Abstract
BackgroundKuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data.ResultsUsing CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification.ConclusionsThis study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.
Highlights
Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus
Nucleotide composition and Parity Rule 2 (PR2)-plot analysis A total of 9414 and 9420 unigenes with lengths larger than 400 bp were screened from M. japonicus and M. pulchricaudatus libraries, respectively (Fig. 1a)
The results indicated that Fragments Per Kilobase per Million (FPKM) was negatively correlated with T3s and A3s (p < 0.05) and positively correlated with other parameters (p < 0.05) in M. japonicus and M. pulchricaudatus
Summary
A major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. For different genes or genomes, the selection of synonymous codons is nonrandom, which is called codon usage bias (CUB) [4, 5]. Correspondence analysis proved that both selection and mutation pressure affect the codon usage pattern in Bungarus species [19]. Based on relative synonymous codon usage (RSCU) values, 27 species were clustered into two primary groups, which was consistent with the evolutionary status of these species [24]. According to these mentioned studies, codon usage showed evolutionary conservation and could be used for taxonomic differentiation
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