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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  • 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

    Leu (L2)1535160066TAA5H
    Gly (G)3943400765TCC0H
    Ala (A)4360442263TGC2H
    Arg (R)4425448763TCG-1H
    Asn (N)4487455165GTT0H
    Ser (S1)4552461867TCT22H
    Thr (T)4641470565TGT2H
    Pro (P)4708477164TGG20L
    Leu (L1)5759582567TAG0L
    His (H)8088815063GTG6L
    Val (V)10,01710,08973TAC0L
    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
    Cyt b13,92315,0571135378ATG/T0H
    Ser (S2)15,05815,12467TGA20H
    Ile (I)15,14515,20965GAT4H
    Met (M)15,21415,28168CAT0H
    Trp (W)16,29116,35868TCA9H
    下载: 导出CSV

    Table  2.   Composition and skewness of V. litterata mitogenome

    Cyt b26.937.514.421.264.4−0.166−0.1931135
    16S rRNA40.439.
    12S rRNA41.438.712.
    下载: 导出CSV

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

    SpeciesA%T%G%C%A + T%AT-
    Cyclograpsus granulosus33.−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.−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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