Characterization of complete mitochondrial genome of coonstriped shrimp <i>Pandalus hypsinotus</i> (Decapoda: Pandalidae)

Kim, Nack-Keun; Andriyono, Sapto; Jung, Kyung Mi; Choi, Gwang Ho; Yoon, Tae-Ho; Kim, Hyun Woo

doi:10.1080/23802359.2018.1542987

Mitochondrial DNA Part B

2018

DOI: 10.1080/23802359.2018.1542987

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Characterization of complete mitochondrial genome of coonstriped shrimp Pandalus hypsinotus (Decapoda: Pandalidae)

Nack-Keun Kim

Sapto Andriyono

Kyung Mi Jung

et al.

Abstract: The complete mitochondrial genome of the coonstriped, Pandalus hypsinotus was determined by the MiSeq sequencing platform. The mitogenome of P. hypsinotus (15,909 bp) encoded the 13 protein-coding genes, 22 tRNA genes, two rRNA genes, non-coding, control region (D-Loop). Phylogenetic analysis based on the full mitochondrial genome sequences showed that P. hypsinotus is most closely related to P. borealis (86%) clustering together with Chlorotocus crassicornis in Pandalidae. The complete mitogenome sequence of … Show more

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Cited by 2 publications

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The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae)

Wang,

Zeng,

Zhang

et al. 2024

Mitochondrial DNA Part B

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We report the complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 . The mitogenome was found to contain 16158 bp with 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that R. brucei was sister to Rhynchocinetes durbanensis (PP= 1), of the same family Rhynchocinetidae. These results are helpful for research on the phylogenetic and evolutionary studies of this group.

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The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae)

Wang,

Zeng,

Zhang

et al. 2024

Mitochondrial DNA Part B

View full text Add to dashboard Cite

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

Cronin

Jones

Baeza

2022

Journal of Crustacean Biology

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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.

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Characterization of complete mitochondrial genome of coonstriped shrimp Pandalus hypsinotus (Decapoda: Pandalidae)

Cited by 2 publications

References 6 publications

The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae)

The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae)

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

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