Fungal ITS2 data from Pyroleae and Monotropa hypopitys germination study

Occurrence
最新バージョン Stockholm University により出版 3月 30, 2026 Stockholm University
公開日:
2026年3月30日
ライセンス:
CC-BY 4.0

DwC-A形式のリソース データまたは EML / RTF 形式のリソース メタデータの最新バージョンをダウンロード：

DwC ファイルとしてのデータ ダウンロード 9,922 レコード English で (2 MB) - 更新頻度: not planned
EML ファイルとしてのメタデータ ダウンロード English で (46 KB)
RTF ファイルとしてのメタデータ ダウンロード English で (17 KB)

説明

This dataset contains ITS metabarcoding data describing fungal communities associated with germinating seeds and early developmental stages of Pyroleae species and Monotropa hypopitys in Sweden. The data were generated using high-throughput sequencing of the ITS2 region to characterize ectomycorrhizal fungal diversity and its relationship to plant development and ecological conditions.DescriptionThe dataset originates from a field-based seed sowing experiment designed to investigate fungal associations during early ontogeny of mycoheterotrophic and partially mycoheterotrophic plants (Johansson et al. 2017). Seed bags were deployed across multiple forest sites and retrieved over multiple years to assess germination, seedling development, and associated fungal communities. DNA was extracted from germinated seedlings and analyzed using ITS metabarcoding of the ITS2 region. The resulting dataset includes operational taxonomic units (OTUs), taxonomic assignments, and sequence read abundances, providing a detailed characterization of fungal diversity associated with early plant life stages.PurposeThe purpose of this dataset is to document the diversity and composition of fungal communities associated with early developmental stages of selected plant species and to support research on plant-fungal interactions, mycoheterotrophy, and forest ecosystem processes, building on the findings presented in Johansson et al. 2017, Mol Ecol, 26: 2591-2604. https://doi.org/10.1111/mec.14050This dataset was published via the SBDI ASV portal.

データ レコード

この オカレンス（観察データと標本) リソース内のデータは、1 つまたは複数のデータ テーブルとして生物多様性データを共有するための標準化された形式であるダーウィン コア アーカイブ (DwC-A) として公開されています。 コア データ テーブルには、9,922 レコードが含まれています。

拡張データ テーブルは2 件存在しています。拡張レコードは、コアのレコードについての追加情報を提供するものです。 各拡張データ テーブル内のレコード数を以下に示します。

Occurrence (コア)
9922
ExtendedMeasurementOrFact 
29766
dnaDerivedData 
9922

この IPT はデータをアーカイブし、データ リポジトリとして機能します。データとリソースのメタデータは、 ダウンロード セクションからダウンロードできます。 バージョン テーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

Johansson V (2026). Fungal ITS2 data from Pyroleae and Monotropa hypopitys germination study. Version 1.1. Stockholm University. Occurrence dataset. https://www.gbif.se/ipt/resource?r=pyrola-its2-2011-2012&v=1.1

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は Stockholm University。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: d19074ea-f1cf-42ba-9109-e99a5e6a50a5が割り当てられています。   GBIF Sweden によって承認されたデータ パブリッシャーとして GBIF に登録されているStockholm University が、このリソースをパブリッシュしました。

キーワード

Occurrence; ITS; metabarcoding; fungal communities; ectomycorrhizal fungi; mycoheterotrophy; seedling development; Pyroleae; Monotropa hypopitys; dust seeds; Sweden

連絡先

Veronika Johansson
  • メタデータ提供者 ●
  • 最初のデータ採集者 ●
  • 連絡先
  • GBIF Sweden Node Manager
Swedish Museum of Natural History
  • Box 50007
104 05 Stockholm
SE
  • +468-51954036
Ove Eriksson
  • 研究代表者
Stockholm University
Stockholm
SE
Urmas Kõljalg
  • 論文著者
University of Tartu
Tartu
EE
Leho Tedersoo
  • 論文著者
University of Tartu
Tartu
EE
Mohammad Bahram
  • 論文著者
Swedish University of Agricultural Sciences
Uppsala
SE

地理的範囲

Sampling was conducted on the island of Öland, Sweden, across multiple forest sites including coniferous and mixed forests.

座標（緯度経度） 南 西 [56.438, 16.387], 北 東 [57.353, 17.093]

生物分類学的範囲

N/A

Kingdom Fungi
Phylum Mortierellomycota, Basidiobolomycota, Entorrhizomycota, Mucoromycota, Ascomycota, Zoopagomycota, Rozellomycota, Basidiomycota, Chytridiomycota
Class Geminibasidiomycetes, Rhizophydiomycetes, Rozellomycota_cls_Incertae_sedis, Tremellomycetes, GS27, Atractiellomycetes, Spizellomycetes, Mortierellomycetes, Microbotryomycetes, Basidiobolomycota_cls_Incertae_sedis, Malasseziomycetes, Pezizomycotina_cls_Incertae_sedis, Dothideomycetes, Candelariomycetes, Eurotiomycetes, Entorrhizomycetes, Umbelopsidomycetes, Exobasidiomycetes, Sordariomycetes, Saccharomycetes, Lobulomycetes, Geoglossomycetes, Mucoromycetes, Pucciniomycetes, Rhizophlyctidomycetes, Archaeorhizomycetes, Arthoniomycetes, Agaricomycetes, Cystobasidiomycetes, Ascomycota_cls_Incertae_sedis, Rozellomycotina_cls_Incertae_sedis, Zoopagomycetes, Pezizomycetes, Basidiobolomycetes, Leotiomycetes, Orbiliomycetes
Order Leucosporidiales, Pezizomycotina_ord_Incertae_sedis, Microthyriales, Filobasidiales, Myrmecridiales, Agaricomycetes_ord_Incertae_sedis, Eurotiomycetidae_ord_Incertae_sedis, Lichenostigmatales, Trichosphaeriales, Microbotryomycetes_ord_Incertae_sedis, Auriculariales, Sordariales, Leotiomycetes_ord_Incertae_sedis, Rhizophlyctidales, Cladosporiales, Mytilinidiales, Orbiliales, Onygenales, Verrucariales, Helicobasidiales, Exobasidiomycetes_ord_Incertae_sedis, Malasseziales, Tremellodendropsidales, Microascales, Cystofilobasidiales, Trichosporonales, Sebacinales, Dothideomycetes_ord_Incertae_sedis, Geminibasidiales, Corticiales, Geoglossales, Acrospermales, Mortierellales, Pseudodactylariales, Rhytismatales, Asterinales, Helotiales, Mucorales, Chaetosphaeriales, Agaricales, GS11, Cephalothecales, Atheliales, Trechisporales, Entorrhizales, Annulatascales, Rozellomycota_ord_Incertae_sedis, Basidiobolomycota_ord_Incertae_sedis, Candelariales, Pleosporales, Umbelopsidales, Pezizales, Glomerellales, Kriegeriales, Spizellomycetales, Polyporales, Sporidiobolales, Zoopagales, Mycosphaerellales, Eurotiales, Capnodiales, Patellariales, GS27_ord_Incertae_sedis, Hymenochaetales, Sclerococcales, Xylariales, Russulales, Hypocreales, Atractiellales, Botryosphaeriales, Tremellales, Chaetothyriales, Venturiales, Exobasidiales, Thelebolales, Tubeufiales, Magnaporthales, Thelephorales, Rhizophydiales, Leotiales, Gloniales, Lobulomycetales, Saccharomycetales, Boletales, Ascomycota_ord_Incertae_sedis, Archaeorhizomycetales, Coniochaetales, Cantharellales, Basidiobolales, Cystobasidiales, Phacidiales, Chaetomellales, Dothideales, Amphisphaeriales

収集方法

Seeds of five plant species (Chimaphila umbellata, Moneses uniflora, Monotropa hypopitys, Pyrola chlorantha, and Pyrola rotundifolia) were collected from mature individuals at each study site. Seeds were placed in mesh seed bags and buried in experimental plots in the field. At each site, seed bags were deployed both in plots containing adult plants (occupied plots) and in control plots without adult individuals (unoccupied plots), allowing comparison of germination and fungal associations under different ecological conditions. Seed bags were retrieved annually over a three-year period following sowing. Upon retrieval, germination status and developmental stage of seedlings were recorded. Seedlings were categorized into developmental stages (germinated, elongated, and branched), and samples of germinated seedlings were collected for molecular analysis of associated fungal communities.

Study Extent The study was conducted on the island of Öland, Sweden, across multiple forest sites representing different habitat types, including old-growth coniferous forests dominated by Pinus sylvestris and mixed coniferous–deciduous forests. The sites were selected to represent suitable habitats for the target plant species and to allow comparison between locations with and without established adult individuals of the studied species.
Quality Control Sequence data were subjected to multiple quality control steps to ensure reliability. Raw reads were filtered to remove low-quality sequences, chimeric sequences, and singletons. Only sequences passing quality thresholds were retained for further analysis. Operational taxonomic units (OTUs) were clustered at a 97 percent sequence similarity threshold. Taxonomic assignments were performed using reference databases, and assignments were accepted based on sequence similarity criteria. Negative controlsitem-0 were included during laboratory procedures to detect contamination, and non-target sequences were excluded from analyses where appropriate (Johansson et al. 2017). Re-annotation against UNITE database took place before publication of this dataset (2026-03-30).

Method step description:

  1. DNA was extracted from germinated seedlings using a soil DNA extraction protocol. The internal transcribed spacer (ITS) region was amplified using PCR with primers targeting fungal ITS regions. Amplicons were normalized, pooled, and sequenced using 454 pyrosequencing technology. Sequence data were processed using bioinformatics pipelines that included demultiplexing, trimming, and clustering into OTUs. Representative sequences for each OTU were compared against reference databases (including UNITE and INSDC) for taxonomic identification. OTUs were assigned to taxonomic levels based on sequence similarity thresholds, and fungal taxa of interest, particularly ectomycorrhizal groups, were identified for further ecological analysis.

追加のメタデータ

はじめに
Getting Started
目的
代替識別子 d19074ea-f1cf-42ba-9109-e99a5e6a50a5
https://www.gbif.se/ipt/resource?r=pyrola-its2-2011-2012