Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

Ying Zhang Li Gong Xinting Lu Zengliang Miao Lihua Jiang Bingjian Liu Liqin Liu Pengfei Li Xu Zhang Zhenming Lü

Ying Zhang, Li Gong, Xinting Lu, Zengliang Miao, Lihua Jiang, Bingjian Liu, Liqin Liu, Pengfei Li, Xu Zhang, Zhenming Lü. Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications[J]. Acta Oceanologica Sinica. doi: 10.1007/s13131-021-1927-7
Citation: Ying Zhang, Li Gong, Xinting Lu, Zengliang Miao, Lihua Jiang, Bingjian Liu, Liqin Liu, Pengfei Li, Xu Zhang, Zhenming Lü. Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications[J]. Acta Oceanologica Sinica. doi: 10.1007/s13131-021-1927-7

doi: 10.1007/s13131-021-1927-7

Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

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    Corresponding author: nblzmnb@163.com
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  • Figure  1.  The base skews of 13 PCGs of 16 Varunidae mitogenomes. (A) GC-skews, (B)AT-skews.

    Figure  2.  Structure of control region in 16 Varunidae mitogenomes. The colored ovals indicate the tandem repeats; the remaining regions are shown with green boxes. The tandem repeat with copy number exceeding 7 is displayed in the format of (motif)n.

    Figure  3.  (A) Sliding window analyses of 13 PCGs and two rRNAs among 16 Varunidae mitogenomes. The red line shows the value of nucleotide diversity (Pi) in a sliding window analysis (a sliding window of 200 bp with a step size of 20 bp). Gene names and the Pi value of each gene are indicated above the graph. (B) Genetic distance (on average) and dN/dS substitution rates of 13 PCGs among 16 Varunidae species.

    Figure  4.  Phylogenetic trees of Varunidae species inferred from 13 PCGs based on different methods. (A) nucleotide sequences based on maximum likelihood (ML) and Bayesian inference (BI) analysis; (B) amino acid sequences based on maximum likelihood (ML) analysis; (C) amino acid sequences based on Bayesian inference (BI) analysis. Node marked with a solid circle indicates 100 maximum likelihood bootstrap value and 100% supporting value.

    Figure  5.  Phylogenetic tree of Brachyuran species inferred from the nucleotide sequences of 13 PCGs based on maximum likelihood (ML) and Bayesian inference (BI) analysis. Node marked with a solid circle indicates 100 maximum likelihood bootstrap value and 100% supporting value.

    Figure  6.  Inferred intermediate steps between the ancestral gene arrangement of crustaceans and Varunidae mitogenomes. (A) The ancestral gene arrangement of crustaceans; (B) The results of one TDRL event and the ancestral gene arrangement of Brachyura; (C) The results of two TDRL events and the final gene arrangement in V. litterata and 15 other varunid species. The duplicated gene block is underlined and the lost genes are labeled with gray.

    Table  1.   Features of the mitochondrial genome of V. litterata

    GenePositionLength
    (bp)
    Amino
    acid
    Start/Stop
    codon
    AnticodonIntergenic
    region
    Strand
    FromTo
    COI115341534511ATG/T0H
    Leu (L2)1535160066TAA5H
    COII16062310705234ATG/TAA12H
    ATP82323248416253ATG/TAA-7H
    ATP624783152675224ATT/TAA-1H
    COIII31523943792263ATG/TAA-1H
    Gly (G)3943400765TCC0H
    ND340084358351116ATT/TAA1H
    Ala (A)4360442263TGC2H
    Arg (R)4425448763TCG-1H
    Asn (N)4487455165GTT0H
    Ser (S1)4552461867TCT22H
    Thr (T)4641470565TGT2H
    Pro (P)4708477164TGG20L
    ND147925727936311ATG/TAA31L
    Leu (L1)5759582567TAG0L
    16S5826719813730L
    12S719980878890L
    His (H)8088815063GTG6L
    ND5815798901734577ATA/TAA126L
    Val (V)10,01710,08973TAC0L
    CR10,09011,18510960H
    Gln (Q)11,18611,25469TTG11L
    Cys (C)11,26611,32863GCA0L
    Tyr (Y)11,32911,39365GTA2L
    Lys (K)11,39611,46570TTT-2H
    Asp (D)11,46411,53168GTC6H
    Glu (E)11,53811,60265TTC2H
    Phe (F)11,60511,66965GAA14L
    ND411,68413,0211338445ATG/TAG-7L
    ND4L13,01513,326312103ATA/TAA87L
    ND613,41413,923510169ATT/TAA-1H
    Cyt b13,92315,0571135378ATG/T0H
    Ser (S2)15,05815,12467TGA20H
    Ile (I)15,14515,20965GAT4H
    Met (M)15,21415,28168CAT0H
    ND215,28216,2921011336ATC/TAG-2H
    Trp (W)16,29116,35868TCA9H
    下载: 导出CSV

    Table  2.   Composition and skewness of V. litterata mitogenome

    A%T%G%C%A+T%AT-skewGC-skewLength(bp)
    Mitogenome35.236.210.817.871.4−0.014−0.24316,368
    PCGs28.240.315.616.068.4−0.177−0.01111,195
    COI27.835.216.920.163.0−0.118−0.0881539
    COII32.534.812.820.067.2−0.034−0.221705
    ATP835.848.83.711.784.6−0.153−0.520162
    ATP628.939.011.720.467.9−0.148−0.272675
    COIII26.837.015.221.163.8−0.160−0.164792
    ND330.841.610.317.472.4−0.150−0.258351
    ND125.443.520.710.468.9−0.2620.333936
    ND528.140.720.910.368.8−0.1840.3421734
    ND428.142.619.79.670.7−0.2050.3421338
    ND4L27.947.418.66.175.3−0.2600.506282
    ND626.747.56.919.074.1−0.280−0.470549
    Cyt b26.937.514.421.264.4−0.166−0.1931135
    ND229.543.78.118.773.2−0.195−0.3951011
    16S rRNA40.439.013.67.079.40.0180.3221373
    12S rRNA41.438.712.77.280.10.0340.277889
    tRNAs38.035.814.911.373.80.0310.1341454
    CR38.042.211.18.780.2−0.0530.1241096
    下载: 导出CSV

    Table  3.   Composition and skewness of mitogenome in 16 Varunidae species

    SpeciesA%T%G%C%A + T%AT-
    skew
    GC-
    skew
    Length
    (bp)
    Cyclograpsus granulosus33.136.111.219.569.3−0.043−0.27216,300
    Pseudohelice subquadrata34.233.510.521.767.70.010−0.34716,898
    Helicana wuana33.035.511.520.068.4−0.037−0.26916,359
    Helice latimera34.035.111.019.969.1−0.017−0.29016,246
    Helice tientsinensis33.935.111.019.969.1−0.017−0.28916,212
    Cyclograpsus intermedius34.735.910.718.770.6−0.017−0.27016,184
    Eriocheir hepuensis35.136.410.817.771.5−0.018−0.24516,335
    Eriocheir sinensis35.336.410.717.771.6−0.015−0.24816,354
    Eriocheir japonica35.236.510.717.771.6−0.018−0.24516,352
    Neoeriocheir leptognathus35.639.010.115.374.6−0.046−0.20616,143
    Hemigrapsus penicillatus34.136.411.418.170.5−0.033−0.22916,486
    Hemigrapsus sanguineus34.335.511.219.169.8−0.018−0.26016,275
    Metaplax longipes37.633.810.617.971.40.053−0.25716,305
    Varuna litterata35.236.210.817.871.4−0.014−0.24316,368
    Varuna yui35.736.510.217.672.2−0.011−0.26515,915
    Gaetice depressus35.437.610.516.573.0−0.030−0.22316,288
    下载: 导出CSV
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