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FEBS Open Bio
2020 Aug 01;108:1587-1600. doi: 10.1002/2211-5463.12914.
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Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers.
Yang F
,
Zhou C
,
Tran NT
,
Sun Z
,
Wu J
,
Ge H
,
Lu Z
,
Zhong C
,
Zhu Z
,
Yang Q
,
Lin Q
.
Abstract
Sea cucumber species are abundant (>1400 species) and widely distributed globally. mtDNA sequencing is frequently used to identify the phylogenetic and evolutionary relationships among species. However, there are no reports on the mitochondrial genome of Phyllophorus liuwutiensis. Here, we performed mtDNA sequencing of P. liuwutiensis to examine its phylogenetic relationships with other echinoderms. Its mitochondrial genome (15 969 bp) contains 37 coding genes, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Except for one protein-coding gene (nad6) and five tRNA genes encoded on the negative strand, all other genes were encoded on the positive strand. The mitochondrial bases of P. liuwutiensis were composed of 29.55% T, 22.16% C, 35.64% A and 12.64% G. The putative control region was 703 bp in length. Seven overlapping regions (1-10 bp) were found. The noncoding region between the genes ranged from 1 to 130 bp in length. One putative control region has been found in the P. liuwutiensis mitogenome. All of the tRNA genes were predicted to fold into a cloverleaf structure. In addition, we compared the gene arrangements of six echinoderms, revealing that the gene order of P. liuwutiensis was a new arrangement.
Fig. 1. The dorsal wall of the P. liuwutiensis. Tabular form (A), plates of sea cucumber (B), type rosettes (C) and type buttons (D). Scale bars: 10 μm (A, C, D); 50 μm (B).
Fig. 2. Gene map of the complete mitochondrial genome of P. liuwutiensis. Genes encoded on the positive and negative strands are shown outside and inside the circular gene map, respectively.
Fig. 3. RSCU in P. liuwutiensis mitogenome.
Fig. 4. Secondary structures of the 22 tRNA genes of P. liuwutiensis.
Fig. 5. Phylogenetic trees based on the concatenated amino acid of 13 PCGs. The Balanoglossus carnosus (NC001887.1) is used as outgroup. The red name highlights the species sequenced in this study. P. liuwutiensis (MN198190), Amphiura digitula (MH791160.1), Apostichopus japonicus (FJ986223.1), P. nigripunctatus (AB525762.1), Parastichopus parvimensis (KU168761.1), Parastichopus californicus (KP398509.1), Stichopus sp. SFâ2010 (HM853683.2), Stichopus horrens (HQ000092.1), Holothuria scabra (KP257577.1), Holothuria forskali (FN562582.1), Cucumaria miniata (AY182376.1), Benthodytes marianensis (MH208310.1), Freyastera benthophila (MG563681.1), Astropecten polyacanthus (AB183560.1), Acanthaster planci (AB231475.1), Echinaster brasiliensis (MG636999.1), Heliocidaris crassispina (KC479025.1), Heterocentrotus mammillatus (KJ680292.1), Strongylocentrotus droebachiensis (EU054306.1), Hemicentrotus pulcherrimus (KC490911.1), Florometra serratissima (NC001878.1), Phanogenia gracilis (DQ068952.1), Ophiura lutkeni (AY184223.1), Peniagone sp. YYHâ2013 (KF915304.1), Amphipholis squamata (FN562578.1) and Astrospartus mediterraneus (NC013878.1).
Fig. 6. Linear representation of gene rearrangements of P. liuwutiensis, Apostichopus japonicus, Florometra serratissima, Strongylocentrotus droebachiensis, Ophiura lutkeni, Acanthaster planci, Cucumaria miniata and Benthodytes marianensis. Gene segments are not drawn to scale. All genes are transcribed from left to right except those indicated by underlining, which are transcribed from right to left. The circling arrows indicate inversions. tRNA genes are represented by the corresponding singleâletter amino acid code, especially S1 (AGN), S2 (UCN), L1 (CUN) and L2 (UUR). rrnL and rrnS are the large and small rRNA subunits, respectively.
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