Potamomics: The Potamopyrgus antipodarum genome/transcriptome projects
Potamopyrgus antipodarum is a New Zealand freshwater snail species characterized by the frequent coexistence of sexually and asexually reproducing individuals. As such, it is a model organism used extensively to study the maintenance of sex and the consequences of asexuality. Potamopyrgus antipodarum has also invaded streams and lakes in Europe, Australia, and North America, and is emerging as a model for invasion biology and ecotoxicology.
Here, we present transcriptomic and genomic data generated via 454 and Illumina high-throughput sequencing technologies. For the 454 project, we used mRNA from individuals representing both diploid sexual and polyploid asexual lineages in order to begin the process of identifying genetic and genomic differences between sexual and asexual P. antipodarum. Sexual P. antipodarum were represented by 5 individuals from each of two sexual lineages (descended from snails sampled from Lake Alexandrina and Lady Lake), and asexuals were represented by 5 individuals from each of two lineages descended from single asexual females from Lake Alexandrina and Lake Mapourika. We extracted and pooled the RNA from each lineage, made normalized cDNA libraries from the extracted RNA pools, and then sequenced the libraries with Roche 454 technology. We produced 494,054 reads with a total length of 116.7 Mbp.
Assembly was carried out with the assembler miraSearchESTSNPs (now available as an option in MIRA) using the default options for de novo assembly of 454 sequences. Assembly produced 41,396 contigs, with 20,900 contigs represented by more than one lineage. The average contig length is 614.7 bp, and a BLASTX search against NCBI's nr database showed that 22.8% of all contigs matched previously known sequences with an e-value of 10-5 or less.
Contig sequences were annotated using the BLAST2GO pipeline using the default cutoff options for annotation cutoff rules.
For the Illumina transcriptome projects, we sequenced the transcriptomes of 24 field-collected sexual diploids (23 females and 1 male), 6 field-collected asexual triploids (5 females and 1 male), and 3 field-collected tetraploids. These data are pooled in the "entire sequences", "ORF nucleotide sequences", and "ORF amino acid sequences" blast databases. We also sequenced the transcriptomes of ovarian tissue extracted from reproductively mature females ("ovary mRNA"). All snails were either collected from the New Zealand lakes Alexandrina, Kaniere, or Selfe or descended from individuals collected from these lakes. For the non-ovary-specific transcriptomes, we extracted and pooled the RNA from each lineage, made normalized cDNA libraries from the extracted RNA pools, and then sequenced the libraries with Illumina HiSeq technology. For the ovarian transcriptomes, we dissected and pooled the ovaries from multiple females, and then conducted RNA extractions, normalization, and Illumina sequencing with the pooled RNA. For the Illumina genomic DNA projects, we sequenced genomic DNA extracted from two different sexual P. antipodarum lineages ("Alexandrina Yellow" and "Ianthe") and three different asexual P. antipodarum lineages (Kaniere, Waikaremoana, and Poerua). We are currently in the process of analyzing the Illumina-generated data.
We are grateful to the Carver Center for Comparative Genomics, John Logsdon, Harsha Doddapaneni, Gery Hehman, Valerie Reeb, Daniela Vergara, Jeffrey Boore, Matthew Brockman, Rachel Gold, Peter Wilton, and Dan Sloan for assistance at various stages of this project. This project is funded in part by NSF-MCB grant #1122176 and in part by the Biological Sciences Funding Program.