msGBS: A new high-throughput approach to quantify relative species abundance in root samples of multi-species plant communities

Wagemaker, Cornelis A. M.; Mommer, Liesje; Visser, Eric J. W.; Weigelt, Alexandra; Gurp, Thomas van; Postuma, Maarten; Smit‐Tiekstra, Annemiek E.; Kroon, Hans de

doi:10.22541/au.159414250.09715006

Cited by 6 publications

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“…gDNA libraries were then prepared largely in accordance with the genotype by sequencing (GBS) approach by Elshire et al. (2011; Wagemaker et al, in review). In short, genome complexity was reduced by digesting 300 ng gDNA by two restriction enzymes ( Pac I and Nsi I) after which two indexed adapters were ligated to each gDNA fragment (Table ).…”

Section: Methodsmentioning

confidence: 99%

“…Root proportions were calculated according to Wagemaker et al (in review) using a multispecies genotype by sequencing (msGBS) approach. This involved mapping of the multispecies root samples taken from the mesocosm compartments to a metareference genome sequence database which contained DNA clusters of each of the mesocosm plant species to determine the proportion of each species root material in the mesocosm root samples.…”

Section: Methodsmentioning

confidence: 99%

“…In the eight‐species mesocosm communities, we left open patches containing soil conditioned by one of the species using inoculum soil from the field site, comparable to the soil conditioning approach used in plant‐soil feedback experiments. During two subsequent growing seasons, we determined root colonization at two soil depths inside the conditioned soil patches using a novel sequencing‐based approach to identify plant roots to species level (Wagemaker et al, in review). Moreover, we injected a mixture of nutrient tracers in the soil patches and measured tracer uptake by the species surrounding the patch.…”

Section: Introductionmentioning

confidence: 99%

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Local soil legacy effects in a multispecies grassland community are underlain by root foraging and soil nutrient availability

et al. 2020

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Local soil legacy effects in a multispecies grassland community are underlain by root foraging and soil nutrient availability

et al. 2020

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“… b Assuming a mean value of 102,155 genomic regions per species (clusters) and 238 bp per cluster (Wagemaker et al, 2021). …”

Section: Amplicon Metabarcoding Genotype By Sequencing Chloroplast Mementioning

confidence: 99%

“… i Although when there are closely related species, many clusters are filtered out for being too similar among species (Wagemaker et al, 2021). …”

Section: Amplicon Metabarcoding Genotype By Sequencing Chloroplast Mementioning

confidence: 99%

Genotype by sequencing: An alternative new method to amplicon metabarcoding and shotgun metagenomics for the assessment of eukaryote biodiversity

Piñol

2021

Molecular Ecology Resources

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The use of high‐throughput DNA sequencing (HTS) has revolutionized the assessment of biodiversity in plant and animal communities. There are two main approaches to estimate the identity and the relative species abundance (RSA) in complex mixtures using HTS: amplicon metabarcoding and shotgun metagenomics. While amplicon metabarcoding targets one or a few genomic regions, shotgun metagenomics randomly explores the genome of the species. In this issue of Molecular Ecology Resources, Wagemaker et al. (2021) present a new method, multi‐species Genotyping by Sequencing (msGBS), as an alternative middle ground between metabarcoding and metagenomics. They apply the technique to mixtures of plant roots and report the remarkable capacity of msGBS to estimate the RSA. If validated in other laboratories and biological communities, msGBS might become a third method to explore the biodiversity of biological communities, especially of plants, where current techniques are struggling to get sufficient taxonomic resolution.

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et al. 2021

Molecular Ecology Resources

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msGBS: A new high-throughput approach to quantify relative species abundance in root samples of multi-species plant communities

Cited by 6 publications

References 0 publications

Local soil legacy effects in a multispecies grassland community are underlain by root foraging and soil nutrient availability

Local soil legacy effects in a multispecies grassland community are underlain by root foraging and soil nutrient availability

Genotype by sequencing: An alternative new method to amplicon metabarcoding and shotgun metagenomics for the assessment of eukaryote biodiversity

Editorial 2022

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