cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20514693.v1
title: Dicom data, MRI Alpine dingo and domestic dog brain

description: Data associated with manuscript: <strong>The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology</strong> <br> Raw Dicom data, Alpine Dingo brain (zip) and domestic dog brain (zip). Brains were scanned using high-resolution magnetic resonance imaging (MRI). A Bruker Biospec 94/20 9.4T high field pre-clinical MRI system located at the Biological Resources imaging Laboratory University of New South Wales (UNSW) was used to acquire MRI data of a fixed dingo and domestic dog brain. The system was equipped with microimaging gradients with a maximum gradient strength of 660mT/m and a 72mm Quadrature volume coil. Images were acquired in transverse and coronal orientation using optimized 2D and 3D Fast Spin Echo (FSE) and Gradient Echo (MGE) methods. Image resolution was 200x200x500 and 300x300 microns isotropic for type 3D and 2D pulse sequences, respectively.
DOI: 10.6084/m9.figshare.20523804.v1
title: Cooinda Alpine Dingo 3D Cranial Landmarks

description: 3D geometric morphometric landmark configuration for Cooinda the Alpine Dingo's cranium, following the 45-landmark system outlined by Koungoulos (2020) ( https://doi.org/10.1007/s00435-019-00475-z). Exported from Stratovan Checkpoint.
DOI: 10.5524/102133
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1070

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001847. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1349100000bp. We have generated 74980000000bp of data, which gives a theoretical coverage of 55.6x.
DOI: 10.5524/102134
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1071

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001849. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 2734970000bp. We have generated 64260000000bp of data, which gives a theoretical coverage of 23.5x.
DOI: 10.5524/102136
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1073

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001851. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 2533260000bp. We have generated 69100000000bp of data, which gives a theoretical coverage of 27.3x.
DOI: 10.5524/102142
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1079

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001857. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 5733010000bp. We have generated 66440000000bp of data, which gives a theoretical coverage of 11.6x.
DOI: 10.5524/102168
title: Genomic data from Erect-crested penguin (<em>Eudyptes sclateri</em>).

description: The Erect-crested penguin is endemic only to the New Zealand Antipodes Islands and Bounty Islands. It is a crested penguin closely related to the extinct Chatham Island crested penguin, and is named after its upright yellow crests. The Erect-crested penguin breeds in large colonies on rocky terrain. Little is known about its biology and breeding habits. Populations have recently declined and the International Union for Conservation of Nature (IUCN) classifies it as endangered. The Erect-crested penguin is a Taonga, or treasured possession in Mori culture.<br>We sequenced the genome of an adult Erect-crested penguin from Antipodes Island, New Zealand sub-Antarctic (provided by Chris Rickard/Sarah Fraser) to a depth of approximately 131x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.25Gb, with the contig and scaffold N50 values of 67.93Kb and 1.83Mb respectively. We identified 15786 protein-coding genes.
DOI: 10.5524/102171
title: Genomic data from Northern rockhopper penguin (<em>Eudyptes moseleyi</em>).

description: The Northern rockhopper penguin (also known as Moseley's rockhopper penguin or Moseley's penguin) is a small crested penguin closely related to the Eastern and Western rockhopper penguins. The Northern rockhopper penguin breeds on Amsterdam and Gough islands. They breed in colonies at sea level, on cliff sides and sometimes inland. Populations of the Northern rockhopper penguin have declined drastically, and the International Union for Conservation of Nature (IUCN) classifies them as endangered.<br>We sequenced the genome of an adult Northern rockhopper penguin from Amsterdam Island, Southern Indian Ocean (provided by Yves Cherel) to a depth of approximately 139x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.23Gb, with the contig and scaffold N50 values of 20.86Kb and 2.14Mb respectively. We identified 16812 protein-coding genes.
DOI: 10.5524/102177
title: Genomic data from White-flippered penguin (<em>Eudyptula minor albosignata</em>).

description: The White-flippered penguin is a small penguin closely related to the New Zealand little blue penguin. It is occasionally considered a unique species or sometimes a subspecies of the New Zealand little blue penguin, however genetic research indicates that the two taxa are probably incipient. The reason it is occasionally considered a separate species or subspecies is because it has white markings on its flippers. Most taxonomists consider it to be a colour morph of the New Zealand little blue penguin. It nests in headlands, caves, rock jumbles and in the sheltered areas at the bases of bays, only on Banks Peninsula and Motunau Island near Christchurch, New Zealand. The white-flippered penguin is a Taonga, or treasured possession in Mori culture. The International Union for Conservation of Nature (IUCN) considers all Eudyptula penguins as least concern.<br>We sequenced the genome of an adult White-flippered penguin from Christchurch Antarctic Centre, originally from Banks Peninsula, Canterbury, New Zealand South Island (provided by Pauline Howard) to a depth of approximately 100x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.3Gb, with the contig and scaffold N50 values of 93.53Kb and 20.85Mb respectively. We identified 17424 protein-coding genes.
DOI: 10.5524/102181
title: Genomic data from Chinstrap penguin (<em>Pygoscelis antarctica</em>).

description: The Chinstrap penguin inhabits a variety of islands and shores in the Southern Pacific and the Antarctic Oceans. It has a narrow black band under its head. They breed in Antarctica, Argentina, Bouvet Island, Chile, the Falkland Islands, the French Southern Territories, and South Georgia and the South Sandwich Islands. Populations of Chinstrap penguin are considered to be decreasing overall, however in many sites the populations are increasing or stable. They are considered as Least Concern by the International Union for Conservation of Nature (IUCN).<br>We sequenced the genome of an adult Chinstrap penguin from Thule Island, South Sandwich Islands (provided by Tom Hart) to a depth of approximately 125x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.24Gb, with the contig and scaffold N50 values of 115.56Kb and 5.89Mb respectively. We identified 15488 protein-coding genes.
DOI: 10.5524/102337
title: Supporting data for "Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals <i>Porites lutea</i> and <i>Isopora palifera</i>"

description: At present our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed towards the millimetre-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals <i>Porites lutea</i> and <i>Isopora palifera</i>, through a compendium of ~400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 microbial classes. Skeletal microbiomes harboured a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (<i>dsyB</i>) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22±15 genes in <i>P. lutea</i> and 28±23 in <i>I. palifera</i> with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulphate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
DOI: 10.5524/102138
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1075

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001854. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 2642270000bp. We have generated 76340000000bp of data, which gives a theoretical coverage of 28.9x.
DOI: 10.5524/102139
title: Genomic data of Nanmaohu Park Cyperaceae plant specimen, RL1076

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001855. Preliminary identification is that it is of the family Cyperaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 4805250000bp. We have generated 68040000000bp of data, which gives a theoretical coverage of 14.2x.
DOI: 10.5524/102141
title: Genomic data of Nanmaohu Park Polygonaceae plant specimen, RL1078

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00002357. Preliminary identification is that it is of the family Polygonaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 4019060000bp. We have generated 68660000000bp of data, which gives a theoretical coverage of 17.1x.
DOI: 10.5524/102143
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1080

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001858. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 2842680000bp. We have generated 55920000000bp of data, which gives a theoretical coverage of 19.7x.
DOI: 10.5524/102166
title: Genomic data from Fiordland-crested penguin (<em>Eudyptes pachyrhynchus</em>).

description: The Fiordland crested penguin (also known as Fiordland penguin, and in Mori it is known as Tawaki) is endemic only to the south-western coasts of New Zealand's South Island as well as on Stewart Island/Rakiura and nearby islands. It is a crested penguin closely related to the Snares crested penguin. Historically, Fiordland crested and Snares crested penguins were considered incipient - however can be distinguished from the Snares crested penguin by having no bare skin around the base of its bill. The Fiordland crested penguin breeds among tree roots and rocks in dense temperate coastal forest, laying a clutch of two eggs where the first-laid egg is much smaller than the second egg, and generally hatches later, with higher mortality. This breeding system demonstrates a brood reduction system that is unique from other avian groups. The Fiordland crested penguin was probably more widely distributed before human arrival to New Zealand ~750 years ago. The International Union for Conservation of Nature (IUCN) classifies the Fiordland crested penguin as vulnerable, and the New Zealand Department of Conservation classifies them as endangered. The Fiordland crested penguin is a Taonga, or treasured possession in Mori culture.<br>We sequenced the genome of an adult Fiordland-crested penguin from Harrison Cove, Milford Sound, New Zealand South Island (provided by Thomas Mattern/Theresa Cole) to a depth of approximately 115x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.17Gb, with the contig and scaffold N50 values of 32.54Kb and 8.39Mb respectively. We identified 19170 protein-coding genes.
DOI: 10.5524/102167
title: Genomic data from Snares-crested penguin (<em>Eudyptes robustus</em>).

description: The Snares crested penguin (also known as Snares penguin, Snares Islands penguin, and in Mori it is known as pokotiwha) is endemic only to the New Zealand Snares Islands and Western Chain. It is a crested penguin closely related to the Fiordland crested penguin. Historically, Snares crested and Fiordland crested penguins were considered incipient - however the Snares crested penguin can be distinguished from the Fiordland crested penguin by having bare skin around the base of its bill. The Snares crested penguin breeds among tree roots and rocks in dense forest or in the open, laying two eggs, the second of which is larger and hatches first rather than being the smallest and last to hatch. The International Union for Conservation of Nature (IUCN) classifies the Snares crested penguin as vulnerable. The Snares crested penguin is a Taonga, or treasured possession in Mori culture.<br>We sequenced the genome of an adult Snares-crested penguin from Dunedin Wildlife Hospital, originally from The Snares, New Zealand sub-Antarctic (provided by David Thompson) to a depth of approximately 138x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.15Gb, with the contig and scaffold N50 values of 29.02Kb and 0.35Mb respectively. We identified 17126 protein-coding genes.
DOI: 10.15468/dl.r5zprn
title: Occurrence Download

description: A dataset containing 341 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "StateProvince is Bayern",
 "TaxonKey is Dactylorhiza majalis (Rchb.) P.F.Hunt & Summerh.",
 "Year 2016-2024"
 ]
}

 The dataset includes 341 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001998-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5524/102096
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1033

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001778. Preliminary identification is that it is of the family Moraceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 714993000bp. We have generated 73800000000bp of data, which gives a theoretical coverage of 103.2x.