Antarctic cryptoendolithic fungal communities ITS amplicon sequencing

メタデータ
最新バージョン SCAR - Microbial Antarctic Resource System により出版 3 19, 2019 SCAR - Microbial Antarctic Resource System
公開日:
2019/03/19
ライセンス:
CC-BY 4.0

メタデータのみリソース のメタデータの最新版をEML または RTF としてダウンロード：

EML ファイルとしてのメタデータ ダウンロード English で (10 KB)
RTF ファイルとしてのメタデータ ダウンロード English で (12 KB)

説明

Amplicon sequencing dataset of cryptoendolithic (sandstone) fungal communities (ITS1 marker gene) in Victoria Land (continental Antarctica).

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。:

Coleine C, Zucconi L, Onofri S, Pombubpa N, Stajich J, Selbman L (2018): Antarctic cryptoendolithic fungal communities ITS amplicon sequencing. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_cryptoendolithic_microbial_fungi_its&v=1.2

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 SCAR - Microbial Antarctic Resource System。 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: b94f714c-e890-4365-81a5-968a20606d37が割り当てられています。   Scientific Committee on Antarctic Research 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SCAR - Microbial Antarctic Resource System が、このリソースをパブリッシュしました。

キーワード

Metadata

連絡先

Claudia Coleine
  • 最初のデータ採集者 ●
  • 連絡先
University of Tuscia
Viterbo
IT
Laura Zucconi
  • 最初のデータ採集者
University of Tuscia
Viterbo
IT
Silvano Onofri
  • 最初のデータ採集者
University of Tuscia
Viterbo
IT
Nuttapon Pombubpa
  • 最初のデータ採集者
University of California
US
Jason Stajich
  • 最初のデータ採集者
University of California
US
Laura Selbman
  • 最初のデータ採集者
University of Tuscia
Viterbo
IT
Maxime Sweetlove
  • メタデータ提供者 ●
  • データ利用者
Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
1000 Brussels

地理的範囲

Victoria Land (Continental Antarctica)

座標（緯度経度） 南 西 [-77.91, 159.233], 北 東 [-74.169, 162.514]

生物分類学的範囲

microbial fungi (ITS1)

Phylum Fungi (Fungi)

プロジェクトデータ

説明がありません

タイトル Antarctic cryptoendolithic fungal communities
ファンデイング Sequencing was supported by funds through United States Department of Agriculture—National Institute of Food and Agriculture Hatch project CA-R-PPA-5062-H. Data analyses were performed on the High-Performance Computing Cluster at the University of California-Riverside in the Institute of Integrative Genome Biology supported by NSF DBI-1429826 and NIH S10-OD016290. Additional support was given through a Royal Thai government fellowship.

プロジェクトに携わる要員:

Claudia Coleine

収集方法

Rock samples were excised aseptically, transported, and stored at −20 °C at the Tuscia University (Viterbo, Italy) until processing.

Study Extent Sandstone rock samples were collected in triplicate in Victoria Land (Continental Antarctica), along a latitudinal transect from 74°10′10.5′′ S 162°25′38.0′′ E (Timber Peak, Northern Victoria Land) to 77°54′43.6′′ S 161°34′39.3′′ E (Finger Mt., Southern Victoria Land) ranging from 834 m a.s.l. (Battleship Promontory, Southern Victoria Land) to 3100 m a.s.l. (Mt. New Zealand, Northern Victoria Land). In addition, rocks with different sun exposures were collected from four visited sites (Battleship Promontory, Siegfried Peak, Finger Mt. and University Valley). All sites were visited during the XXXII Italian Antarctic Expedition (2015–2016).

Method step description:

  1. Rocks were crushed using a Grinder MM 400 RETSCH (Verder Scientific, Bologna, Italy) in sterile conditions to avoid contamination.
  2. Metagenomic DNA was extracted from 0.3 g of rocks using MOBIO Power Soil DNA Extraction kit (MOBIO Laboratories, Carlsbad, CA, USA), according to the manufacturer’s instructions. ITS1F (CTTGGTCATTTAGAGGAAGTAA) and ITS2 (GCTGCGTTCTTCATCGATGC) primers were used to amplify the internal transcribed spacer 1 region (ITS1). PCR reactions were performed in a total volume of 25 μL, containing 1 μL of each primer, 12.5 μL of Taq DNA Polymerase (Thermo Fischer Scientific Inc., Waltham, MA, USA), 9.5 μL of nuclease-free water (Sigma-Aldrich, St. Louis, MO, USA) and 5 ng of DNA, following Coleine et al. PCR conditions were initial denaturation at 93 °C for 3 min, 35 cycles of denaturation at 95 °C for 45 s, annealing at 50 °C for 1 min, extension at 72°C for 90 s, followed by a final extension at 72 °C for 10 min in an automated thermal cycler (BioRad, Hercules, CA, USA). Amplicons, purified with Qiagen PCR CleanUp kit (Macherey-Nagel, Hoerdt, France) and quantified using the Qubit dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, USA), were tagged with unique barcodes to enable identification of each sample, and then pooled for run sequencing.
  3. Sequencing (paired-end reads, 2 × 300 bp) of the pooled libraries was performed on a single Illumina MiSeq flowcell at the Institute for Integrative Genome Biology, University of California, Riverside.

書誌情報の引用

  1. Coleine, C., Zucconi, L., Onofri, S., Pombubpa, N., Stajich, J., & Selbmann, L. (2018). Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities. Life, 8(2), 19.

追加のメタデータ