Two complete mitogenomes of Ocypodoidea (Decapoda: Brachyura), Cleistostoma dilatatum (Camptandriidae) and Euplax sp. (Macrophthalmidae) and its phylogenetic implications
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Abstract: Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and molecular evolution. In the present study, two newly sequenced mitogenomes of Ocypodoidea (Cleistostoma dilatatum and Euplax sp.) were reported for the first time, which are 15 444 bp and 16 129 bp in length, respectively. Cleistostoma dilatatum is the first species in the family Camptandriidae whose complete mitogenome was sequenced. Each mitogenome contains an entire set of 37 genes and a putative control region, but their gene arrangements are largely different. Tandem duplication and random loss model is proposed to account for their gene arrangements. Comparative genomic analyses of 19 mitogenomes clustering in one branch reveal that 18 of them shared the same gene rearrangement, while that of C. dilatatum mitogenome was consistent with the ancestral gene arrangement of Brachyura. The dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. Phylogenetic analyses show that all Macrophalmidae species cluster together as a group, and then form a sister clade with Camptandriidae. Moreover, the polyphyly of three superfamilies (Ocypodoidea, Eriphioidea, and Grapsoidea) is reconfirmed. These findings help to confirm the phylogenetic position of Camptandriidae, as well as provide new insights into the phylogeny of Brachyura.
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Key words:
- Camptandriidae /
- Macrophthalmidae /
- mitogenome /
- gene rearrangement /
- phylogenetic analysis
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Figure 1. Gene maps of Cleistostoma dilatatum (a) and Euplax sp. (b) mitogenomes. Genes encoded on the heavy or light strands are shown outside or inside the circular gene map, respectively.
Figure 2. Amino acid composition in the mitogenome of Cleistostoma dilatatum (a) and Euplax sp. (b); relative synonymous codon usage in the mitogenome of C. dilatatum (c) and Euplax sp. (d). RSCU: relative synonymous codon usage.
Figure 3. Genetic distance (on average) and dN/dS substitution rates of 13 PCGs among 19 mitogenomes.
Figure 4. Multiple genome alignments of 19 mitogenomes. The mitogenome of Eriocheir sinensis at the top as the reference genome. All genomes are started from the COI gene. The number at the top of each genome shows nucleotide positions. Within each of the alignments, local collinear blocks are represented by blocks of the same color connected by lines.
Figure 5. Gene arrangements in Cleistostoma dilatatum (A) and Euplax sp. (B) mitogenome.
Figure 6. Inferred intermediate steps between the ancestral gene arrangement of crustaceans and two newly sequenced mitogenomes. The ancestral gene arrangement of crustaceans (A); the results of one tandem duplication and random loss (TDRL) event, the ancestral gene arrangement in Brachyuran mitogenome, and the final gene arrangement in Cleistostoma dilatatum mitogenome (B); the results of two TDRL events, the ancestral gene arrangement in Varunidae and Macrophthalmidae mitogenomes, and the final gene arrangement in Euplax sp. mitogenome (C). The duplicated gene block is underlined and the lost genes are labeled with gray.
Figure 7. Phylogenetic tree of brachyuran species inferred from the nucleotide sequences of 13 PCGs based on maximum likelihood (ML) and Bayesian inference (BI) analyses. The node marked with a solid circle indicates 100 ML bootstrap support and 100% BI posterior probability. The numbers after the species name are the GenBank accession number.
Table 1. Features of the mitochondrial genome of Cleistostoma dilatatum
Gene Position Length/bp Amino acid Start/Stop codon Anticodon Intergenic region Strand From To COI 1 bp 1534 bp 1534 511 ATG/T – 0 H Leu (L2) 1535 bp 1599 bp 65 – – TAA 6 H COII 1606 bp 2293 bp 688 229 ATG/T 0 H Lys (K) 2294 bp 2363 bp 70 – – TTT 0 H Asp (D) 2364 bp 2424 bp 61 – – GTC 1 H ATP8 2426 bp 2584 bp 159 52 ATG/TAA – –4 H ATP6 2581 bp 3252 bp 672 223 ATA/TAA – –1 H COIII 3252 bp 4041 bp 790 263 ATG/T – 0 H Gly (G) 4042 bp 4105 bp 64 – – TCC –3 H ND3 4103 bp 4456 bp 354 117 ATT/TAA – 4 H Ala (A) 4461 bp 4525 bp 65 – – TGC 4 H Arg (R) 4530 bp 4593 bp 64 – – TCG 0 H Asn (N) 4594 bp 4662 bp 69 – – GTT 0 H Ser (S1) 4663 bp 4729 bp 67 – – TCT 0 H Glu (E) 4730 bp 4795 bp 66 – – TTC 2 H His (H) 4798 bp 4862 bp 65 – – GTG 1 L Phe (F) 4864 bp 4928 bp 65 – – GAA –1 L ND5 4928 bp 6643 bp 1716 571 ATT/TAA – 53 L ND4 6697 bp 8034 bp 1338 445 ATG/TAA – –7 L ND4L 8028 bp 8330 bp 303 100 ATG/TAA – 9 L Thr (T) 8340 bp 8405 bp 66 – – TGT 0 H Pro (P) 8406 bp 8470 bp 65 – – TGG 2 L ND6 8473 bp 8976 bp 504 167 ATT/TAA – –1 H Cyt b 8976 bp 10 110 bp 1135 378 ATG/T – 0 H Ser (S2) 10 111 bp 10 177 bp 67 – – TGA 15 H ND1 10 193 bp 11 131 bp 939 312 ATA/TAA – 34 L Leu (L1) 11 166 bp 11 232 bp 67 – – TAG 0 L 16S 11 233 bp 12 546 bp 1314 – – – 0 L Val (V) 12 547 bp 12 619 bp 73 – – TAC 0 L 12S 12 620 bp 13 435 bp 816 – – – 0 L CR 13 436 bp 14 024 bp 589 – – – 0 H Ile (I) 14 025 bp 14 090 bp 66 – – GAT –3 H Gln (Q) 14 088 bp 14 156 bp 69 – – TTG 8 L Met (M) 14 165 bp 14 234 bp 70 – – CAT 0 H ND2 14 235 bp 15 245 bp 1011 336 ATT/TAG – –2 H Trp (W) 15 244 bp 15 315 bp 72 – – TCA 1 H Cys (C) 15 317 bp 15 380 bp 64 – – GCA 0 L Tyr (Y) 15 381 bp 15 444 bp 64 – – GTA –1 L Note: – represents no data. 
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Table 2. Features of the mitochondrial genome of Euplax sp.
Gene Position Length/bp Amino acid Start/Stop codon Anticodon Intergenic region Strand From To COI 1 bp 1539 bp 1539 512 ATG/TAA – –5 H Leu (L2) 1535 bp 1600 bp 66 – – TAA 8 H COII 1609 bp 2296 bp 688 229 ATG/T – 28 H ATP8 2325 bp 2486 bp 162 53 ATT/TAA – –4 H ATP6 2 483 bp 3154 bp 672 223 ATA/TAA – –1 H COIII 3154 bp 3943 bp 790 263 ATG/T – 0 H Gly (G) 3 944 bp 4006 bp 63 – – TCC –3 H ND3 4004 bp 4357 bp 354 117 ATA/TAA – 1 H Ala (A) 4359 bp 4422 bp 64 – – TGC 1 H Arg (R) 4424 bp 4487 bp 64 – – TCG 0 H Asn (N) 4488 bp 4554 bp 67 – – GTT 0 H Ser (S1) 4555 bp 4621 bp 67 – – TCT 6 H Thr (T) 4 628 bp 4689 bp 62 – – TGT 16 H Pro (P) 4 706 bp 4770 bp 65 – – TGG 10 L ND1 4781 bp 5707 bp 927 308 ATA/TAG – 33 L Leu (L1) 5741 bp 5807 bp 67 – – TAG 0 L 16S 5808 bp 7170 bp 1363 – – – 0 L 12S 7171 bp 8048 bp 878 – – – 0 L His (H) 8 049 bp 8113 bp 65 – – GTG –1 L ND5 8113 bp 9813 bp 1701 566 ATG/TAA – 125 L Val (V) 9939 bp 10 011 bp 73 – – TAG 0 L CR 10 012 bp 10 806 bp 795 – – – 0 H Gln (Q) 10 807 bp 10 875 bp 69 – – TTG 7 L Cys (C) 10 883 bp 10 944 bp 62 – – GCA 0 L Tyr (Y) 10 945 bp 11 010 bp 66 – – GTA 37 L Lys (K) 11 048 bp 11 116 bp 69 – – TTT 0 H Asp (D) 11 117 bp 11 182 bp 66 – – GTC 4 H Glu (E) 11 187 bp 11 249 bp 63 – – TTC –1 H Phe (F) 11 249 bp 11 314 bp 66 – – GAA 7 L ND4 11 322 bp 12 659 bp 1338 445 ATG/TAA – –7 L ND4L 12 653 bp 12 955 bp 303 100 ATG/TAA – 169 L ND6 13 125 bp 13 649 bp 525 174 ATT/TAA – –20 H Cyt b 13 630 bp 14 764 bp 1135 378 ATG/T – 0 H Ser (S2) 14 765 bp 14 830 bp 66 – – TGA 76 H Ile (I) 14 907 bp 14 971 bp 65 – – GAT 2 H Met (M) 14 974 bp 15 042 bp 69 – – CAT 0 H ND2 15 043 bp 16 053 bp 1011 336 ATG/TAG – –2 H Trp (W) 16 052 bp 16 121 bp 70 – – TCA 7 H Note: – represents no data.
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