The complete mitochondrial genome of the spot prawn,Pandalus platycerosBrandt in von Middendorf, 1851 (Decapoda: Caridea: Pandalidae), assembled from linked-reads sequencing

Abstract

Pandalus platyceros Brandt in von Middendorf, 1851, the spot prawn, is a commercially important pandalid shrimp that sustains a small fishery in the northeastern Pacific Ocean. We report, for the first time, the complete mitochondrial genome of P. platyceros, while also testing whether linked-reads sequencing (10X Genomics) data can be used to assemble complete and accurate mitochondrial genomes. The pipeline GetOrganelle assembled and circularized the complete mitochondrial chromosome of P. platyceros with an average coverage of 28.2x from a dataset of 5 M pairs of linked reads. The AT-rich mitochondrial genome of P. platyceros is 16,628 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 24 transfer RNA genes. One copy of all tRNA genes was present, except for tRNA-G, which had three copies. A single 1,077 bp-long intergenic space was assumed to be the D-loop/Control region. Selective pressure analysis indicated the PCGs were under purifying selection, although levels differed among genes. The highest KA:KS ratios were found in nad4 and nad4l, suggesting weaker purifying selection and environmental constraints on these genes. The KA:KS ratios for cob and cox1 were a magnitude lower than the ratios in other PCGs, suggesting strong purifying selection acting upon these genes. A maximum likelihood phylogenetic analysis based on all PCGs that included a total of 91 species of shrimps supported the monophyly of the infraorder Caridea and family Pandalidae. Furthermore, the monophyly of other caridean families, including Alvinocaridae, Atyidae, Thoridae, Lysmatidae, and Palaemonidae was also supported by the same analysis. Our results thus suggest that mitochondrial PCGs have enough phylogenetic information to resolve relationships at high taxonomic levels (families) in Caridea. This study contributes new genomic resources for this commercially important species and demonstrates that linked-reads sequencing can be used to assemble accurate mitochondrial genomes.

Comparison of Mitochondrial Genome Sequences between Two Palaemon Species of the Family Palaemonidae (Decapoda: Caridea): Gene Rearrangement and Phylogenetic Implications

“…to the distinct computational methods used [65]. However, our research results regarding the fourth major branch do not align with Cronin et al's study [19], where the family Rhynchocinetidae formed a separate branch, while the families Hippolytidae, Lysmatidae, and Thoridae were most closely related (Figure 7F).…”

“…Similarly, trnA, trnF, trnM, and trnT were also unable to form a secondary structure due to the lack of a TΨC loop. The phenomenon of tRNA gene loss of the TψC loop has also been observed in the genomes of some previous metazoans [13,19,64]. However, the remaining tRNAs of two species were capable of folding into a typical cloverleaf structure (Figure 4).…”

“…Using five nuclear genes, they constructed both Bayesian inference (BI) and maximum likelihood (ML) phylogenetic trees, which indicated a closer affinity between Alpheidae and Hippolytidae, while Palaemonidae formed a separate branch. Moreover, the internal phylogenetic positions of various families within Caridea have also shown discrepancies in previous molecular systematic studies [13,14,[17][18][19].…”

“…In the BI tree, the relationships of these four families were (((Hippolytidae + Rhynchocinetidae) + Thoridae) + Lysmatidae))). In order to better explore the phylogenetic relationships among the families within Caridea, we compiled the research findings of previous studies and represented the simplified phylogenetic relationships of these families in Figure 7, including A [13], B [14], C [15,16], D&E [18], F [19], G [17], H [20] (Figure 7).…”

“…The taxonomic status of the Palaemonidae family has also been a subject of interest in previous molecular systematic studies of the suborder Caridea. Most studies have proposed a close relationship between the Palaemonidae family and Alpheidae [13][14][15][16][17][18][19], but Li et al's research yielded different results [20]. Using five nuclear genes, they constructed both Bayesian inference (BI) and maximum likelihood (ML) phylogenetic trees, which indicated a closer affinity between Alpheidae and Hippolytidae, while Palaemonidae formed a separate branch.…”