De novo assembly and characterization of the invasive Northern Pacific Seastar transcriptome

Invasive species are a major threat to global biodiversity but can also serve as valuable model systems to examine important evolutionary processes. While the ecological aspects of invasions have been well documented, the genetic basis of adaptive change during the invasion process has been hampered by a lack of genomic resources for the majority of invasive species. Here we report the first larval transcriptomic resource for the Northern Pacific Seastar, Asterias amurensis, an invasive marine predator in Australia. Approximately 117.5 million 100 base-pair (bp) paired-end reads were sequenced from a single RNA-Seq library from a pooled set of full-sibling A. amurensis bipinnaria larvae. We evaluated the efficacy of a pre-assembly error correction pipeline on subsequent de novo assembly. Error correction resulted in small but important improvements to the final assembly in terms of mapping statistics and core eukaryotic genes representation. The error-corrected de novo assembly resulted in 115,654 contigs after redundancy clustering. 41,667 assembled contigs were homologous to sequences from NCBI's non-redundant protein and UniProt databases. We assigned Gene Ontology, KEGG Orthology, Pfam protein domain terms and predicted protein-coding sequences to > 36,000 contigs. The final transcriptome dataset generated here provides functional information for 18,319 unique proteins, comprising at least 11,355 expressed genes. Furthermore, we identified 9,739 orthologs to P. miniata proteins, evaluated our annotation pipeline and generated a list of 150 candidate genes for responses to several environmental stressors that may be important for adaptation of A. amurensis in the invasive range. Our study has produced a large set of A. amurensis RNA contigs with functional annotations that can serve as a resource for future comparisons to other echinoderm transcriptomes and gene expression studies. Our data can be used to study the genetic basis of adaptive change and other important evolutionary processes during a successful invasion.

Preference for feeding at habitat edges declines among juvenile blue crabs as oyster reef patchiness increases and predation risk grows

Both habitat patchiness and behaviorally-mediated indirect effects (BMIEs; predator- induced changes in prey behavior that affect the prey's resources) are important in many food webs, but the relationships between these 2 factors have yet to be investigated. To explore effects of habitat patchiness and variation in perceived risk of predation on food-web dynamics, we conducted a factorial experiment in a model aquatic food chain of predator-prey-resource using 2 contrasting predators (adult blue crab Callinectes sapidus and toad fish Opsanus tau), juvenile blue crab as prey, and mussel Geukensia demissa as resource. Both predator presence and habitat patchiness influenced the prey's preference for consuming resources at patch edges instead of interiors. The preference of prey for consuming resources at habitat edges was 4 times stronger in continuous oyster reef habitat than in smaller habitat patches. This suggests that interior resources in continuous habitat experience a refuge from consumption, but this refuge is largely lost in patchy habitat. The mere presence of predators reduced the prey's preference for consuming resources at habitat edges. This BMIE was significant for the ambush predator (toadfish) and the treatment containing both predators, but not for the actively hunting predator (adult blue crab). We conclude that habitat patchiness and predator presence can jointly affect resource distribution by inducing shifts in prey foraging behavior, revealing a need to incorporate BMIEs into habitat fragmentation studies. This conclusion has broad and growing relevance as anthropogenic factors increasingly modify predator abundances and fragment coastal habitats. © Inter-Research 2012.