Item talk:Q253895
From geokb
{
"USGS Publications Warehouse": { "@context": "https://schema.org", "@type": "Article", "additionalType": "Journal Article", "name": "A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands", "identifier": [ { "@type": "PropertyValue", "propertyID": "USGS Publications Warehouse IndexID", "value": "70232205", "url": "https://pubs.usgs.gov/publication/70232205" }, { "@type": "PropertyValue", "propertyID": "USGS Publications Warehouse Internal ID", "value": 70232205 }, { "@type": "PropertyValue", "propertyID": "DOI", "value": "10.1093/g3journal/jkac122", "url": "https://doi.org/10.1093/g3journal/jkac122" } ], "journal": { "@type": "Periodical", "name": "G3 Genes, Genomes, Genetics", "volumeNumber": "12", "issueNumber": "7" }, "inLanguage": "en", "isPartOf": [ { "@type": "CreativeWorkSeries", "name": "G3 Genes, Genomes, Genetics" } ], "datePublished": "2022", "dateModified": "2022-07-08", "abstract": "Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000\u2009km2\u00a0in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata\u00a0subsp.\u00a0tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome;\u00a0n\u2009=\u20099). The assembly contains an estimated 43,377 genes based on\u00a0ab initio\u00a0gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the\u00a0Artemisia tridentata\u00a0subsp.\u00a0tridentata\u00a0genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.", "description": "jkac122, 9 p.", "publisher": { "@type": "Organization", "name": "Oxford University Press" }, "author": [ { "@type": "Person", "name": "Germino, Matthew", "givenName": "Matthew", "familyName": "Germino", "identifier": { "@type": "PropertyValue", "propertyID": "ORCID", "value": "0000-0001-6326-7579", "url": "https://orcid.org/0000-0001-6326-7579" }, "affiliation": [ { "@type": "Organization", "name": "Forest and Rangeland Ecosystem Science Center", "url": "https://www.usgs.gov/centers/forest-and-rangeland-ecosystem-science-center" } ] }, { "@type": "Person", "name": "Melton, Anthony E.", "givenName": "Anthony E.", "familyName": "Melton", "affiliation": [ { "@type": "Organization", "name": "Boise State University" } ] }, { "@type": "Person", "name": "Child, Andrew W.", "givenName": "Andrew W.", "familyName": "Child", "affiliation": [ { "@type": "Organization", "name": "University of Idaho, Moscow ID" } ] }, { "@type": "Person", "name": "Beard, Richard S. Jr.", "givenName": "Richard S.", "familyName": "Beard", "affiliation": [ { "@type": "Organization", "name": "Boise State University" } ] }, { "@type": "Person", "name": "Dumaguit, Carlos Dave C.", "givenName": "Carlos Dave C.", "familyName": "Dumaguit", "affiliation": [ { "@type": "Organization", "name": "Boise State University" } ] }, { "@type": "Person", "name": "Self, Desiree", "givenName": "Desiree", "familyName": "Self", "affiliation": [ { "@type": "Organization", "name": "Boise State University" } ] }, { "@type": "Person", "name": "Serpe, Marcelo D.", "givenName": "Marcelo D.", "familyName": "Serpe", "affiliation": [ { "@type": "Organization", "name": "Boise State University" } ] }, { "@type": "Person", "name": "Buerki, Sven", "givenName": "Sven", "familyName": "Buerki", "affiliation": [ { "@type": "Organization", "name": "Boise State University" } ] }, { "@type": "Person", "name": "Kliskey, Andrew", "givenName": "Andrew", "familyName": "Kliskey" }, { "@type": "Person", "name": "Leitch, Ilia J.", "givenName": "Ilia J.", "familyName": "Leitch", "affiliation": [ { "@type": "Organization", "name": "Royal Botanic Gardens" } ] }, { "@type": "Person", "name": "Forbey, Jennifer S.", "givenName": "Jennifer S.", "familyName": "Forbey" }, { "@type": "Person", "name": "de Graaff, Marie-Anne", "givenName": "Marie-Anne", "familyName": "de Graaff" }, { "@type": "Person", "name": "Martinez, Peggy", "givenName": "Peggy", "familyName": "Martinez", "affiliation": [ { "@type": "Organization", "name": "Boise State University" } ] }, { "@type": "Person", "name": "Novak, Stephen J.", "givenName": "Stephen J.", "familyName": "Novak", "affiliation": [ { "@type": "Organization", "name": "Boise State University" } ] }, { "@type": "Person", "name": "Pellicer, Jaume", "givenName": "Jaume", "familyName": "Pellicer", "affiliation": [ { "@type": "Organization", "name": "Royal Botanic Gardens" } ] }, { "@type": "Person", "name": "Richardson, Bryce A.", "givenName": "Bryce A.", "familyName": "Richardson" } ], "funder": [ { "@type": "Organization", "name": "Forest and Rangeland Ecosystem Science Center", "url": "https://www.usgs.gov/centers/forest-and-rangeland-ecosystem-science-center" } ], "spatialCoverage": [ { "@type": "Place", "additionalType": "country", "name": "United States", "url": "https://geonames.org/4074035" }, { "@type": "Place", "additionalType": "state", "name": "Arizona" }, { "@type": "Place", "additionalType": "state", "name": "California" }, { "@type": "Place", "additionalType": "state", "name": "Colorado" }, { "@type": "Place", "additionalType": "state", "name": "Idaho" }, { "@type": "Place", "additionalType": "state", "name": "Montana" }, { "@type": "Place", "additionalType": "state", "name": "Nebraska" }, { "@type": "Place", "additionalType": "state", "name": "Nevada" }, { "@type": "Place", "additionalType": "state", "name": "New Mexico" }, { "@type": "Place", "additionalType": "state", "name": "North Dakota" }, { "@type": "Place", "additionalType": "state", "name": "Oregon" }, { "@type": "Place", "additionalType": "state", "name": "South Dakota" }, { "@type": "Place", "additionalType": "state", "name": "Utah" }, { "@type": "Place", "additionalType": "state", "name": "Washington" }, { "@type": "Place", "additionalType": "state", "name": "Wyoming" }, { "@type": "Place", "geo": [ { "@type": "GeoShape", "additionalProperty": { "@type": "PropertyValue", "name": "GeoJSON", "value": { "type": "FeatureCollection", "features": [ { "type": "Feature", "properties": {}, "geometry": { "type": "Polygon", "coordinates": [ [ [ -121.28906250000001, 35.817813158696616 ], [ -103.3154296875, 35.817813158696616 ], [ -103.3154296875, 48.980216985374994 ], [ -121.28906250000001, 48.980216985374994 ], [ -121.28906250000001, 35.817813158696616 ] ] ] } } ] } } }, { "@type": "GeoCoordinates", "latitude": 42.3990150720358, "longitude": -112.30224609374999 } ] } ] }, "OpenAlex": { "_id": "https://openalex.org/w4280616755", "abstract_inverted_index": { "Increased": [ 0 ], "ecological": [ 1 ], "disturbances,": [ 2 ], "species": [ 3, 16, 28 ], "invasions,": [ 4 ], "and": [ 5, 20, 29, 43, 76, 114, 167, 214, 226, 229 ], "climate": [ 6 ], "change": [ 7 ], "are": [ 8, 18, 38 ], "creating": [ 9 ], "severe": [ 10 ], "conservation": [ 11, 42 ], "problems": [ 12 ], "for": [ 13, 40, 51, 99, 234 ], "several": [ 14 ], "plant": [ 15, 209, 222 ], "that": [ 17 ], "widespread": [ 19 ], "foundational.": [ 21 ], "Understanding": [ 22 ], "the": [ 23, 60, 80, 85, 94, 126, 148, 172, 194, 197, 205 ], "genetic": [ 24 ], "diversity": [ 25 ], "of": [ 26, 82, 84, 104, 134, 147, 177, 193, 204 ], "these": [ 27, 36 ], "how": [ 30 ], "it": [ 31 ], "relates": [ 32 ], "to": [ 33, 35, 211, 224 ], "adaptation": [ 34, 223 ], "stressors": [ 37 ], "necessary": [ 39 ], "guiding": [ 41 ], "restoration": [ 44, 87 ], "efforts.": [ 45 ], "This": [ 46, 216 ], "need": [ 47 ], "is": [ 48 ], "particularly": [ 49 ], "acute": [ 50 ], "big": [ 52, 105 ], "sagebrush": [ 53, 106 ], "(Artemisia": [ 54 ], "tridentata;": [ 55 ], "Asteraceae),": [ 56 ], "which": [ 57 ], "was": [ 58, 185 ], "once": [ 59 ], "dominant": [ 61 ], "shrub": [ 62 ], "over": [ 63 ], "1,000,000": [ 64 ], "km2": [ 65 ], "in": [ 66 ], "western": [ 67 ], "North": [ 68 ], "America": [ 69 ], "but": [ 70 ], "has": [ 71, 78 ], "since": [ 72 ], "retracted": [ 73 ], "by": [ 74 ], "half": [ 75 ], "thus": [ 77 ], "become": [ 79 ], "target": [ 81 ], "one": [ 83, 203 ], "largest": [ 86 ], "seeding": [ 88 ], "efforts": [ 89 ], "globally.": [ 90 ], "Here,": [ 91 ], "we": [ 92 ], "present": [ 93 ], "first": [ 95 ], "reference-quality": [ 96 ], "genome": [ 97, 202, 217 ], "assembly": [ 98, 132, 155, 184, 218 ], "an": [ 100, 157 ], "ecologically": [ 101 ], "important": [ 102 ], "subspecies": [ 103 ], "(A.": [ 107 ], "tridentata": [ 108, 199, 201 ], "subsp.": [ 109, 200 ], "tridentata)": [ 110 ], "based": [ 111, 161 ], "on": [ 112, 162, 221 ], "short": [ 113 ], "long": [ 115 ], "reads,": [ 116 ], "as": [ 117, 119 ], "well": [ 118 ], "chromatin": [ 120 ], "proximity": [ 121 ], "ligation": [ 122 ], "data": [ 123, 169 ], "analyzed": [ 124, 170 ], "using": [ 125, 171 ], "HiRise": [ 127 ], "pipeline.": [ 128 ], "The": [ 129, 154, 182 ], "final": [ 130, 183 ], "4.2-Gb": [ 131 ], "consists": [ 133 ], "5,492": [ 135 ], "scaffolds,": [ 136 ], "with": [ 137, 175, 188 ], "nine": [ 138 ], "pseudo-chromosomal": [ 139 ], "scaffolds": [ 140, 142 ], "(nine": [ 141 ], "comprising": [ 143, 191 ], "at": [ 144 ], "least": [ 145 ], "90%": [ 146 ], "assembled": [ 149 ], "genome;": [ 150 ], "n": [ 151 ], "=": [ 152 ], "9).": [ 153 ], "contains": [ 156 ], "estimated": [ 158 ], "43,377": [ 159 ], "genes": [ 160 ], "ab": [ 163 ], "initio": [ 164 ], "gene": [ 165 ], "discovery": [ 166 ], "transcriptional": [ 168 ], "MAKER": [ 173 ], "pipeline,": [ 174 ], "91.37%": [ 176 ], "BUSCOs": [ 178 ], "being": [ 179 ], "completely": [ 180 ], "assembled.": [ 181, 215 ], "highly": [ 186, 207 ], "repetitive,": [ 187 ], "repeat": [ 189 ], "elements": [ 190 ], "77.99%": [ 192 ], "genome,": [ 195 ], "making": [ 196 ], "Artemisia": [ 198 ], "most": [ 206 ], "repetitive": [ 208 ], "genomes": [ 210 ], "be": [ 212 ], "sequenced": [ 213 ], "advances": [ 219 ], "studies": [ 220 ], "drought": [ 225 ], "heat": [ 227 ], "stress": [ 228 ], "provides": [ 230 ], "a": [ 231 ], "valuable": [ 232 ], "tool": [ 233 ], "future": [ 235 ], "genomic": [ 236 ], "research.": [ 237 ] }, "apc_list": { "value": 2400, "currency": "USD", "value_usd": 2400, "provenance": "doaj" }, "apc_paid": { "value": 2400, "currency": "USD", "value_usd": 2400, "provenance": "doaj" }, "authorships": [ { "author_position": "first", "author": { "id": "https://openalex.org/A5084009126", "display_name": "Anthony E. Melton", "orcid": "https://orcid.org/0000-0003-4882-6664" }, "institutions": [ { "id": "https://openalex.org/I120156002", "display_name": "Boise State University", "ror": "https://ror.org/02e3zdp86", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I120156002" ] } ], "countries": [ "US" ], "is_corresponding": true, "raw_author_name": "Anthony E Melton", "raw_affiliation_strings": [ "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA" ], "affiliations": [ { "raw_affiliation_string": "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA", "institution_ids": [ "https://openalex.org/I120156002" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5089636203", "display_name": "Andrew Wright Child", "orcid": "https://orcid.org/0000-0001-6666-0739" }, "institutions": [ { "id": "https://openalex.org/I155093810", "display_name": "University of Idaho", "ror": "https://ror.org/03hbp5t65", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I155093810" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Andrew W Child", "raw_affiliation_strings": [ "University of Idaho , Moscow, ID 83844, USA" ], "affiliations": [ { "raw_affiliation_string": "University of Idaho , Moscow, ID 83844, USA", "institution_ids": [ "https://openalex.org/I155093810" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5048206844", "display_name": "Richard S. Beard", "orcid": "https://orcid.org/0000-0001-8545-3014" }, "institutions": [ { "id": "https://openalex.org/I120156002", "display_name": "Boise State University", "ror": "https://ror.org/02e3zdp86", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I120156002" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Richard S Beard", "raw_affiliation_strings": [ "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA" ], "affiliations": [ { "raw_affiliation_string": "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA", "institution_ids": [ "https://openalex.org/I120156002" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5019741613", "display_name": "Carlos Dave C. Dumaguit", "orcid": "https://orcid.org/0000-0003-0411-7129" }, "institutions": [ { "id": "https://openalex.org/I120156002", "display_name": "Boise State University", "ror": "https://ror.org/02e3zdp86", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I120156002" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Carlos Dave C Dumaguit", "raw_affiliation_strings": [ "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA" ], "affiliations": [ { "raw_affiliation_string": "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA", "institution_ids": [ "https://openalex.org/I120156002" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5091003981", "display_name": "Jennifer S. Forbey", "orcid": "https://orcid.org/0000-0001-6069-4049" }, "institutions": [ { "id": "https://openalex.org/I120156002", "display_name": "Boise State University", "ror": "https://ror.org/02e3zdp86", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I120156002" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Jennifer S Forbey", "raw_affiliation_strings": [ "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA" ], "affiliations": [ { "raw_affiliation_string": "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA", "institution_ids": [ "https://openalex.org/I120156002" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5002624848", "display_name": "Matthew J. Germino", "orcid": "https://orcid.org/0000-0001-6326-7579" }, "institutions": [ { "id": "https://openalex.org/I1286329397", "display_name": "United States Geological Survey", "ror": "https://ror.org/035a68863", "country_code": "US", "type": "government", "lineage": [ "https://openalex.org/I1286329397", "https://openalex.org/I1335927249" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Matthew Germino", "raw_affiliation_strings": [ "Forest and Rangeland Ecosystem Science Center, United States Geological Survey , Boise, ID 83706, USA" ], "affiliations": [ { "raw_affiliation_string": "Forest and Rangeland Ecosystem Science Center, United States Geological Survey , Boise, ID 83706, USA", "institution_ids": [ "https://openalex.org/I1286329397" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5069220744", "display_name": "Marie\u2010Anne de Graaff", "orcid": "https://orcid.org/0000-0001-5668-7647" }, "institutions": [ { "id": "https://openalex.org/I120156002", "display_name": "Boise State University", "ror": "https://ror.org/02e3zdp86", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I120156002" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Marie-Anne de Graaff", "raw_affiliation_strings": [ "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA" ], "affiliations": [ { "raw_affiliation_string": "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA", "institution_ids": [ "https://openalex.org/I120156002" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5041297130", "display_name": "Andrew Kliskey", "orcid": "https://orcid.org/0000-0002-2146-2015" }, "institutions": [ { "id": "https://openalex.org/I155093810", "display_name": "University of Idaho", "ror": "https://ror.org/03hbp5t65", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I155093810" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Andrew Kliskey", "raw_affiliation_strings": [ "University of Idaho , Moscow, ID 83844, USA" ], "affiliations": [ { "raw_affiliation_string": "University of Idaho , Moscow, ID 83844, USA", "institution_ids": [ "https://openalex.org/I155093810" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5001350920", "display_name": "Ilia J. Leitch", "orcid": "https://orcid.org/0000-0002-3837-8186" }, "institutions": [ { "id": "https://openalex.org/I2799614521", "display_name": "Royal Botanic Gardens, Kew", "ror": "https://ror.org/00ynnr806", "country_code": "GB", "type": "archive", "lineage": [ "https://openalex.org/I2799614521" ] } ], "countries": [ "GB" ], "is_corresponding": false, "raw_author_name": "Ilia J Leitch", "raw_affiliation_strings": [ "Royal Botanic Gardens , Richmond TW9 3AE, UK" ], "affiliations": [ { "raw_affiliation_string": "Royal Botanic Gardens , Richmond TW9 3AE, UK", "institution_ids": [ "https://openalex.org/I2799614521" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5014817789", "display_name": "Peggy Martinez", "orcid": "https://orcid.org/0000-0001-5043-6839" }, "institutions": [ { "id": "https://openalex.org/I120156002", "display_name": "Boise State University", "ror": "https://ror.org/02e3zdp86", "country_code": "US", "type": "education", "lineage": [ "https://openalex.org/I120156002" ] } ], "countries": [ "US" ], "is_corresponding": false, "raw_author_name": "Peggy Martinez", "raw_affiliation_strings": [ "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA" ], "affiliations": [ { "raw_affiliation_string": "Department of Biological Sciences, Boise State University , Boise, ID 83725, USA", "institution_ids": [ "https://openalex.org/I120156002" ] } ] }, { "author_position": "middle", "author": { "id": "https://openalex.org/A5027929508", "display_name": "Stephen J. 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