De novo assembly of the transcriptome of an invasive snail and its multiple ecological applications

Abstract

Studying how invasive species respond to environmental stress at the molecular level can help us assess their impact and predict their range expansion. Development of markers of genetic polymorphism can help us reconstruct their invasive route. However, to conduct such studies requires the presence of substantial amount of genomic resources. This study aimed to generate and characterize genomic resources using high throughput transcriptome sequencing for Pomacea canaliculata, a nonmodel gastropod indigenous to Argentina that has invaded Asia, Hawaii and southern United States. De novo assembly of the transcriptome resulted in 128,436 unigenes with an average length of 419 bp (range: 150-8556 bp). Many of the unigenes (2439) contained transposable elements, showing the existence of a source of genetic variability in response to stressful conditions. A total of 3196 microsatellites were detected in the transcriptome; among 20 of the randomly tested microsatellites, 10 were validated to exhibit polymorphism. A total of 15,412 single-nucleotide polymorphisms (SNPs) were detected in the ORFs. LC-MS/MS analysis of the proteome of juveniles revealed 878 proteins, of which many are stress related. This study has demonstrated the great potential of high throughput DNA sequencing for rapid development of genomic resources for a nonmodel organism. Such resources can facilitate various molecular ecological studies, such as stress physiology and range expansion.

Gene Discovery through Transcriptome Sequencing for the Invasive Mussel Limnoperna fortunei

“…Furthermore, taxonomically-restricted genes (TRGs) that allow species to adapt to specific ecological niches [16] usually account for 10 to 20% of total genes, with no resemblance in other species. The annotation generally tends to improve as more studies investigating the molecular mechanisms of mollusks are being developed [17], [18], [19].…”

Insights from an Integrated View of the Biology of Apple Snails (Caenogastropoda: Ampullariidae)

“…Sun et al (2012a) have made a significant step forward by conducting a de novo assembly of the transcriptome of P. canaliculata. They reported the identification of 128,436 unigenes with an average length of 419 bp and listed a number of genomic resources that may be useful for ecological and physiological studies including 2,439 unigenes with transposable elements, 3,196 microsatellites and 15,412 single-nucleotide polymorphisms.…”

Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi

“…Recent studies have attempted to elucidate the strategies responsible for various abiotic stresses in plants such as hybrids of Hordeum vulgare L. x Saccharum spp. (Janska et al, 2013;Guo et al, 2014), fish such as Pangasianodon hypophthalmus and Pagothenia borchgrevinki (Thanh et al, 2014;Bilyk and Cheng, 2014), and molluscs such as Mytilus galloprovincialis (Lockwood et al, 2010;Lockwood and Somero, 2011) and Pomacea canaliculata (Sun et al, 2012). As invasive species rapidly spread and successfully colonized throughout varying environments, they offer a great opportunity to study the causes and consequences of adaptability to rapidly changing environments.…”