Adaptive Differences in Gene Expression in Farm-Impacted Seedbeds of the Native Blue Mussel Mytilus chilensis

Abstract

The study of adaptive population differences is relevant for evolutionary biology, as it evidences the power of selective local forces relative to gene flow in maintaining adaptive phenotypes and their underlying genetic determinants. However, human-mediated hybridization through habitat translocations, a common and recurrent aquaculture practice where hybrids could eventually replace local genotypes, risk populations' ability to cope with perturbations. The endemic marine mussel Mytilus chilensis supports a booming farming industry in the inner sea of Chiloé Island, southern Chile, which entirely relies on artificially collected seeds from natural beds that are translocated to ecologically different fattening centers. A matter of concern is how farm-impacted seedbeds will potentially cope with environmental shifts and anthropogenic perturbations. This study provides the first de novo transcriptome of M. chilensis; assembled from tissue samples of mantles and gills of individuals collected in ecologically different farm-impacted seedbeds, Cochamó (41°S) and Yaldad (43°S). Both locations and tissue samples differentially expressed transcripts (DETs) in candidate adaptive genes controlling multiple fitness traits, involved with metabolism, genetic and environmental information processing, and cellular processes. From 189,743 consensus contigs assembled: 1,716 (Bonferroni p _value ≤ 0.05) were DETs detected in different tissues of samples from different locations, 210 of them (fold change ≥ | 100|) in the same tissue of samples from a different location, and 665 (fold change ≥ | 4|) regardless of the tissue in samples from a different location. Site-specific DETs in Cochamó (169) and Yaldad (150) in candidate genes controlling tolerance to temperature and salinity shifts, and biomineralization exhibit a high number of nucleotide genetic variants with regular occurrence (frequency > 99%). This novel M. chilensis transcriptome should help assessing and monitoring the impact of translocations in wild and farm-impacted mussel beds in Chiloé Island. At the same time, it would help designing effective managing practices for conservation, and translocation traceability.

Keywords: Mytilus chilensis; adaptative differences; farm-impacted seedbeds; gene expression; genetic variants; transcriptome.

FIGURE 1

(A) A map indicating the geographical locations of the samplings, Cochamó (north) and Yaldad (south), and seawater temperature for March 2018. (B) Seawater conditions variations between June 2017 and May 2018.

FIGURE 2

3D-PCA plot (A) resulting from the principal components analysis by replicating local samples from Cochamó and Yaldad. Heat map (B) representing a visual distribution by tissue and location of the up-regulated DETs of individuals from Cochamó and Yaldad. LCo, local individuals from Cochamó and LYa, locals from Yaldad. _m, mantle samples and _g, gill samples.

FIGURE 3

Intra-location by tissue comparison. The number (bars) of differentially expressed transcripts (DETs) by location are in the central plot (A); the number of up-regulated (UR-) DET from mantle tissue by location is in negative values. Also are showed the top twenty exclusive annotated UR-DETs from gills (B) and mantle (C) tissues for samples from Cochamó (left) and Yaldad (right, D,E, respectively). LCo, local individuals from Cochamó and LYa, locals from Yaldad. _m, mantle samples and _g, gill samples.

FIGURE 4

Inter-location by tissue comparison. The number (bars) of differentially expressed transcripts (DETs) by tissue are in the central plot (A); the number of up-regulated (UR-) DETs from gills and mantle tissues for Yaldad are in negative values. Also are showed the top twenty exclusive annotated UR-DETs from gill samples from Cochamó (B) and Yaldad (C). Top twenty exclusive annotated UR-DETs from the mantle are in (D) for Cochamó and (E) samples for Yaldad. LCo, local individuals from Cochamó and LYa, locals from Yaldad. _m, mantle samples and _g, gill samples.

FIGURE 5

Comparison by location. The number of differentially expressed transcripts (DETs) by location (bars) are in the central plot (A); the number of the up-regulated (UR-) DETs of samples from Yaldad are in negative values. Also are showed, sorted by fold change, the top thirty-five exclusive annotated UR-DETs for samples from Cochamó (B) and Yaldad (C). LCo, local individuals from Cochamó and LYa, locals from Yaldad.

FIGURE 6

KEGG categorization of differentially expressed transcripts (DETs) for intra-location by tissue comparison. The KEGG terms represented by up-regulated (UR-) DETs from Cochamó are in (A) and those represented by samples from UR-DETs from Yaldad in (B). LCo, local individuals from Cochamó and LYa, locals from Yaldad. _m, mantle samples and _g, gill samples.

FIGURE 7

KEGG categorization of differentially expressed transcripts (DETs) for inter-location by tissue comparison. The KEGG terms represented by samples from gills tissue are in (A) and those represented by samples from mantle are in (B). LCo, local individuals from Cochamó and LYa, locals from Yaldad. _m, mantle samples and _g, gill samples.

FIGURE 8

KEGG categorization of the differentially expressed transcripts (DETs) of the comparison by location. LCo, local individuals from Cochamó and LYa, locals from Yaldad.