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

Jianbo Yuan,Yamin Sun,Shihao Li,Lu Feng,Min Wang,Yi Gao,Guangyi Fan,Chengsong Zhang,Chengzhang Liu,Jianhai Xiang,Xiaojun Zhang,Xiaoxi Zhang,Yang Yu,Fei Liu,Fuhua Li,Jie Kong

doi:10.1038/s42003-021-01716-y

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.

Highlights

Simple sequence repeats (SSRs) are rare in most genomes and are generally considered to have no function
Based on the genome described in our previous study[2], we updated the genome assembly of L. vannamei to the chromosome level and de novo assembled the genome of another important penaeid shrimp, Fenneropenaeus chinensis
Based on the various sequencing data (Supplementary Tables 1–3), a high-quality de novo reference genome assembly of F. chinensis was obtained with a total length of 1.58 Gb and a contig N50 of 59.00 kb, comparable to that of the previously constructed genome assembly of L. vannamei[2]

Summary

Introduction

Simple sequence repeats (SSRs) are rare (approximately 1%) in most genomes and are generally considered to have no function. 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. A high proportion of SSRs (~10%) have been identified in the draft genomes of other penaeid shrimp[6] These findings raise questions about the functions of these significantly expanded SSRs, including their role in the adaptation and evolution of SSR-rich species. The penaeid shrimp, whose Penaeidae ancestor originated in the Late Devonian[18,19], are especially interesting in this regard as this group might have undergone at least three worldwide mass extinctions during its evolutionary history[2,20] These species present different ecological distributions and environmental adaptability traits[21]. Genome assembly Chromosome number Total length Scaffold number Contig N50 Scaffold N50 GC content Genome annotation Transposable elements SSRs Protein-coding genes

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Conclusion