Details regarding DNA isolation and sequencing of Bhaga and Jamy individuals are given in Mishra and coauthors [26 (link)]. The remaining 16 individuals representing a wide range of the species distribution were collected from Siemianice provenance trial [28 ]. Detailed geographic locations are presented in Table 1 and Figure S1 . DNA was isolated from leaves with a GeneMATRIX Plant & Fungi DNA Purification Kit (EURx, Poland), after storing them in the dark for 48 h. Genomic library preparation and sequencing was done by an external service provider (IGA Technology Services s.r.l.) with Illumina HiSeq 2500 device in 125-bp PE mode. The obtained reads were purified from adapters and trimmed with Trimmomatic [29 (link)]. Raw reads were deposited in SRA under the accession numbers listed in Table 1 .
Genematrix plant fungi dna purification kit
Manufactured by EURx
Sourced in Poland
The GeneMATRIX Plant & Fungi DNA Purification Kit is a laboratory product designed to extract and purify DNA from plant and fungal samples. The kit utilizes a silica-based membrane technology to efficiently capture and isolate DNA, allowing for subsequent analysis and applications.
Automatically generated - may contain errors
Lab products found in correlation
Nanodrop nd 100, by Thermo Fisher Scientific (2 mentions)
Nanodrop 2000c, by Thermo Fisher Scientific (2 mentions)
Nanodrop, by Thermo Fisher Scientific (2 mentions)
Hiseq 2500, by Illumina (1 mentions)
Dneasy mericon food kit, by Qiagen (1 mentions)
Genematrix bacterial yeast genomic dna purification kit, by EURx (1 mentions)
Clean up concentrator, by A&A Biotechnology (1 mentions)
Hiseq 2500 platform, by Illumina (1 mentions)
Quantus fluorometer, by Promega (1 mentions)
Novaseq 6000, by Macrogen (1 mentions)
Kb240, by Binder (1 mentions)
Purification kit, by EURx (1 mentions)
8 protocols using genematrix plant fungi dna purification kit
1
DNA Isolation and Sequencing of Bhaga and Jamy
2
Bacterial and Fungal DNA Extraction
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genomic bacterial DNA was isolated using the Genomic Mini bacterial DNA Purification Kit (A&A Biotechnology, Poland), the DNeasy Mericon Food Kit (Qiagen, Hilden, Germany) or Whole Blood and Tissue kit (Qiagen, Germantown, MD, USA), according to the manufacturer’s instructions. The total fungal DNA was extracted from 100 mg of mycelia scraped from 10-day-old PDA cultures with the GeneMatrix Plant & Fungi DNA Purification Kit (EURx, Gdańsk, Poland) according to the manufacturer’s instructions. The quality and total DNA concentration was estimated with a NanoDrop ND-100 or NanoDrop 2000c (ThermoFisherScientific, Waltham, MA, USA).
3
Rapid Genomic DNA Purification Kits
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Two commercially available kits, designed for rapid purification of genomic DNA, based on specific buffer formulations and DNA-binding silica membrane columns, were tested, namely GeneMATRIX Bacterial & Yeast Genomic DNA Purification Kit (EurX®, Gdańsk, Poland), in combination with lyticase (100 μg/mL) and β-mercaptoethanol (β-ME, 1 μL/mL) (Sigma, Saint Louis, USA) (K1) and GeneMATRIX Plant & Fungi DNA Purification Kit (EurX®, Gdańsk, Poland) (K2). When using both kits, all steps were performed strictly in accordance with instructions provided by the manufacturer.
4
Molecular Markers Amplification Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Small pieces of thalli (approx. 2 mm2) were put into Eppendorf tubes. Then DNA was extracted using a GeneMATRIX Plant & Fungi 1 . Electrophoresis was performed on a 1% agarose gel to determine whether amplification of target molecular markers was successful. PCR products were purified using Clean-Up Concentrator (A&A Biotechnology). Sequencing was performed by Macrogen (The Netherlands). All newly-generated sequences were deposited in GenBank and their GenBank Acc. Numbers are presented in Table 1 .
5
DNA Extraction and Sequencing Protocols
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total DNA was extracted from the young leaves of 300 sampled individuals from dataset A using the GeneMATRIX Plant & Fungi DNA Purification Kit (EURx, Poland), following the manufacturer's instructions. Extracted DNA was quantified using the Eppendorf BioPhotometer and Quantus Fluorometer (Promega). Genomic DNA was digested with SphI and MboI. Library preparation and double‐digest restriction site‐associated DNA (ddRAD) sequencing using an Illumina HiSeq 2500 platform with 125 bp paired‐end reads were performed at IGA Technology Services (Udine, Italy).
DNA extraction from 20 individuals from dataset B was based on the method described by Wang et al. (2012 (link)). The quality of the isolated genomic DNA was checked using both a Quantus Fluorometer (Promega) and gel electrophoresis. Library preparation using Truseq PCR‐free with 350 bp inserts, and whole‐genome sequencing using NovaSeq6000 with 150 bp paired‐end reads was performed by Macrogen (Amsterdam, The Netherlands).
DNA extraction from 20 individuals from dataset B was based on the method described by Wang et al. (2012 (link)). The quality of the isolated genomic DNA was checked using both a Quantus Fluorometer (Promega) and gel electrophoresis. Library preparation using Truseq PCR‐free with 350 bp inserts, and whole‐genome sequencing using NovaSeq6000 with 150 bp paired‐end reads was performed by Macrogen (Amsterdam, The Netherlands).
6
DNA Isolation from Young Plant Seedlings
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For DNA isolation, fragments of young seedlings of analyzed genotypes were collected and frozen in liquid nitrogen. Each sample consisted of plant material from 6 plants. DNA extraction was performed using the GeneMATRIX Plant & Fungi DNA purification kit (EURx, Gdańsk, Poland) according to the manufacturer protocol. The isolated DNA was quantified and qualified using a NanoDrop (Thermo Scientific, Madison, USA) spectrophotometer.
7
Optimized DNA Extraction for Reduced-Representation Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The sequencing of reduced-representation libraries demands high molecular weight DNA >50 kb, with a concentration >30 ng/µL and total mass of 1.5-3 µg [50] (link). To meet these requirements, we collected flushing leaf buds. Sampled material was dried to ≈10% humidity with a phytotron (BINDER WTC KB 240) for 24 h at 30 • C; afterwards, 30 mg of tissue was stacked in sterile 2 mL Eppendorf tubes and ground at 30 Hz in a laboratory mill (Mixer Mill MM 400, Retsch, Haan, Germany). DNA was isolated using GeneMATRIX Plant & Fungi DNA Purification Kit (EURx, Gda ńsk, Poland), with slight modifications to the manufacturer's protocol (for details, see Supplementary Materials).
Isolated DNA was shipped to external service providers for enzyme optimization, library construction, and sequencing: GBS-Cornell University (Ithaca, NY, USA); RADseq-Floragenex Inc. (Portland, OR, USA); and ddRAD-IGA Technology Services (Udine, Italy). Details of library construction and sequencing are presented in Table 1.
Isolated DNA was shipped to external service providers for enzyme optimization, library construction, and sequencing: GBS-Cornell University (Ithaca, NY, USA); RADseq-Floragenex Inc. (Portland, OR, USA); and ddRAD-IGA Technology Services (Udine, Italy). Details of library construction and sequencing are presented in Table 1.
8
Extraction and Purification of Plant and Fungal DNA
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
In the preliminary stage, the collected leaves were crushed in a mortar in the presence of liquid nitrogen. Genetic material was isolated using two different methods. One involved using the GeneMATRIX Plant & Fungi DNA Purification Kit (EURx, Gdańsk, Poland). The procedure was Purification Kit (EURx, Gdańsk). Procedurę wykonano zgodnie z instrukcją producenta. Druga metoda opierała się na procesie izolacji DNA z grzybów opracowanym przez Murraya i Thomsona. Po pomyślnej izolacji oznaczono stężenie i czystość DNA metodą spektrofotometryczną przy użyciu aparatu NanoDrop 1000 (Thermo Fisher Scientific).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!