Optimization of the second internal transcribed spacer (ITS2) for characterizing land plants from soil. 2020

Emma K Timpano, and Melissa K R Scheible, and Kelly A Meiklejohn
Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America.

Molecular-based taxonomy, specifically DNA barcoding, has streamlined organism identification. For land plants, the recommended 2-locus barcode of rbcL and matK is not suitable for all groups, thus the second subunit of the nuclear internal transcribed spacer (ITS2) has received attention as a possible alternative. To date, evaluations of ITS2 have mostly been limited in scope to specific plant orders/families and single source material. Prior to using ITS2 to routinely characterize land plants present in environmental samples (i.e., DNA metabarcoding), a wet lab protocol optimized for bulk sample types is needed. To address this gap, in this study we determined the broad recoverability across land plants when using published ITS2 primer pairs, and subsequently optimized the PCR reaction constituents and cycling conditions for the best two performing primer pairs (ITS2F/ITSp4 and ITSp3/ITSu4). Using these conditions, both primer pairs were used to characterize land plants present in 17 diverse soils collected from across the US. The resulting PCR amplicons were prepared into libraries and pooled for sequencing on an Illumina® MiniSeq. Our existing bioinformatics workflow was used to process raw sequencing data and taxonomically assign unique ITS2 plant sequences by comparison to GenBank. Given strict quality criteria were imposed on sequences for inclusion in data analysis, only 43.6% and 7.5% of sequences from ITS2F/ITSp4 and ITSp3/ITSu4 respectively remained for taxonomic comparisons; ~7-11% of sequences originated from fungal co-amplification. The number of orders and families recovered did differ between primer pairs, with ITS2F/ITSp4 consistently outperforming ITSp3/ITSu4 by >15%. Primer pair bias was observed in the recovery of certain taxonomic groups; ITS2F/ITSp4 preferentially recovered flowering plants and grasses, whereas ITSp3/ITSu4 recovered more moss taxa. To maximize data recovery and reduce potential bias, we advocate that studies using ITS2 to characterize land plants from environmental samples such as soil use a multiple primer pair approach.

UI MeSH Term Description Entries
D012987 Soil The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants. Peat,Humus,Soils
D016133 Polymerase Chain Reaction In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships. Anchored PCR,Inverse PCR,Nested PCR,PCR,Anchored Polymerase Chain Reaction,Inverse Polymerase Chain Reaction,Nested Polymerase Chain Reaction,PCR, Anchored,PCR, Inverse,PCR, Nested,Polymerase Chain Reactions,Reaction, Polymerase Chain,Reactions, Polymerase Chain
D044002 Bryophyta A division of the plant kingdom. Bryophyta contains the subdivision, Musci, which contains the classes: Andreaeopsida, BRYOPSIDA, and SPHAGNOPSIDA. Andreaeopsida,Mosses, Granite,Musci,Mosses,Andreaeopsidas,Bryophytas,Granite Mosse,Granite Mosses,Mosse,Mosse, Granite,Muscus
D056186 Metagenomics The systematic study of the GENOMES of assemblages of organisms. Community Genomics,Environmental Genomics,Population Genomics,Genomics, Community,Genomics, Environmental,Genomics, Population
D058893 DNA Barcoding, Taxonomic Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode". DNA Barcode, Taxonomic,Phylogenetic DNA Barcode,Phylogenetic DNA Barcoding,Taxonomic DNA Barcode,Taxonomic DNA Barcodes,Taxonomic DNA Barcoding,Barcode, Phylogenetic DNA,Barcode, Taxonomic DNA,Barcodes, Phylogenetic DNA,Barcodes, Taxonomic DNA,Barcoding, Phylogenetic DNA,Barcoding, Taxonomic DNA,Barcodings, Phylogenetic DNA,Barcodings, Taxonomic DNA,DNA Barcode, Phylogenetic,DNA Barcodes, Phylogenetic,DNA Barcodes, Taxonomic,DNA Barcoding, Phylogenetic,DNA Barcodings, Phylogenetic,DNA Barcodings, Taxonomic,Phylogenetic DNA Barcodes,Phylogenetic DNA Barcodings,Taxonomic DNA Barcodings
D018744 DNA, Plant Deoxyribonucleic acid that makes up the genetic material of plants. Plant DNA
D019684 Magnoliopsida A class of vascular plants which produce flowers and seeds. They include monocotyledons, dicotyledons, and about 80% of all known plant species. Angiosperms,Angiosperma,Angiospermae,Arecidae,Asteridae,Caryophyllidae,Commelinidae,Dicotyledoneae,Dilleniidae,Flowering Plants,Hamamelidae,Hamamelididae,Icacinales,Liliatae,Liliidae,Liliopsida,Magnoliatae,Metteniusales,Oncothecales,Rosidae,Vahliales,Zingiberidae,Angiosperm,Flowering Plant,Icacinale,Metteniusale,Oncothecale,Plant, Flowering,Plants, Flowering,Vahliale
D021901 DNA, Intergenic Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions. DNA, Junk,DNA, Spacer,Intergenic DNA,Junk DNA,Spacer DNA,Intercistronic Region,Intercistronic Sequence,Intergenic Region,Intergenic Sequence,Sequence, Intergenic,DNAs, Intergenic,DNAs, Junk,DNAs, Spacer,Intercistronic Regions,Intercistronic Sequences,Intergenic DNAs,Intergenic Regions,Intergenic Sequences,Junk DNAs,Region, Intercistronic,Region, Intergenic,Regions, Intercistronic,Regions, Intergenic,Sequence, Intercistronic,Sequences, Intercistronic,Sequences, Intergenic,Spacer DNAs
D029624 Ferns Seedless nonflowering plants of the class Filicinae. They reproduce by spores that appear as dots on the underside of feathery fronds. In earlier classifications the Pteridophyta included the club mosses, horsetails, ferns, and various fossil groups. In more recent classifications, pteridophytes and spermatophytes (seed-bearing plants) are classified in the Subkingdom TRACHEOPHYTA (also known as Tracheophyta). Blechnum,Blechnums,Fern

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