Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids

Abstract

Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor‐joining distance tree constructed using over 2,500 one‐to‐one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression.

Evolution and genetics of bighead and silver carps: Native population conservation versus invasive species control

“…Several studies suggest that a combination of genetic and environmental factors may contribute to the success of bighead and silver carp hybrids in the Mississippi River Basin (Lamer et al., 2019; Wang, Lamer, et al, 2016; Wang, Gaughan, et al, 2019). Further investigations using tracking systems such as a stationary acoustic telemetry array are needed to identify environmental factors that may drive the hybridization of bigheaded carp in the MRB (Coulter, Brey, et al, 2018).…”

“…We conducted a transcriptomic analysis of pure and hybrid bigheaded carps and found one of four hybrids studied had a significantly lower number of transcripts in important biological processes, indicating a potential loss of fitness in F1 hybrids (Wang, Lamer, & Gaughan, 2016). The transcriptomic comparison of pure and hybrid bighead carps allowed confident detection of introgression and hybridization history (Wang, Lamer et al, 2016).…”

Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin

“…We know very little about the evolutionary dynamics of parental species and their hybrids and the fate of further genomic introgression between them. We showed previously in a transcriptomic study that F 1 and backcrossed hybrids possessed pronounced variation in some Gene Ontology categories (Wang et al, ). Does this variation suggest the hybrids, even with the same genotypes, could have dissimilar fitness?…”

Stress response to low temperature: Transcriptomic characterization in Crassostrea sikamea × Crassostrea angulata hybrids

“…Pathway analysis was based on KEGG enrichment (Wang et al., ), in which a total of 13,207 unigenes were divided into five major classifications containing environmental information processing, metabolism, cellular processes, organismal systems and genetic information processing. The most significantly represented pathways were as follows: transport and catabolism (859, 6.5%), signal transduction (1649, 12.5%), translation (947, 7.2%), carbohydrate metabolism (964, 7.3%) and Endocrine system (902, 6.8%), respectively (Figure ).…”