Dataset Information

Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

ABSTRACT:

Background

Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel.

Methodology/principle findings

Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups.

Conclusions

Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

SUBMITTER: Lindeque PK

PROVIDER: S-EPMC3820580 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Publications

Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

Lindeque Penelope K PK Parry Helen E HE Harmer Rachel A RA Somerfield Paul J PJ Atkinson Angus A

PloS one 20131107 11

<h4>Background</h4>Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from wh ...[more]

PMID: 24244737

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Project description:Structural and functional impacts of copy number variations (CNVs) on livestock genomes are not yet well understood. In this study, we have identified 1853 CNV regions (CNVRs) using population-scale sequencing data generated from 75 cattle of 8 breeds (Holstein, Angus, Jersey, Limousin, Romagnola, Brahman, Gir and Nelore). Individual genome sequence coverage ranged from 4 to 30 fold, with a mean of 11.8 fold. A total of 3.1% (87.5 Mb) of the cattle genome is predicted to be copy number variable, representing a substantial increase over the previous estimates (~2%). This dataset was highly correlated with array CGH data (r2 = 0.761) and was validated to be accurate with an estimated 12% false positive rate and a 19% false negative rate based on qPCR and array CGH, respectively. Hundreds of CNVs were found to be either breed specific or differentially variable across breeds, including the RICTOR gene in dairy breeds and the PNPLA3 gene in the beef breeds. In contrast, clusters of the PRP and PAG genes are duplicated in all sequenced animals, implicating that subfunctionalization, neofunctionalization or overdominance play a role in diversifying these fertility related genes. Further population-genetic analyses based on CNVs revealed the population structures of these taurine and indicine breeds and uncovered hundreds of positively selected CNV candidates near important functional genes. These CNV results provide a new glimpse of diverse selections during cattle speciation, domestication, breed formation, and recent genetic improvement. 25 animals were analyzed using a custom Nimblegen aCGH chip with 2.1 million probes. The reference animal chosen was L1 Dominette, a Hereford cow of European ancestry. The array was subjected to a dye-swap with the reference sample to test probe intensity fidelity. Single channel intensity data from the array was used in a digital aCGH analysis to compare aCGH copy number estimates to copy number estimates derived from sequence data. Briefly, the reference signal from all analyzed arrays was collected and a median signal intensity was calculated from probe intensities within the BTF3 gene. The copy number of the reference animal was then inferred by division of single channel probe intensities with the median intensity of the BTF3 gene. Next, test sample intensities were normalized by taking the log2 ratio of the test intensity divided by the normalized reference copy number for the probe. CN values derived from sequence data were also normalized in this fashion by taking the log2 of the ratio of NGS CN divided by aCGH reference copy number.

Dataset Information

Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

Background

Methodology/principle findings

Conclusions

Publications

Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

Similar Datasets

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