USAP-DC

{"dp_type": "Project", "free_text": "genome assembly"}

[{"awards": "1645087 Catchen, Julian", "bounds_geometry": null, "dataset_titles": "Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus\u2014The Closest Ancestral Proxy of Antarctic Cryonotothenioids; Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki; Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish", "datasets": [{"dataset_uid": "200380", "doi": "", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA857989"}, {"dataset_uid": "200330", "doi": "", "keywords": null, "people": null, "repository": "NCBI ", "science_program": null, "title": "Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA861284"}, {"dataset_uid": "200381", "doi": "", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus\u2014The Closest Ancestral Proxy of Antarctic Cryonotothenioids", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA917608"}, {"dataset_uid": "200331", "doi": "10.5061/dryad.ghx3ffbs3", "keywords": null, "people": null, "repository": "Dryad", "science_program": null, "title": "Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki", "url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.ghx3ffbs3"}], "date_created": "Mon, 10 Oct 2022 00:00:00 GMT", "description": "As plate tectonics pushed Antarctica into a polar position, by ~34 million years ago, the continent and its surrounding Southern Ocean (SO) became geographically and thermally isolated by the Antarctic Circumpolar Current. Terrestrial and marine glaciation followed, resulting in extinctions as well as the survival and radiation of unique flora and fauna. The notothenioid fish survived and arose from a common ancestral stock into tax with 120 species that dominates today\u0027s SO fish fauna. The Notothenioids evolved adaptive traits including novel antifreeze proteins for survival in extreme cold, but also suffered seemingly adverse trait loss including red blood cells in the icefish family, and the ability to mount cellular responses to mitigate heat stress ? otherwise ubiquitous across all life. This project aims to understand how the notothenoid genomes have changed and contributed to their evolution in the cold. The project will sequence, analyze and compare the genomes of two strategic pairs of notothenioid fishes representing both red-blooded and white-blooded species. Each pair will consist of one Antarctic species and one that has readapted to the temperate waters of S. America or New Zealand. The project will also compare the Antarctic species genomes to a genome of the closet non-Antarctic relative representing the temperate notothenioid ancestor. The work aims to uncover the mechanisms that enabled the adaptive evolution of this ecologically vital group of fish in the freezing Southern Ocean, and shed light on their adaptability to a warming world. The finished genomes will be made available to promote and advance Antarctic research and the project will host a symposium of Polar researchers to discuss the cutting edge developments regarding of genomic adaptations in the polar region.\u003cbr/\u003eDespite subzero, icy conditions that are perilous to teleost fish, the fish fauna of the isolated Southern Ocean (SO) surrounding Antarctica is remarkably bountiful. A single teleost group - the notothenioid fishes - dominate the fauna, comprising over 120 species that arose from a common ancestor. When Antarctica became isolated and SO temperatures began to plunge in early Oligocene, the prior temperate fishes became extinct. The ancestor of Antarctic notothenioids overcame forbidding polar conditions and, absent niche competition, it diversified and filled the SO. How did notothenioids adapt to freezing environmental selection pressures and achieve such extraordinary success? And having specialized to life in chronic cold for 30 myr, can they evolve in pace with today\u0027s warming climate to stay viable? Past studies of Antarctic notothenioid evolutionary adaptation have discovered various remarkable traits including the key, life-saving antifreeze proteins. But life specialized to cold also led to paradoxical trait changes such as the loss of the otherwise universal heat shock response, and of the O2-transporting hemoglobin and red blood cells in the icefish family. A few species interestingly regained abilities to live in temperate waters following the escape of their ancestor out of the freezing SO. \u003cbr/\u003eThis proposed project is the first major effort to advance the field from single trait studies to understanding the full spectrum of genomic and genetic responses to climatic and environmental change during notothenioid evolution, and to evaluate their adaptability to continuing climate change. To this end, the project will sequence the genomes of four key species that embody genomic responses to different thermal selection regimes during notothenioids\u0027 evolutionary history, and by comparative analyses of genomic structure, architecture and content, deduce the responding changes. Specifically, the project will (i) obtain whole genome assemblies of the red-blooded T. borchgrevinki and the S. American icefish C. esox; (ii) using the finished genomes from (i) as template, obtain assemblies of the New Zealand notothenioid N. angustata, and the white-blooded icefish C. gunnari, representing a long (11 myr) and recent (1 myr) secondarily temperate evolutionary history respectively. Genes that are under selection in the temperate environment but not in the Antarctic environment can be inferred to be directly necessary for that environment and the reverse is also true for genes under selection in the Antarctic but not in the temperate environment. Further, genes important for survival in temperate waters will show parallel selection between N. angustata and C. esox despite the fact that the two fish left the Antarctic at far separated time points. Finally, gene families that expanded due to strong selection within the cold Antarctic should show a degradation of duplicates in the temperate environment. The project will test these hypotheses using a number of techniques to compare the content and form of genes, the structure of the chromosomes containing those genes, and through the identification of key characters, such as selfish genetic elements, introns, and structural variants.", "east": null, "geometry": null, "instruments": null, "is_usap_dc": true, "keywords": "Mcmurdo Sound; Genome Assembly; FISH; Icefish; SHIPS; Notothenioid; Puerto Natales, Chile", "locations": "Mcmurdo Sound; Puerto Natales, Chile", "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Catchen, Julian; Cheng, Chi-Hing", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e SHIPS", "repo": "NCBI", "repositories": "Dryad; NCBI; NCBI ", "science_programs": null, "south": null, "title": "Evolutionary Genomic Responses in Antarctic Notothenioid Fishes", "uid": "p0010384", "west": null}, {"awards": "1643825 Bucklin, Ann", "bounds_geometry": "POLYGON((-74.57 -60.9,-72.487 -60.9,-70.404 -60.9,-68.321 -60.9,-66.238 -60.9,-64.155 -60.9,-62.072 -60.9,-59.989 -60.9,-57.906 -60.9,-55.823 -60.9,-53.74 -60.9,-53.74 -61.537,-53.74 -62.174,-53.74 -62.811,-53.74 -63.448,-53.74 -64.085,-53.74 -64.722,-53.74 -65.359,-53.74 -65.996,-53.74 -66.633,-53.74 -67.27,-55.823 -67.27,-57.906 -67.27,-59.989 -67.27,-62.072 -67.27,-64.155 -67.27,-66.238 -67.27,-68.321 -67.27,-70.404 -67.27,-72.487 -67.27,-74.57 -67.27,-74.57 -66.633,-74.57 -65.996,-74.57 -65.359,-74.57 -64.722,-74.57 -64.085,-74.57 -63.448,-74.57 -62.811,-74.57 -62.174,-74.57 -61.537,-74.57 -60.9))", "dataset_titles": "Alongtrack data collected continuously by the ship\u0027s underway acquisition system from ARSV Laurence M. Gould cruise LMG1110 in the Southern Ocean in 2011 ; Bucklin, A., R.J. O\u0027Neill, D. Payne (2018) Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean. Biological and Chemical Oceanography Data Management Office (BCO-DMO). ; Bucklin, A., R.J. O\u0027Neill, D. Payne (2018) Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2. Biological and Chemical Oceanography Data Management Office (BCO-DMO).; CTD data from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project) ; CTD data from MOCNESS tows taken in the Antarctic in 2011 from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project) ; Scientific sampling event log from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from Nov. 2011 (Salp_Antarctic project) ", "datasets": [{"dataset_uid": "200227", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Bucklin, A., R.J. O\u0027Neill, D. Payne (2018) Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2. Biological and Chemical Oceanography Data Management Office (BCO-DMO).", "url": "https://www.bco-dmo.org/dataset/672600"}, {"dataset_uid": "200230", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Scientific sampling event log from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from Nov. 2011 (Salp_Antarctic project) ", "url": "https://www.bco-dmo.org/dataset/3565/data"}, {"dataset_uid": "200228", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Bucklin, A., R.J. O\u0027Neill, D. Payne (2018) Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean. Biological and Chemical Oceanography Data Management Office (BCO-DMO). ", "url": "https://www.bco-dmo.org/dataset/675040/data"}, {"dataset_uid": "200231", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Alongtrack data collected continuously by the ship\u0027s underway acquisition system from ARSV Laurence M. Gould cruise LMG1110 in the Southern Ocean in 2011 ", "url": "https://www.bco-dmo.org/dataset/3636/data"}, {"dataset_uid": "200232", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "CTD data from MOCNESS tows taken in the Antarctic in 2011 from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project) ", "url": "https://www.bco-dmo.org/dataset/488871/data"}, {"dataset_uid": "200229", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "CTD data from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project) ", "url": "https://www.bco-dmo.org/dataset/559174/data"}], "date_created": "Sat, 03 Jul 2021 00:00:00 GMT", "description": "The Antarctic salp, Salpa thompsoni, is an increasingly important player in the vulnerable Southern Ocean pelagic ecosystem. Field studies have documented rapid population growth under favorable environmental conditions, resulting in dense blooms of salps that can out-compete and displace other species, and significantly perturb the pelagic ecosystem. A comprehensive reference genome for the Antarctic salp will enable the identification of genes and gene networks underlying physiological responses and allow detection of natural selection driving the species\u2019 adaptation to climate change. The primary hypothesis driving this research is that predicted S. thompsoni orthologs (i.e., genes of the same function that share a common ancestor) that show evidence of rapid evolution are indicative of positive selection, and further that these genes and associated gene networks provide the basis for rapid adaptation of the Antarctic salp to environmental variation associated with climate change. Our genome assembly strategy builds upon methods developed during our previous award (PLR-1044982), including both paired-end short read and linked-read sequencing approaches. This project used state-of-the-art approaches: Oxford Nanopore long read sequencing, de novo assembly, and comprehensive transcriptomics. The results include a new reference genome for S. thompsoni, consisting of 8,815 sequences (contigs), with less fragmentation (N50 = 188 kb), and genome coverage of 78%. We have discovered strong secondary structures that dramatically affect sequencing efficiency. Our analyses of these secondary structures led to the discovery of abundant G-quadruplex sequences distributed throughout the genome at a significantly higher frequency compared to other tunicate species, suggesting the structures are a defining feature of this salp genome. These results provide novel insights into the function of unique genomic features in the regulation of genome stability, despite the complex life history, including sexual and asexual reproduction of the Southern Ocean salp. The completed salp reference genome will provide a valuable foundational resource for other scientists (including ecologists, oceanographers, and climate change experts), working on this species. ", "east": -53.74, "geometry": "POINT(-64.155 -64.085)", "instruments": null, "is_usap_dc": true, "keywords": "SHIPS; PELAGIC; Southern Ocean", "locations": "Southern Ocean", "north": -60.9, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Bucklin, Ann; O\u0027Neill, Rachel J", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e SHIPS", "repo": "BCO-DMO", "repositories": "BCO-DMO", "science_programs": null, "south": -67.27, "title": "Genome Assembly and Analysis of the Bloom Forming Southern Ocean Salp, Salpa thompsoni", "uid": "p0010224", "west": -74.57}, {"awards": "1443554 Buys, Emmanuel", "bounds_geometry": "POLYGON((166.163 -76.665,166.2635 -76.665,166.364 -76.665,166.4645 -76.665,166.565 -76.665,166.6655 -76.665,166.766 -76.665,166.8665 -76.665,166.967 -76.665,167.0675 -76.665,167.168 -76.665,167.168 -76.782,167.168 -76.899,167.168 -77.016,167.168 -77.133,167.168 -77.25,167.168 -77.367,167.168 -77.484,167.168 -77.601,167.168 -77.718,167.168 -77.835,167.0675 -77.835,166.967 -77.835,166.8665 -77.835,166.766 -77.835,166.6655 -77.835,166.565 -77.835,166.4645 -77.835,166.364 -77.835,166.2635 -77.835,166.163 -77.835,166.163 -77.718,166.163 -77.601,166.163 -77.484,166.163 -77.367,166.163 -77.25,166.163 -77.133,166.163 -77.016,166.163 -76.899,166.163 -76.782,166.163 -76.665))", "dataset_titles": "Biosamples and observations from Weddell Seal colonies in McMurdo Sound during the 2015-2016 Antarctic field season", "datasets": [{"dataset_uid": "601028", "doi": "10.15784/601028", "keywords": "Antarctica; Biota; Mcmurdo Sound; Ross Sea; Sample/collection Description; Sample/Collection Description; Seals", "people": "Hindle, Allyson; Buys, Emmanuel", "repository": "USAP-DC", "science_program": null, "title": "Biosamples and observations from Weddell Seal colonies in McMurdo Sound during the 2015-2016 Antarctic field season", "url": "https://www.usap-dc.org/view/dataset/601028"}], "date_created": "Fri, 26 May 2017 00:00:00 GMT", "description": "The Weddell seal is a champion diving mammal. The physiology that permits these animals to sustain extended breath-hold periods and survive the extreme pressure of diving deep allows them to thrive in icy Antarctic waters. Key elements of their physiological specializations to breath-hold diving are their ability for remarkable adjustment of their heart and blood vessel system, coordinating blood pressure and flow to specific body regions based on their metabolic requirements, and their ability to sustain periods without oxygen. Identifying the details of these strategies has tremendous potential to better inform human medicine, helping us to develop novel therapies for cardiovascular trauma (e.g. stroke, heart attack) and diseases associated with blunted oxygen delivery to tissues (e.g. pneumonia, sepsis, or cancer). The goal of this project is to document specific genes that control these cardiovascular adjustments in seals, and to compare their abundance and activity with humans. Specifically, the investigators will study a signaling pathway that coordinates local blood flow. They will also use tissue samples to generate cultured cells from Weddell seals that can be used to study the molecular effects of low oxygen conditions in the laboratory. The project will further the NSF goals of training new generations of scientists and of making scientific discoveries available to the general public. The project will train a pre-veterinary student researcher will conduct public outreach via a center for community health improvement, a multicultural affairs office, and a public aquarium. The goal of this study is to unravel the molecular mechanisms underlying the dive response. A hallmark of the dive response is tissue-specific vascular system regulation, likely resulting from variation in both nerve inputs and in production of local signaling molecules produced by blood vessel cells. The investigators will use emerging genomic information to begin to unravel the genetics underlying redistribution of the circulation during diving. They will also directly test the hypothesis that modifications in the signaling system prevent local blood vessel changes under low oxygen conditions, thereby allowing the centrally mediated diving reflex to override local physiological responses and to control the constriction of blood vessel walls in Weddell seals. They will perform RNA-sequencing of Weddell seal tissues and use the resulting sequence, along with information from other mammals such as dog, to obtain a full annotation (identifying all genes based on named features of reference genomes) of the existing genome assembly for the Weddell seal, facilitating comparative and species-specific genomic research. They will also generate a Weddell seal pluripotent stem cell line which should be a valuable research tool for cell biologists, molecular biologists and physiologists that will allow them to further test their hypotheses. It is expected that the proposed studies will advance our knowledge of the biochemical and physiological adaptations that allow the Weddell seal to thrive in the Antarctic environment.", "east": 167.168, "geometry": "POINT(166.6655 -77.25)", "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": -76.665, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Buys, Emmanuel; Costa, Daniel; Zapol, Warren; Hindle, Allyson", "platforms": "Not provided", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -77.835, "title": "Unraveling the Genomic and Molecular Basis of the Dive Response: Nitric Oxide Signaling and Vasoregulation in the Weddell Seal", "uid": "p0000072", "west": 166.163}]

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