Data from: A metagenetic approach for revealing community structure of marine planktonic copepods

Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure

Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association

Bombyx Vasa assembles Vasa bodies, the site of transposon silencing by Siwi and Ago3-piRISC formation. Here, the authors show Vasa sequesters transposon mRNAs in Vasa bodies via phase separation requiring RNA binding and self-association of Vasa

MOTU table for field-collected samples

MOTU list for field-collected samples at the 97% similarity threshold, with information of number of sequence reads in each station, Blast result, and representative sequences. The taxonomic order determined by the naϊve Bayesian classifier implemented in mothur is also listed

Raw data of morphological analysis

Morphological analysis of field-collected samples. Numbers of individuals (Inds.) and total dry weight (DW) for all species identified from each sampling location. Numbers of individuals and DW are calibrated into unsplit (1/1) samples

Sequence file for classification

Sequence file for the naϊve Bayesian classifier implemented in mothu

MOTU table for field-collected samples (99% similarity)

MOTU list for field-collected samples at the 99% similarity threshold, with information of number of sequence reads in each station, and representative sequences

Aligned LSU sequences of copepods

Aligned sequences of LSU D2 region registered in this study (GenBank accessions AB796399–AB796431 and AB820728–AB820803

MOTU table for artificial community sample

MOTU list for artificial community sample (33 morphologically identified species) at the 97% threshold, with information of number of sequence reads, Blast result and representative sequence

Taxonomy file for classification

Taxonomy file for the naϊve Bayesian classifier implemented in mothu

MID tag information

MID tag used in this study. Each sample was differentiated by unique multiplex identifier (MID) adaptors in GS Titanium Rapid Library MID Adaptors Kit (Roche)