Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis.

Koushirou Suga,David Mark Welch,Atsushi Hagiwara,Yoshitaka Sakakura,Yukari Tanaka

doi:10.1371/journal.pone.0000671

Abstract

BackgroundRotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking.Methodology/Principal FindingsWe generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy.Conclusions/SignificanceDespite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and can be browsed and searched at gmod.mbl.edu.

Highlights

Rotifera is one of the largest microinvertebrate phyla, in terms of both biomass and number of species
The fungal species Atkinsiella parasitica was isolated from eggs and body of B. plicatilis [29], and PCR with primers to small subunit ribosomal RNA (SSU rRNA) demonstrated the presence of bacteria including Afipia, Bosea, and Delftia, protozoa including Hartmannella, and fungi including Catenaria in seemingly axenic cultures (DMW, unpublished)
We obtained 2220 non-rRNA ESTs from our B. plicatilis cDNA library, which assembled into 530 unique contigs, 98 of which contained reads in forward and reverse orientation

Summary

Introduction

Rotifera is one of the largest microinvertebrate phyla, in terms of both biomass and number of species. The most well-studied are the euryhaline rotifers of the Brachionus plicatilis species complex Their widespread distribution and ease of culturing make this group a useful model system for studies of population dynamics [5,6,7,8,9], speciation [10,11,12,13,14], the evolution of sexual reproduction [15,16], and ecotoxicology [17,18,19,20]. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and can be browsed and searched at gmod.mbl.edu

Methods

Results

Conclusion