Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass

Abstract

Seagrasses are marine flowering plants found in tropical and sub-tropical areas that live in coastal regions between the sea and land. All seagrass species evolved from terrestrial monocotyledons, providing the opportunity to study plant adaptation to sea environments. Here, we sequenced the chloroplast genomes (cpGenomes) of three <i>Zostera</i> species, then analyzed and compared their cpGenome structures and sequence variations. We also performed a phylogenetic analysis using published seagrass chloroplasts and calculated the selection pressure of 17 species within seagrasses and nine terrestrial monocotyledons, as well as estimated the number of shared genes of eight seagrasses. The cpGenomes of <i>Zosteraceae</i> species ranged in size from 143,877 bp (<i>Zostera marina</i>) to 152,726 bp (<i>Phyllospadix iwatensis</i>), which were conserved and displayed similar structures and gene orders. Additionally, we found 17 variable hotspot regions as candidate DNA barcodes for <i>Zosteraceae</i> species, which will be helpful for studying the phylogenetic relationships and interspecies differences between seagrass species. Interestingly, nine genes had positive selection sites, including two ATP subunit genes (<i>atpA</i> and <i>atpF</i>), two ribosome subunit genes (<i>rps4</i> and <i>rpl20</i>), two DNA-dependent RNA polymerase genes (<i>rpoC1</i> and <i>rpoC2</i>), as well as <i>accD</i>, <i>clpP</i>, and <i>ycf2</i>. These gene regions may have played key roles in the seagrass adaptation to diverse environments. The Branch model analysis showed that seagrasses had a higher rate of evolution than terrestrial monocotyledons, suggesting that seagrasses experienced greater environmental pressure. Moreover, a branch-site model identified positively selected sites (PSSs) in <i>ccsA</i>, suggesting their involvement in the adaptation to sea environments. These findings are valuable for further investigations on <i>Zosteraceae</i> cpGenomes and will serve as an excellent resource for future studies on seagrass adaptation to sea environments.