High-quality genome assembly of Chinese shrimp (Fenneropenaeus
chinensis) suggests genome contraction and adaptation to the environment
Abstract
A high-quality reference genome is necessary to determine the molecular
mechanisms underlying important biological phenomena; therefore, in the
present study, a chromosome-level genome assembly of the Chinese shrimp
Fenneropenaeus chinensis was performed. Muscle of a male shrimp was
sequenced using PacBio platform, and assembled by Hi-C technology. The
assembled F. chinensis genome was 1,465.32 Mb with contig N50 of 472.84
Kb, including 57.73% repetitive sequences, and was anchored to 43
pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026
protein-coding genes were predicted. The genome size of F. chinensis
showed significant contraction in comparison with that of other penaeid
species, which is likely related to migration observed in this species.
However, the F. chinensis genome included several expanded gene families
related to cellular processes and metabolic processes, and the
contracted gene families were associated with virus infection process.
The findings signify the adaptation of F. chinensis to the selection
pressure of migration and cold environment. Furthermore, the selection
signature analysis identified genes associated with metabolism,
phototransduction, and nervous system in cultured shrimps when compared
with wild population, indicating targeted, artificial selection of
growth, vision, and behavior during domestication. The construction of
the genome of F. chinensis provided valuable information for the further
genetic mechanism analysis of important biological processes, and will
facilitate the research of genetic changes during evolution.