Abstract
Background: Marsupenaeus japonicus, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Due to the lack of genomic information, little is known about the correlations among codon usage bias, gene expression, and evolutionary trends in Marsupenaeus orthologs.Results: Using the CodonW 1.4.2 software, we performed the codon bias analysis of two Marsupenaeus species transcriptomes. The average contents of GC and ENc were 51.61% and 52.1 for VI (M. japonicus), 51.54% and 52.22 for VII (M. pulchricaudatus), respectively. Parity Rule 2 (PR2) plot analysis showed that purines (A and G) were used more frequently than pyrimidines (C and T) in two Marsupenaeus species. The average ENc value was 52.1 and 52.22 for M. japonicus and M. pulchricaudatus, respectively. Overall, orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that experienced purifying selection (ω < 1). In M. japonicus, the relationships were highly significant positive about Axis 1 and A3, T3 and ENc (p < 0.01). However, all relationships in M. pulchricaudatus were the opposite. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively. Two Marsupenaeus species had 31 different codon pairs. The results of multi-species clustering based on codon preference were consistent with traditional classification. Conclusions: We characterized the codon usage patterns of the two Marsupenaeus species and the evolutionary trends in Marsupenaeus orthologs, which provides new insights into the genetic divergence and the phylogenetic relationships of two Marsupenaeus species.