The checklist of macrofungi of raised bogs: barcoding of accumulated collection following the 9-year plot-based monitoring in Northwestern Siberia

Study Extent

For molecular identification we used ITS region using primers ITS1F, ITS4 (for a few specimens other regions and primers accordingly).

Sampling

DNA extraction was done from dry exsiccata or freshly collected material using Diatom DNA Prep 200 or TransDirect® Plant Tissue PCR Kit following the standard protocols of these kits. The PCR was made using ready mix for PCR 5X ScreenMix (Evrogen). PCR and sequence reaction products were purified using Cleanup Standard (Evrogen), CleanMag DNA (Evrogen) and Dynabeads™ Sequencing Clean-Up kits. The sequencing was done with BrilliantDye™ Terminator (v3.1) Cycle Sequencing kit (NimaGen) using Applied Biosystems® Sanger Sequencing 3500 Series Genetic Analyzer.

Method steps

1. Sequence processing was made using BaseAlign and Mega11 software. The search of the nearest sequence was done through BLAST at NCBI and using UNITE SH matching. The resulted sequences were uploaded to GenBank and BOLD.
2. Fields in the Occurrence table: occurrenceID - ID of the record identificationRemarks - "Current identification is based on morphological and sequence analyses." for all specimens kingdom - Fungi verbatimIdentification - Previous identification based on morphological characters ScientificName - Current identification based on morpho- and sequence analysis identificationQualifier - Aff., sp Genbank Accession Number - Number of associated sequences in GenBank catalogNumber - Catalog number otherCatalogNumbers - Alternative catalog numbers basisOfRecord - Preserved specimen collectionCode - YSU-F country - Russian Federation stateProvince - Region county - Rayon locality - Locality decimalLatitude - Latitude decimalLongitude - Longitude eventDate - Date of specimen collection habitat - Vegetation description geodeticDatum - Datum recordedBy - Name of collector fieldNotes - Substrate associatedMedia - Macro- and micro- morphological images of the specimen Fields in the DNA-derived-data table: occurrenceID - key field target_subfragment - ITS, LSU, TEF seq_meth - Sanger sequencing pcr_primer_forward - sequence of formard primer used for pcr pcr_primer_reverse - sequence of formard primer used for pcr pcr_primer_name_forward - name of the forward primer used for pcr pcr_primer_name_reverse - name of the reverse primer used for pcr pcr_primer_reference - citation of the primer in literature DNA_sequence - sequence FASTA

The study site – the Mukhrino field station and the Mukhrino bog – located in the middle taiga zone of Western Siberia, nearby Khanty-Mansiysk (60.89N, 68.68E). The Mukhrino bog is an ombrotrophic landscape covering about 10 x 15 km, and located in the northern border of the large paludified area “Kondinskaya nizmennost”, on the left terrace of Irtysh river close to its confluence with Ob river. The vegetation of the raised bog represented by typical ombrotrophic or oligo-mesotrophic communities from classes Scheuchzerio-Caricetea nigrae, Oxycocco-Sphagnetea and Vaccinio-Piceetea.