Project description:As an ancient jawless vertebrate species, the lamprey offers an important model to probe the evolutionary history of retinal cells. In this study, we generated a cell atlas of the adult sea lamprey retina using single-cell RNA sequencing
Project description:This project is designed to measure changes in gene expression during sea lamprey development and in the adult germline RNA was extracted in biological triplicate from sea lamprey embryos at 1, 2, 2.5, 3, 4, and 5 days post-fertilization and in technical replicates from adult testes using trizol extraction. RNA was analyzed on the Nanostring nCounter gene expression assay to measure changes in gene expression across developmental time points and in adult testes
Project description:This project is designed to measure changes in gene expression during sea lamprey development RNA was extracted from sea lamprey embryos at 1, 2, 2.5, 3, 4, and 5 days post-fertilization and used to generate RNAseq data
Project description:During early embryogenesis, the sea lamprey Petromyzon marinus undergoes a dynamic form of genome rearrangement whereby several specific chromosomes are selectively eliminated from somatic progenitor cells. These elimination events effectively silence all genes on these chromosomes in all somatic cells., and Pprevious studies in lamprey and other eliminating species have provided strong evidence that other epigenetic silencing marks (DNA and histone posttranslational modifications) are enriched in the germline-restricted chromosomes and contribute to micronucleus packaging during elimination. These silencing marks include the histone marks H3K9me3 and H4K20me3, which are respectively deposited by KMT1A/SUV39 and KMT5/SUV420 methyltransferases in . To test whether lamprey homologs of methyltransferases contribute to deposition of these marks on elimination micronuclei and whether these marks contribute to the highly coordinated process of DNA elimination in sea lamprey, we leveraged CRISPR/Cas9 gene editing and lightsheet imaging to investigate their potential roles during early development and during the progression of DNA elimination. Analysis of knockout embryos for four methyltransferases show that these KMT genes contribute to the deposition of repressive histone marks on micronuclei, but are not essential for programmed DNA elimination per se. Analyses of later embryogenic stages suggests that these marks may contribute to interim silencing of germline-specific chromosomes, and reveals major impacts on post-blastula survival and developmental patterning.
Project description:Strand-specific RNA-seq libraries from different sea lamprey tissues (brain, heart, liver, kidney, ovary, testis) were produced in order to enhance the genome annotation for protein coding genes.
Project description:The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.
Project description:The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.