (ROS) accumulation were concomitantly elevated, indicating a disruption of mitochondrial energy-redox homeostasis. Further functional analyses demonstrated that anther-specific overexpression of atp8 directly induced premature programmed cell death (PCD) in the tapetum, accompanied by extensive transcriptional reprogramming of pathways associated with energy metabolism and ROS responses.. Collectively, our findings propose that atp8-mediated disruption of mitochondrial energy-ROS homeostasis represents a central molecular mechanism driving cytoplasmic male sterility in M. sativa, and they provide new insights into mitochondrial regulation of male fertility in plants.
Project description:We assembled de novo transcriptomes for three Antarctic invertebrate species: the limpet Nacella concinna (foot muscle tissue), the amphipod Paracerodocus miersii (body wall tissue) and the urchin Sterechinus neumayeri (coelomic fluid). Individuals (n = 5 per treatment) were sampled following exposure to different rates of warming: 1°C per hour, 1°C per day, 1°C per 3 days, or after acclimation to 2°C for 3 months. For longer term experiments (1°C per day, 1°C per 3 days and acclimation), control animals were sampled at both the start and end of the experiment to identify possible seasonal effects. For the shorter term experiment (1°C per hour) only one set of controls was needed.
Project description:The mitochondrial genome encodes 13 well-characterized mRNAs but, similar to the nuclear genome, it has the potential to encode many additional proteins through previously unannotated open reading frames. Using MitoRiboSeq, we detected dozens of new mitochondrial-derived microproteins in both cell lines and liver tissues. We demonstrate that MOTS-c, a previously described microprotein, shows a significant decrease during senescence induction, and its supplementation is sufficient to prevent key cellular dysfunctions associated with this process. This work significantly deepens our understanding of the mitochondrial genome and underscores its relevance for functional and therapeutic discoveries.
Project description:We introduce FACIL (http://www.cmbi.ru.nl/FACIL), a fast, reliable tool to evaluate nucleic acid sequences for non-standard codes that detects alternative genetic codes even in species distantly related to known organisms. Results are visualized in a Genetic Code Logo. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens. These are particularly challenging data, as the genome is highly fragmented and incomplete. Approximately 10,000 single-cell Globobulimina pseudospinescens organisms were isolated by hand from Gullmar Fjord Sweden sediment. After washing, total DNA was extracted and sequenced by Illumina sequencing. The reads were assembled using Edena. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens, an organism without any sequenced relatives in the databases. These are particularly challenging data, as the genome is highly fragmented and incomplete. DNA isolated from approximately 10,000 single-cell Globobulimina pseudospinescens organisms
Project description:The proper replication of mitochondrial DNA is key to the maintenance of this crucial organelle. Multiple studies aimed at understanding the mechanisms of replication of the mitochondrial genome have been conducted in the past several decades; however, while highly informative, they were conducted using relatively low-sensitivity techniques. Here, we established a high-throughput approach based on next-generation sequencing to identify replication start sites with nucleotide-level resolution and applied it to the genome of mitochondria from different human and mouse cell types. We found complex and highly reproducible patterns of mitochondrial initiation sites, both previously annotated and newly discovered in this work, that showed differences among different cell types and species. These results suggest that the patterns of the replication initiation sites are dynamic and might reflect, in some yet unknown ways, the complexities of mitochondrial and cellular physiology. Overall, this work suggests that much remains unknown about the details of mitochondrial DNA replication in different biological states, and the method established here opens up a new avenue in the study of the replication of mitochondrial and potentially other genomes.
2023-06-14 | GSE220621 | GEO
Project description:Microbiomes of geminate gastropods