cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102234
title: Supporting data for "Association Mapping Across a Multitude of Traits Collected in Diverse Environments in Maize"

description: Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data -- 18M markers -- from two partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least seven US states and scored for 162 distinct trait datasets enabled the identification of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be three genes based a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g. above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype by environment interaction.
DOI: 10.6084/m9.figshare.19175888
title: Maize_WiDiv_SAM_1051Genotype.vcf.gz genotype file

description: The genotype dataset with 17,717,568 SNPs was used for a resampling-based genome-wide association study on 162 phenotypes from two partially overlapping maize association panels viz, SAM and WiDiv panels. SNPs were filtered to remove markers with a minor allele frequency of less than 0.01 or proportion of heterozygous SNP calls greater than 0.1 to produce the final SNP set
DOI: 10.5524/101950
title: Image data of Nanmaohu Park vascular plant specimen, RL0887

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: 10.5524/101957
title: Image data of Nanmaohu Park vascular plant specimen, RL0894

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: 10.5524/101974
title: Genomic data of Nanmaohu Park vascular plant specimen, RL0911

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_00001572. Preliminary identification is that it is of the family Araceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 4054850000bp. We have generated 71700000000bp of data, which gives a theoretical coverage of 17.7x.
DOI: 10.5524/101975
title: Genomic data of Nanmaohu Park vascular plant specimen, RL0912

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_00001635. Preliminary identification is that it is of the family Dioscoreaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 587797000bp. We have generated 78900000000bp of data, which gives a theoretical coverage of 134.2x.
DOI: 10.5524/101977
title: Genomic data of Nanmaohu Park Combretaceae plant specimen, RL0914

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_00001617. Preliminary identification is that it is of the family Combretaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 954909000bp. We have generated 56940000000bp of data, which gives a theoretical coverage of 59.6x.
DOI: 10.5524/102193
title: The haplotype-resolved chromosome pairs and transcriptome data of a heterozygous diploid African cassava cultivar

description: Cassava (<i>Manihot esculenta</i>) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult to assemble genome. <br>Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler Hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present two chromosome scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy above QV46, contig N50 above 18 Mbp, BUSCO completeness of 99%, and 35 K phased gene loci, it is the most accurate, continuous, complete and haplotype-resolved cassava genome assembly so far. <i>Ab initio</i> gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20-30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue-specific and inconsistent across different tissues. Direction-shifting was observed in less than 2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome re-arrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR-retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding.<br>The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy and continuity.
DOI: 10.5524/102202
title: Supporting data for Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

description: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.
DOI: 10.5524/102205
title: Supporting data for "Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding"

description: The sequencing of the wheat (<i>Triticum aestivum</i>) genome has been a methodological challenge for many years due to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read whole genome sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost. Here, we report on an optimized procedure based on long-reads produced on the ONT (Oxford Nanopore Technology) PromethION device to assemble the genome of the French bread wheat cultivar Renan. We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date, a resource that will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide the methodological standards to generate high-quality assemblies of complex genomes.
DOI: 10.5524/102230
title: Chromosome-scale assembly of the caddisfly <i>Eubasilissa regina</i>

description: Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic sequences for the caddisfly <i>Eubasilissa regina</i>. The <i>Eubasilissa regina</i> genome was highly contiguous (N50 = 32.4 Mbp, L50 = 11) and complete (BUSCO Complete = 95.5%), with complete and contiguous recovery of silk <i>heavy fibroin</i> gene sequences. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.
DOI: 10.5524/101935
title: Genomic data of Nanmaohu Park vascular plant specimen, RL0872

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_00002273. Preliminary identification is that it is of the family Hamelia patens. <br>The K-mer distribution of the sequencing predicted the genome size to be 2788090000bp. We have generated 61960000000bp of data, which gives a theoretical coverage of 22.2x.
DOI: 10.5524/101944
title: Genomic data of Nanmaohu Park vascular plant specimen, RL0881

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_00001546. Preliminary identification is that it is of the family Arecaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1697330000bp. We have generated 77640000000bp of data, which gives a theoretical coverage of 45.7x.
DOI: 10.5524/101945
title: Genomic data of Nanmaohu Park vascular plant specimen, RL0882

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_00001564. Preliminary identification is that it is of the family Asparagaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be Not recordedbp. We have generated 69780000000bp of data, which gives a theoretical coverage of x.
DOI: 10.5524/101946
title: Genomic data of Nanmaohu Park vascular plant specimen, RL0883

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_00001547. Preliminary identification is that it is of the family Arecaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1560170000bp. We have generated 70820000000bp of data, which gives a theoretical coverage of 45.4x.
DOI: 10.5524/101947
title: Image data of Nanmaohu Park vascular plant specimen, RL0884

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: 10.5524/101948
title: Image data of Nanmaohu Park vascular plant specimen, RL0885

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: 10.5524/101949
title: Image data of Nanmaohu Park vascular plant specimen, RL0886

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.