Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp

Abstract

Simple sequence repeats (SSRs) are rare (approximately 1%) in most genomes and are generally considered to have no function. However, penaeid shrimp genomes have a high proportion of SSRs (>23%), raising the question of whether these SSRs play important functional and evolutionary roles in these SSR-rich species. Here, we show that SSRs drive genome plasticity and adaptive evolution in two penaeid shrimp species, Fenneropenaeus chinensis and Litopenaeus vannamei. Assembly and comparison of genomes of these two shrimp species at the chromosome-level revealed that transposable elements serve as carriers for SSR expansion, which is still occurring. The remarkable genome plasticity identified herein might have been shaped by significant SSR expansions. SSRs were also found to regulate gene expression by multi-omics analyses, and be responsible for driving adaptive evolution, such as the variable osmoregulatory capacities of these shrimp under low-salinity stress. These data provide strong evidence that SSRs are an important driver of the adaptive evolution in penaeid shrimp.

Fig. 1. Comparative genomics of penaeid shrimp and other arthropods.

a The pictures of F. chinensis and L. vannamei. b Synteny of the chromosome-level genomes assembled based on Hi-C data and a high-density linkage map of L. vannamei. Rearrangements were identified in four pseudochromosomes (red circles), and a Hi-C scaffold was found to be composed of two linkage groups (green circle). c Phylogenetic placement of penaeid shrimp in the arthropod phylogenetic tree. The numbers on the branches indicate the estimated divergence times (MYA). Error bars indicate 95% confidence levels. The SSR content for each species is shown in the right bar plot. d Comparison of the physical coverage and read mapping rates of the two penaeid shrimp genomes based on the Illumina sequencing data of various penaeid shrimp species. A positive value of log₂(Cov_Fch/Cov_Lva) indicates that the genome sequences of the corresponding species were more similar to that of F. chinensis, while a negative value indicates that the genome sequences of the corresponding species were more similar to that of L. vannamei. The line indicates the median value, the square symbol indicates the mean, the upper and lower box edges indicate the 75% and 25% quartiles, respectively, and the “X” indicates the outliers. * indicates significant difference between two groups of values (p < 0.01). e Principal component analysis (PCA) of SSR composition among arthropod genomes. f Comparison of SSR length and density of each type among three decapod genomes. The orange star indicates a significant variation (p < 0.05) between F. chinensis and L. vannamei, and the black star indicates a significant variation between L. vannamei and E. sinensis.

Fig. 2. Relationship between TEs and SSR expansion.

a Age distribution of major expanded TEs in the two penaeid shrimp genomes. According to previous studies, the substitution rate of decapods is 2 × 10⁻⁹ substitutions per site per year. b Percentage of TEs harboring SSRs in the two shrimp genomes. The SSRs located within TEs (hide bar) and 100 bp up- and downstream of TEs (orange and green bars) were counted separately. *Indicates significant difference (p < 0.05) of the TEs harboring SSRs between L. vannamei and F. chinensis. c Comparison of ancient and recent TEs that carrying SSRs. d Distribution of the number of TEs containing variable lengths of SSRs. Two peaks representing short and long SSRs were identified in the curve plot. e Comparison of TEs containg short and long SSRs. The stars indicate the significant differences with p < 0.05. The short and long SSRs were selected according to a curve plot of the numbers of TEs with different SSR lengths (Supplementary Fig. 19). Since a single peak (representing short SSRs) was observed in the length distribution of (AAT)_n, long (AAT)_n SSRs were considered those with lengths longer than 35 bp. f Comparison of SSR density in various TEs of F. chinensis and L. vannamei. A positive value of log₂(Density_Fch/Density_Lva) indicates that the SSR density in correspondent TE was higher in F. chinensis than L. vannamei, and verse versa. g Synteny of recently transposed TEs (Penelope). SSR elongations and new insertions (green circle) were identified in the transposed TEs.

Fig. 3. Intrachromosomal rearrangement in penaeid shrimp genomes.

a Heatmap of the orthologous gene numbers in each pair of chromosomes from the two shrimp genomes. b Intrachromosomal rearrangement between the homologous chromosomes of the two shrimp genomes. c Synteny of Hox genes and neighboring genes on the homologous chromosomes of the two shrimp species. d Relationship between rearrangement sites and SSRs. The rearrangement sites were calculated according to the paired-end read (Illumina 170 bp libraries) mapping results. When the distance between the paired mapping reads was longer than 50 kb, the site considered a candidate rearrangement site. The number of rearrangement sites in a window of 10 kb was calculated and compared between the shrimp used for genome sequencing and other populations of L. vannamei (Mexico, USA, and Thailand). The blue boxes show areas that have high chromosomal rearrangements and low SSR content, but sharp peaks of high SSR content adjacently.

Fig. 4. Multi-omic analyses of two penaeid shrimp species under low-salinity stress.

a KEGG enrichment analysis of the DEGs of L. vannamei (Lva) and F. chinensis (Fch). Only the pathways with significantly enriched DEGs (p < 0.05) are shown on the heatmap. NA indicates no DEGs identified in related pathways. b Expression patterns of the DEGs in different pathways. The number of DEGs and their corresponding expression patterns are shown in the yellow box at right. c Differentially regulated metabolites in penaeid shrimp under low-salinity stress. Metabolite levels were compared between the two shrimp species, and the metabolites were divided into four groups, namely, those differentially regulated in only L. vannamei (yellow background), those differentially regulated in only F. chinensis (orange background), those up- or downregulated consistently in both shrimp species (light blue background), and those with different regulation patterns between the two shrimp species (green background). A white background indicates no significant difference. d Correlations between DEGs and differentially regulated metabolites in the pathway of glycine, serine, and threonine metabolism in both the L. vannamei and F. chinensis genomes. e SSR contents in all identified peaks at 3% and 30% salinity and only the differential peaks (3% vs. 30%) identified by ATAC-seq. The differential peaks were identified according to various p values from differential analyses of ATAC-seq. f ATAC peak distribution and structure comparison of the glyA gene in both L. vannamei and F. chinensis. The brown lines indicate orthologous regions of the differential peaks in the genes.

Fig. 5. SSR expansion during penaeid shrimp evolutionary history.

Timescale of SSR expansion and relationships with the origination and divergence of penaeid shrimp.