Fungal ITS2 data from Pyroleae and Monotropa hypopitys germination study

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說明

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.

資料紀錄

此資源出現紀錄的資料已發佈為達爾文核心集檔案（DwC-A），其以一或多組資料表構成分享生物多樣性資料的標準格式。核心資料表包含 9,922 筆紀錄。

亦存在 2 筆延伸集的資料表。延伸集中的紀錄補充核心集中紀錄的額外資訊。每個延伸集資料表中資料筆數顯示如下。

9922

29766

9922

此 IPT 存放資料以提供資料儲存庫服務。資料與資源的詮釋資料可由「下載」單元下載。「版本」表格列出此資源的其它公開版本，以便利追蹤其隨時間的變更。

版本

以下的表格只顯示可公開存取資源的已發布版本。

如何引用

研究者應依照以下指示引用此資源。:

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

權利

研究者應尊重以下權利聲明。:

此資料的發布者及權利單位為 Stockholm University。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: d19074ea-f1cf-42ba-9109-e99a5e6a50a5。 Stockholm University 發佈此資源，並經由GBIF Sweden同意向GBIF註冊成為資料發佈者。

關鍵字

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

聯絡資訊

Veronika Johansson

元數據提供者 ●
出處 ●
連絡人

GBIF Sweden Node Manager

Swedish Museum of Natural History

Box 50007

104 05 Stockholm

veronika.johansson@nrm.se

+468-51954036

https://orcid.org/https://orcid.org/0000-0002-3028-9947

Ove Eriksson

研究主持人

Stockholm University

Stockholm

ove.eriksson@su.se

Urmas Kõljalg

作者

University of Tartu

Tartu

urmas.koljalg@ut.ee

Leho Tedersoo

作者

University of Tartu

Tartu

leho.tedersoo@ut.ee

Mohammad Bahram

作者

Swedish University of Agricultural Sciences

Uppsala

mohammad.bahram@slu.se

地理涵蓋範圍

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

界定座標範圍	緯度南界經度西界 [56.438, 16.387], 緯度北界經度東界 [57.353, 17.093]

分類群涵蓋範圍

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

取樣方法

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.

研究範圍	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.
品質控管	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).

研究範圍

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.

品質控管

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).

方法步驟描述:

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.

額外的詮釋資料

Introduction
Getting Started
目的
替代的識別碼	d19074ea-f1cf-42ba-9109-e99a5e6a50a5
	https://www.gbif.se/ipt/resource?r=pyrola-its2-2011-2012