cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102150
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1087

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_00001863. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 2811400000bp. We have generated 65420000000bp of data, which gives a theoretical coverage of 23.3x.
DOI: 10.5524/102151
title: Image data of Nanmaohu Park vascular plant specimen, RL1088

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 images from the plant vouchered as not provided. Preliminary identification is that it is of the family uncharacterized vascular plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/102152
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1089

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_00001931. Preliminary identification is that it is of the family Saururaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 2401780000bp. We have generated 66620000000bp of data, which gives a theoretical coverage of 27.7x.
DOI: 10.5524/102153
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1090

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_00001876. Preliminary identification is that it is of the family Polygonaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1824350000bp. We have generated 73260000000bp of data, which gives a theoretical coverage of 40.2x.
DOI: 10.5524/102154
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1091

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_00001628. Preliminary identification is that it is of the family Cucurbitaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1043280000bp. We have generated 68000000000bp of data, which gives a theoretical coverage of 65.2x.
DOI: 10.5524/102155
title: Image data of Nanmaohu Park uncharacterized vascular plant plant specimen, RL1092

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 images from the plant vouchered as not provided. Preliminary identification is that it is of the family uncharacterized vascular plant plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/102156
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1093

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_00002326. Preliminary identification is that it is of the family Flemingia stricta. <br>The K-mer distribution of the sequencing predicted the genome size to be 1238480000bp. We have generated 74080000000bp of data, which gives a theoretical coverage of 59.8x.
DOI: 10.5524/102160
title: Genome data of the bird of paradise, Paradisaea rubra

description: The Paradisaea rubra, also called red bird-of-paradise or cendrawasih merah, is a large bird-of-paradise up to 72 cm long, brown and yellow with a dark brown iris, grey legs and yellow bill. The male has an emerald green face, a pair of elongated black corkscrew-shaped tail wires, dark green feather pompoms above each eye and a train of glossy crimson red plumes with whitish tips at either side of the breast. The male measures up to 72 cm long, including the ornamental red plumes that require at least six years to reach full length. The female is similar but smaller in size, with a dark brown face and has no ornamental red plumes. The diet consists mainly of fruits, berries and arthropods. An Indonesian endemic, the red bird-of-paradise is distributed to lowland rainforests of Waigeo and Batanta islands of Raja Ampat, West Papua. This species shares its home with another bird-of-paradise, the Wilson's bird-of-paradise.(Wikipedia). <br> Here we extracted DNA from the footpad of a museum specimen collected collected nearly 70 years ago. Due to the natural degradation of the DNA it was not possible to make denovo assembly of the genome so the reads were mapped to the genome assembly of a closely related species, Ptiloris paradiseus. The map reads provide 16822 coding gene sequences, and BUSCO analysis demonstrates a coverage of 94.9%.
DOI: 10.5524/102161
title: Genome data of the bird of paradise, Pteridophora alberti

description: The Pteridophora alberti is also know as the King of Saxony bird of paradise. It is endemic to montane forest in New Guinea. The adult King of Saxony bird-of-paradise is approximately 22 cm long. The male is black and yellow with a dark brown iris, brownish-grey legs, a black bill with a bright aqua-green gape, and two remarkably long (up to 50 cm) scalloped, enamel-blue brow-plumes that can be independently erected at the bird's will. The unadorned female is greyish brown with barred underparts. The diet consists mainly of fruits, berries and arthropods.(Wikipedia). <br> Here we extracted DNA from the footpad of a museum specimen collected collected nearly 70 years ago. Due to the natural degradation of the DNA it was not possible to make de novo assembly of the genome so the reads were mapped to the genome assembly of a closely related species, Ptiloris paradiseus. The map reads provide 16721 coding gene sequences, and BUSCO analysis demonstrates a coverage of 94.8%.
DOI: 10.5524/102162
title: The genome and transcriptome of the Antarctic toothfish Dissostichus mawsoni

description: The Antarctic toothfish <i>Dissostichus mawsoni</i> can grow to giant sizes (2.0 m in length and 140 kg in mass) and is an iconic species of the Antarctic notothenioid radiation, with wide distributions in freezing waters of high latitude Antarctic coasts, as far south as 77.5o 107 S, the southern limit of Antarctic marine life. It thus exemplifies the stenothermal cold-adapted character state. Despite its large size, it is the only notothenioid species that achieved complete neutral buoyancy as adults; thus this species serves as the best model for examining the evolutionary underpinning of secondary pelagicism in the Antarctic clade. <br> Here we provide the chromosome-level genome assembly of <i>D.mawsoni</i> using the Illumina, PacBio, and Hi-C sequencing data. A total of ~107Gb of raw data covering the predicted genome length ~840Mb to ~ 139× read depth. The de novo genome assembly of ~757 Mb generated a scaffold N50 of ~2.2Mb with 22,516 intact predicted protein-coding gene models. BUSCO evaluation demonstrated that the genome completeness reached 97.2%. Additionally we demonstrat expression profiles and sequence variations with RNA seq data from 13 tissues (liver, gill, stomach, white muscle, red muscle, skin, small intestine, brain, head kidney, caudal kidney, spleen, and ovary ).
DOI: 10.5524/102163
title: The genome and transcriptome of the Patagonia robalo Eleginops maclovinus

description: <i>Eleginops maclovinus</i>, the Patagonian robalo, is a species of notothenioid fish found in coastal and estuarine habitats around southernmost South America, ranging as far north as Valparaíso on the Pacific side, and Uruguay on the Atlantic side. It is the only member of its genus, which is the only member of the family Eleginopsidae. It is an omnivore, tending towards carnivore. In some parts of its range, it is especially fond of Paracorophium, but it is opportunistic, and its exact diet depends on the availability in the habitat where the individual fish lives. It reaches about 105 cm (3.44 ft) in length, and can live for 10 years. It is a protandric hermaphrodite, and males predominate in lengths below 52 cm (1.71 ft), while female predominate above.<br> Here we provide the chromosome-level genome assembly of <i>E. maclovinus</i> using the Illumina, PacBio, and Hi-C sequencing data. A total of ~411Gb of raw data covering the predicted genome length ~780Mb to ~ 590× read depth. The de novo genome assembly of ~727 Mb generated a scaffold N50 of ~0.69 Mb with 22,959 intact predicted protein-coding gene models. BUSCO evaluation demonstrated that the genome completeness reached 95.0%. Additionally we demonstrat expression profiles and sequence variations with RNA seq data from 13 tissues (liver, gill, stomach, white muscle, red muscle, skin, small intestine, brain, head kidney, caudal kidney, spleen, and ovary ).
DOI: 10.5524/102165
title: Genomic data from Macaroni penguin (<em>Eudyptes chrysolophus chrysolophus</em>).

description: The Macaroni penguin is a crested penguin with golden-yellow crests found widely on subantarctic islands to the Antarctic peninsula. The Macaroni penguin is often considered a separate species from the Royal penguin, given its unique black facial plumage and wide breeding range. Several recent genetic studies, however, have demonstrated that the Macaroni penguin and Royal penguin are probably incipient. They are the most numerous penguin species. However, widespread declines have been recorded in many populations and the International Union for Conservation of Nature (IUCN) classifies the Macaroni penguin as vulnerable.<br>We sequenced the genome of an adult Macaroni penguin from Marion Island, Prince Edward Islands (provided by Peter Ryan) to a depth of approximately 109x 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 160.01Kb and 13.16Mb respectively. We identified 16311 protein-coding genes.
DOI: 10.5524/102170
title: Genomic data from Western rockhopper penguin (<em>Eudyptes chrysocome</em>).

description: The Western rockhopper penguin (also known as the Southern rockhopper penguin or American Southern rockhopper penguin) is a small crested penguin. It is closely related to the Eastern rockhopper penguin, and there is still some debate about whether both are considered incipient species, sub-species or distinct species. Recent genetic work suggests they are probably separate species. The Western rockhopper penguin breeds on subantarctic islands of the western Pacific and Indian Oceans, as well as around the southern coasts of South America. The International Union for Conservation of Nature (IUCN) classifies the Southern rockhopper penguin group (including both the Western and the Eastern rockhopper penguin) as vulnerable.<br>We sequenced the genome of an adult Western rockhopper penguin from Falkland Islands/Malvinas (provided by Dee Boersma) to a depth of approximately 162x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.26Gb, with the contig and scaffold N50 values of 64.46Kb and 1.86Mb respectively. We identified 16280 protein-coding genes.
DOI: 10.5524/102178
title: Genomic data from Little blue penguin (<em>Eudyptula minor minor</em>).

description: The New Zealand little blue penguin (also known as fairy penguin, blue penguin, little penguin and koror in Mori) is one of the smallest penguins. It is found on the coastlines of New Zealand and the Chatham Islands. They have a slate-blue plumage. Recent genetic, morphological and behavioral research has demonstrated that the New Zealand little blue penguin is a seperate species to the Australian fairy penguin, however this still remains controversial. Populations have recently declined, and they are considered as Least Concern by the International Union for Conservation of Nature (IUCN), however this assessment still classifies the Australian and New Zealand species as conspecific. The New Zealand little penguin is a Taonga, or treasured possession in Mori culture.<br>We sequenced the genome of an adult Little blue penguin from National Aquarium of New Zealand, New Zealand North Island (provided by Helen Taylor) to a depth of approximately 87x 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 86.12Kb and 20.15Mb respectively. We identified 17802 protein-coding genes.
DOI: 10.5524/102180
title: Genomic data from Gentoo penguin (<em>Pygoscelis papua</em>).

description: The Gentoo penguin is easily recognized by the wide white stripe extending across the top of its head, and its bright orange-red bill. It has a long tail. Gentoos are the third-largest species of penguin after the Emperor penguin and the King penguin. Gentoos are well adapted to extremely cold and harsh climates. Breeding colonies are located on ice-free surfaces. Gentoos breed on many sub-Antarctic islands, with main colonies are on the Falkland Islands, South Georgia and the South Sandwich Islands, and Kerguelen Islands. Gentoo penguins exhibit population genetic structure, and different populations are occasionally considered to represent several subspecies. They are considered as Least Concern by the International Union for Conservation of Nature (IUCN).<br>We sequenced the genome of an adult Gentoo penguin from West Antarctic Peninsula, Antarctica (provided by Tom Hart) to a depth of approximately 105x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.26Gb, with the contig and scaffold N50 values of 91.59Kb and 2.65Mb respectively. We identified 16698 protein-coding genes.
DOI: 10.5524/102356
title: Supporting data for "The Australasian dingo archetype: <i>De novo</i> chromosome-length genome assembly, DNA methylome, and cranial morphology"

description: There is no reference specimen for Australias top-order predator the dingo. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. Here we link a high-quality <i>de novo</i> long read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies.Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published <i>de novo</i> canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog.These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
DOI: 10.5524/102360
title: Supporting data for "Honey bee (<i>Apis mellifera</i>) wing images: a tool for identification and conservation"

description: The honey bee (<i>Apis mellifera</i>) is an ecologically and economically important species that provides pollination services to natural and agricultural systems. The biodiversity of the honey bee in parts of its native range is endangered by migratory beekeeping and commercial breeding. In consequence, some honey bee populations that are well adapted to the local environment are threatened with extinction. A crucial step for the protection of honey bee biodiversity is reliable differentiation between native and non-native bees. One of the methods that can be used for this is the geometric morphometrics of wings. This method is fast, low-cost, and does not require expensive equipment. Therefore, it can be easily used by both scientists and beekeepers. However, wing geometric morphometrics is challenging due to the lack of reference data that can be reliably used for comparisons between different geographic regions.<br>Here, we provide an unprecedented collection of 26,481 honey bee wing images representing 1,725 samples from 13 European countries. The wing images are accompanied by the coordinates of 19 landmarks and the geographic coordinates of the sampling locations. We present an R script that describes the workflow for analysing the data and identifying an unknown sample. We compared the data with available reference samples for lineage and found general agreement with them.<br>The extensive collection of wing images available on the Zenodo website can be used to identify the geographic origin of unknown samples and therefore assist in the monitoring and conservation of honey bee biodiversity in Europe.