dna sequencing files  (Biotechnology Information)

Journal: Molecular Ecology Resources

Article Title: Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch

doi: 10.1111/1755-0998.14056

Figure Lengend Snippet: File size reduction (contig count) and runtime of our pipeline. Reported values are from one randomly selected individual of each Betula host species in the multiple individual datasets.

Article Snippet: Using several datasets of publicly available raw Betula DNA sequence files from the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), we demonstrate how our pipeline can detect and inform on the abundance and rarity of plant‐associated fungi (including fungi not previously known to infect plants) and characterise the fungal communities of Betula , a non‐model organism with ample sequence data across individuals.

Techniques:

Journal: Molecular Ecology Resources

Article Title: Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch

doi: 10.1111/1755-0998.14056

Figure Lengend Snippet: Contig lengthening using metagenomic assembly prior to fungal detection and proportion of contigs classified to fungi. Samples belong to the same individual in B. nana and different individuals for all other taxa. Classified fungal sequences are reported at all confidence levels.

Article Snippet: Using several datasets of publicly available raw Betula DNA sequence files from the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), we demonstrate how our pipeline can detect and inform on the abundance and rarity of plant‐associated fungi (including fungi not previously known to infect plants) and characterise the fungal communities of Betula , a non‐model organism with ample sequence data across individuals.

Techniques: Sequencing

Journal: Molecular Ecology Resources

Article Title: Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch

doi: 10.1111/1755-0998.14056

Figure Lengend Snippet: Fungal genera detected in three Betula taxa ( Betula ermanii, B. pendula , B. platyphylla ), Buddleja alternifolia and Panicum virgatum . All phyla, and class, order, and family taxonomic groups with > 1 genus detected among samples, are labelled. Fungal genera are highlighted to indicate FUNGuild designation to endophyte or pathogen guilds. Black circles next to fungal genera indicate support from flanking region (ITS or 5.8S). At right, a heatmap of the plant host taxa with detected fungal genera relative frequencies shown.

Article Snippet: Using several datasets of publicly available raw Betula DNA sequence files from the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), we demonstrate how our pipeline can detect and inform on the abundance and rarity of plant‐associated fungi (including fungi not previously known to infect plants) and characterise the fungal communities of Betula , a non‐model organism with ample sequence data across individuals.

Techniques:

Journal: Molecular Ecology Resources

Article Title: Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch

doi: 10.1111/1755-0998.14056

Figure Lengend Snippet: PCoA of Sørenson dissimilarity across fungal communities (one or more taxa) detected from Betula ermanii, B. pendula , B. platyphylla , Buddleja alternifolia and Panicum virgatum . Different plant individuals are represented by blue circles. Plant taxa are represented by ‘spiders’.

Article Snippet: Using several datasets of publicly available raw Betula DNA sequence files from the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), we demonstrate how our pipeline can detect and inform on the abundance and rarity of plant‐associated fungi (including fungi not previously known to infect plants) and characterise the fungal communities of Betula , a non‐model organism with ample sequence data across individuals.

Techniques:

Journal: Molecular Ecology Resources

Article Title: Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch

doi: 10.1111/1755-0998.14056

Figure Lengend Snippet: Comparison of fungal taxa classified in a single individual. All classifications were made at species rank to taxa at BLAST scores over 0.99, using genomic libraries of different insert sizes prepared from Betula nana tissue.

Article Snippet: Using several datasets of publicly available raw Betula DNA sequence files from the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), we demonstrate how our pipeline can detect and inform on the abundance and rarity of plant‐associated fungi (including fungi not previously known to infect plants) and characterise the fungal communities of Betula , a non‐model organism with ample sequence data across individuals.

Techniques: Comparison