DOI: 10.5061/dryad.k98sf7mhh
title: Data for: Harnessing environmental DNA (eDNA) to explore frugivorous interactions: A case study in Papaya (<em>Carica papaya</em>) and pineapple (<em>Ananas comosus</em>)

description: Plant-animal interactions (PAIs) are critical in ecosystem function,
 mediating energy flow and species interactions. Traditional methods of
 tracking PAIs, such as morphological identification and camera trapping,
 are limited in speed and scalability, posing challenges for comprehensive
 biodiversity monitoring. Recently, environmental DNA (eDNA) metabarcoding
 has emerged as a promising technique for detecting species interactions
 non-destructively. This pilot study explores the application of eDNA
 metabarcoding to investigate interactions involving partially consumed and
 intact fruits of Carica papaya and Ananas comosus. eDNA metabarcoding was
 performed from 36 partially consumed and 6 intact fruit samples.
 Metabarcoding of mitochondrial COI gene fragments revealed a diverse range
 of taxa, with Arthropoda, particularly insects, being the most abundant.
 Results indicated significant differences in taxonomic composition between
 pineapple and papaya samples, where both the fruits hold some unique as
 well as shared taxa. Furthermore, the diversity also differed between
 consumed and intact fruits, suggesting that partially consumed fruits
 serve as rich eDNA sources, capturing interactions with various frugivores
 and decomposers. Signals from various organisms detected through eDNA
 metabarcoding from consumed and damaged fruits allowed us to capture a
 wide array of taxa, revealing insights into species composition and
 ecological relationships. The unique ASVs associated with each fruit type
 suggest that certain taxa may be showing preferences based on fruit
 characteristics such as sugar content, texture, or chemical profile. The
 present work highlighted the importance of eDNA-based methods in
 unraveling the taxonomic composition of fruit-associated plant-animal
 interactions. This method needs limited taxonomic expertise, less labor,
 fast and effective, which can be implemented in monitoring ecological and
 economic species interactions.
description: Environmental DNA samples were sequenced through the Illumina
 MiSeq sequencing platform. 
description: # Data for: Harnessing environmental DNA (eDNA) to explore frugivorous
 interactions: A case study in Papaya (*Carica papaya*) and pineapple
 (*Ananas comosus*)
 [https://doi.org/10.5061/dryad.k98sf7mhh](https://doi.org/10.5061/dryad.k98sf7mhh) [https://doi.org/10.1002/edn3.70196](https://doi.org/10.1002/edn3.70196) ## Description of the data and file structure **1. General Information** **Title of Dataset** Harnessing Environmental DNA (eDNA) to Explore Frugivorous Interactions: A Case Study in Papaya (*Carica papaya*) and Pineapple (*Ananas comosus*) **Authors and Affiliations** * **Pritam Banerjee** - Department of Environmental Science, Policy, and Management, University of California * **Jyoti Prakash Maity** - Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, India * **Nalonda Chatterjee** - Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology * **Sven Weber** - Department of Environmental Science, Policy, and Management, University of California * **Gobinda Dey** - Department of Earth and Environmental Sciences, National Chung Cheng University, Taiwan * **Raju Kumar Sharma** - Department of Earth and Environmental Sciences, National Chung Cheng University, Taiwan * **Chien-Yen Chen** - Department of Earth and Environmental Sciences, National Chung Cheng University, Taiwan **Date of Data Collection** * Sampling Period: March-May, 2022 **Geographic Location** * Sampling Sites: Minxiong Township, Chiayi County, Taiwan **Contact Information** * **Contact Person:** Pritam Banerjee * **Email:** [[pritam8683@gmail.com](mailto:pritam8683@gmail.com)] * **Affiliation:** *Department of Environmental Science, Policy, and Management, University of California, University Avenue and Oxford St, Berkeley, CA 94720, USA* **2. Abstract** This dataset supports the study investigating plant-animal interactions (PAIs) using environmental DNA (eDNA) metabarcoding. The study focuses on partially consumed and intact fruits of papaya (*Carica papaya*) and pineapple (*Ananas comosus*). Using eDNA metabarcoding of mitochondrial COI gene fragments, the dataset reveals taxonomic compositions, highlighting significant differences between fruit types and consumption statuses. These findings emphasize the utility of eDNA-based approaches for ecological studies, offering insights into frugivory and decomposition. **3. Dataset Description** **Files Included** * taxonomy tables - Taxonomic assignments for Amplicon Sequence Variants (ASVs), including abundance data. * ASV_tax_species.tsv * ASV_tax.tsv * abundance tables - ASV tables used for the study (see in R scripts) * abundance_table.tsv * ASV_table.tsv * data analysis - R scripts for processing raw sequence data, conducting diversity analysis, and visualizing results. * 2024_eDNA_fruit.Rproj * 00source.R * 01xlsx.qmd * alpha_diversity.qmd * beta_diversity.qmd * tenary_plots.qmd * venn_diagrams.qmd * Raw Illumina files - Contains raw sequencing files in FASTQ format. * PN1.R1.fastq.gz * PN1.R2.fastq.gz * PN2.R1.fastq.gz * PN2.R2.fastq.gz * PN3.R1.fastq.gz * PN3.R2.fastq.gz * PN4.R1.fastq.gz * PN4.R2.fastq.gz * PN5.R1.fastq.gz * PN5.R2.fastq.gz * PN6.R1.fastq.gz * PN6.R2.fastq.gz * PNC.R1.fastq.gz * PNC.R2.fastq.gz * PP1.R1.fastq.gz * PP1.R2.fastq.gz * PP2.R1.fastq.gz * PP2.R2.fastq.gz * PP3.R2.fastq.gz * PP4.R1.fastq.gz * PP4.R2.fastq.gz * PP5.R1.fastq.gz * PP5.R2.fastq.gz * PP6.R1.fastq.gz * PP6.R2.fastq.gz * PPC.R1.fastq.gz * PPC.R2.fastq.gz * Raw Illumina stats - Sequencing facility stats * stats.txt **Variables in metadata.csv (only created in the script)** | **Column Name** | **Description** | | :--------------- | :---------------------------------------------------------- | | Sample\_ID | Unique identifier for each sample. | | Fruit\_Type | Type of fruit sampled (e.g., Papaya or Pineapple). | | Status | Consumption status of the fruit (e.g., Intact or Consumed). | | Location | Geographic location of the sampling site. | | Collection\_Date | Date the sample was collected. | **Variables in taxonomy_table.csv** | **Column Name** | **Description** | | :-------------- | :------------------------------------------------------------------------ | | ASV\_ID | Unique identifier for each Amplicon Sequence Variant (ASV). | | Taxonomy | Taxonomic classification of the ASV (e.g., Class, Order, Genus, Species). | | Abundance | Number of sequence reads associated with each ASV. | **4. Methods** **Sample Collection** * Samples of partially consumed and intact fruits were collected from Minxiong Township, Chiayi County, Taiwan 62102. * A total of 36 partially consumed and 6 intact fruit samples were processed. **DNA Extraction and Sequencing** * DNA was extracted using the DNeasy Blood & Tissue Kit. * The mitochondrial COI gene was amplified for metabarcoding. * Sequencing was conducted on the Illumina MiSeq. **Data Analysis** * Sequence reads were quality filtered and trimmed using Cutadapt (v3.4), DADA2. * Taxonomic assignments were performed using NCBI Blast. * Diversity analyses and visualizations were carried out in R using the vegan and phyloseq packages. **5. Usage Notes** * **Raw Data:** * FASTQ files can be re-analyzed using bioinformatics pipelines such as QIIME2 or DADA2. * **R Scripts:** * The provided R script includes all steps for preprocessing, diversity analysis, and visualization. **6. Licensing and Citation** **License** CC0 **Citation** Please cite this dataset as:\ Banerjee, P., et al. (2024). Dataset for: Harnessing Environmental DNA (eDNA) to Explore Frugivorous Interactions: A Case Study in Papaya (*Carica papaya*) and Pineapple (*Ananas comosus*). Dryad Digital Repository. [https://doi.org/10.xxxx](https://doi.org/10.xxxx) **7. Limitations** * The dataset reflects observations from specific geographic locations and sampling conditions. * Interpretation of species interactions may require consideration of environmental and ecological context.