Melin, A. D. — Page 2 | bioRxiv Science

bioRxiv2019

De novo transcriptome analysis of dermal tissue from the rough-skinned newt, Taricha granulosa, enables investigation of tetrodotoxin expression

BackgroundTetrodotoxin (TTX) is a potent neurotoxin used in anti-predator defense by several aquatic species, including the rough-skinned newt, Taricha granulosa. While several possible biological sources of newt TTX have been investigated, mounting evidence suggests a genetic, endogenous origin. We present here a de novo transcriptome assembly and annotation of dorsal skin samples from the tetrodotoxin-bearing species T. granulosa, to facilitate the study of putative genetic mechanisms of TTX expression.\n\nFindingsApproximately 211 million read pairs were assembled into 245,734 transcripts using the Trinity de novo assembly method. Of the assembled transcripts, we were able to annotate 34% by comparing them to databases of sequences with known functions, suggesting that many transcripts are unique to the rough-skinned newt. Our assembly has near-complete sequence information for an estimated 83% of genes based on Benchmarking Universal Single Copy Orthologs. We also utilized other comparative methods to assess the quality of our assembly. The T. granulosa assembly was compared with that of the Japanese fire-belly newt, Cynops pyrrhogaster, and they were found to share a total of 30,556 orthologous sequences (12.9% gene set).\n\nConclusionsWe provide a reference assembly for Taricha granulosa that will enable downstream differential expression and comparative transcriptomics analyses. This publicly available transcriptome assembly and annotation dataset will facilitate the investigation of a wide range of questions concerning amphibian adaptive radiation, and the elucidation of mechanisms of tetrodotoxin defense in Taricha granulosa and other TTX-bearing species.

genomics↗

bioRxiv2018

Unbiased whole genomes from mammalian feces using fluorescence-activated cell sorting

Ecological flexibility, extended lifespans, and large brains, have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have the largest relative brain size of any monkey and a lifespan that exceeds 50 years, despite their small (3-5 kg) body size. We assemble a de novo reference genome for Cebus imitator and provide the first genome annotation of a capuchin monkey. Through high-depth sequencing of DNA derived from blood, various tissues and feces via fluorescence activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of non-invasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides new insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity. SIGNIFICANCESurviving challenging environments, living long lives, and engaging in complex cognitive processes are hallmark characteristics of human evolution. Similar traits have evolved in parallel in capuchin monkeys, but their genetic underpinnings remain unexplored. We developed and annotated a reference assembly for white-faced capuchin monkeys to explore the evolution of these phenotypes. By comparing populations of capuchins inhabiting rainforest versus dry forests with seasonal droughts, we detected selection in genes associated with kidney function, muscular wasting, and metabolism, suggesting adaptation to periodic resource scarcity. When comparing capuchins to other mammals, we identified evidence of selection in multiple genes implicated in longevity and brain development. Our research was facilitated by our new method to generate high- and low-coverage genomes from non-invasive biomaterials.

genomics↗