Semi-automated curation and manual addition of sequences to build reliable and extensive reference databases for ITS2 vascular plant DNA (meta-)barcoding

Quaresma, Andreia; García, Carlos Ariel Yadró; Rufino, José; Honrado, Mónica; Amaral, Joana S.; Brodschneider, Robert; Brusbardis, Valters; Gratzer, Kristina; Hatjina, Fani; Kilpinen, Ole; Pietropaoli, Marco; Roessink, Ivo; Steen, Jozef van der; Vejsnæs, Flemming; Pinto, M. Alice; Keller, Alexander

doi:10.1101/2023.06.12.544582

Cited by 2 publications

(1 citation statement)

References 63 publications

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“…Reads were first directly mapped iteratively with global alignments using VSEARCH against five flowering plant ITS2 reference databases (see below for construction details) for the study region and an identity cut-off threshold of at least 97% (higher percentages are prioritized). These references databases were created with BCdatabaser, then automatically curated 35 from GenBank entries with default parameters (length between 200 and 2000 bp, maximum nine sequences per species), from the following species lists: 1) all plant species recorded from IBGE. This database was then manually curated to remove voucher-less entries for greater trustworthiness.…”

Section: Methodsmentioning

confidence: 99%

Contrasting patterns of foraging behavior in neotropical stingless bees using pollen and honey metabarcoding

Martins,

Proença,

Vasconcelos

et al. 2023

Sci Rep

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Stingless bees are major flower visitors in the tropics, but their foraging preferences and behavior are still poorly understood. Studying stingless bee interactions with angiosperms is methodologically challenging due to the high tropical plant diversity and inaccessibility of upper canopy flowers in forested habitats. Pollen DNA metabarcoding offers an opportunity of assessing floral visitation efficiently and was applied here to understand stingless bee floral resources spectra and foraging behavior. We analyzed pollen and honey from nests of three distantly related stingless bee species, with different body size and social behavior: Melipona rufiventris, Scaptotrigona postica and Tetragonisca angustula. Simultaneously, we evaluate the local floristic components through seventeen rapid botanical surveys conducted at different distances from the nests. We discovered a broad set of explored floral sources, with 46.3 plant species per bee species in honey samples and 53.67 in pollen samples. Plant families Myrtaceae, Asteraceae, Euphorbiaceae, Melastomataceae and Malpighiaceae dominated the records, indicating stingless bee preferences for abundant resources that flowers of these families provide in the region. Results also reinforce the preference of stingless bees for forest trees, even if only available at long distances. Our high-resolution results encourage future bee-plant studies using pollen and honey metabarcoding in hyper-diverse tropical environments.

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Section: Methodsmentioning

confidence: 99%

Contrasting patterns of foraging behavior in neotropical stingless bees using pollen and honey metabarcoding

Martins,

Proença,

Vasconcelos

et al. 2023

Sci Rep

Self Cite

View full text Add to dashboard Cite

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High Resource Overlap and a Consistently Generalised Pattern of Interactions in a Bat–Flower Network in a Seasonally Dry Landscape

Tremlett,

Chapman,

Maher

et al. 2024

Ecology and Evolution

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Pollination is an ecosystem process that is crucial to maintain biodiversity and ecosystem function. Bats are important pollinators in the tropics and are an integral part of complex plant–pollinator interaction networks. However, network analysis–based approaches are still scarce at the plant species and bat community levels. We used metabarcoding to identify plant taxa present in pollen from fur and faecal samples collected across 1 year from three nectar‐feeding bat roosts in central Mexico. We calculated the frequency of occurrence of plant taxa and assembled a zoocentric network of bat–plant interactions. We constructed a year‐long network, encompassing the entire period of sampling, two seasonal networks comprising the wet and dry seasons, and six individual networks from sampling at two‐month intervals across the year. Four species of nectar‐feeding bats interacted with 36 plant species from 16 families. We found highly generalised interaction patterns across networks corresponding with opportunistic feeding behaviour by bats, with little seasonal variation in network structure. There was high resource overlap between bat species, and bats visited a diverse range of plant species even during periods with a high abundance of particular resources in the landscape. The diverse diet of nectar‐feeding bats emphasises the importance of floristically rich natural habitats in the landscape to provide reliable foraging resources year‐round in a seasonally variable system. While a generalised network structure is thought to increase robustness, further research is necessary to understand how fluctuations in pollinator abundance and diversity in the face of land use and climate change may impact bat–flower networks and the consequences to plant communities.

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Semi-automated curation and manual addition of sequences to build reliable and extensive reference databases for ITS2 vascular plant DNA (meta-)barcoding

Cited by 2 publications

References 63 publications

Contrasting patterns of foraging behavior in neotropical stingless bees using pollen and honey metabarcoding

Contrasting patterns of foraging behavior in neotropical stingless bees using pollen and honey metabarcoding

High Resource Overlap and a Consistently Generalised Pattern of Interactions in a Bat–Flower Network in a Seasonally Dry Landscape

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