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.

Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species

“…The Illumina paired-end sequencing data of four penaeid shrimp species ( L. vannamei , F. chinensis , P. monodon , and M. japonicus ) were collected from previous studies with the sequencing read length of 150 bp (PRJNA438564, PRJNA627295, PRJNA387410) ( Yuan et al, 2018 , 2021 ; Zhang et al, 2019 ). A total of 361.5 Gb data for L. vannamei , 160.9 Gb data for F. chinensis , 127.3 Gb data for P. monodon , and 127.5 Gb data for M. japonicus were collected.…”

“…The raw sequencing data were trimmed to filter out low-quality data and adapter contaminants by using the NGS QC Toolkit with the parameters of “2 A -c 10” ( Patel and Jain, 2012 ). The PacBio long-read sequencing data of L. vannamei and F. chinensis were collected from previous studies with the PacBio sequencing read N50 length of 11,205 and 9,813 bp, respectively (PRJNA438564 and PRJNA627295) ( Zhang et al, 2019 ; Yuan et al, 2021 ). A total of 132.8 Gb PacBio data for L. vannamei and 160.3 Gb PacBio data for F. chinensis were collected.…”

“…A total of 132.8 Gb PacBio data for L. vannamei and 160.3 Gb PacBio data for F. chinensis were collected. The final genome assembly sequences of L. vannamei , F. chinensis , and P. monodon were downloaded from the NCBI with the accession number of QCYY00000000 , JABKCB000000000 , and JABERT000000000 , respectively ( Zhang et al, 2019 ; Uengwetwanit et al, 2021 ; Yuan et al, 2021 ). These three genome assemblies were all assembled based on PacBio sequencing data.…”

“…However, the detailed mechanisms of these biological features are far from understood. Thus, numerous recent studies have tried to investigate these mechanisms through whole-genome sequencing (WGS) of penaeid shrimp ( Yuan et al, 2018 , 2021 ; Zhang et al, 2019 ; Uengwetwanit et al, 2021 ).…”

“…However, due to the high degree of genome complexity, penaeid shrimp has encountered extreme difficulties in genome sequencing and assembly, and the first penaeid shrimp genome was not completed until 2019 ( Zhang et al, 2019 ). Nowadays, only three high-quality genomes of penaeid shrimp have been reported, namely, L. vannamei , F. chinensis , and P. monodon ( Zhang et al, 2019 ; Uengwetwanit et al, 2021 ; Yuan et al, 2021 ). The draft assembly of M. japonicus is highly fragmented ( Yuan et al, 2018 ).…”