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

doi:10.1007/s13131-021-1927-7

Volume 41 Issue 6

Jun. 2022

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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, 2022, 41(6): 119-131. 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, 2022, 41(6): 119-131. 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, 2022, 41(6): 119-131. doi: 10.1007/s13131-021-1927-7

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Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

doi: 10.1007/s13131-021-1927-7

Ying Zhang^{1, 2},
Li Gong^{1, 2, 3},
Xinting Lu^{1, 2},
Zengliang Miao²,
Lihua Jiang^{1, 2},
Bingjian Liu^{1, 2},
Liqin Liu^{1, 2},
Pengfei Li³,
Xu Zhang⁴,
Zhenming Lü^{1, 2
,
,}

1.
National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan 316022, China
2.
Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
3.
Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China
4.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China

Funds: The Natural Science Foundation of Zhejiang Province under contract No. LY21C190007.

More Information

Corresponding author: nblzmnb@163.com
Received Date: 2021-02-07
Accepted Date: 2021-03-29

Available Online: 2022-03-16

Publish Date: 2022-06-16

Abstract

Abstract

Complete mitochondrial genomes (mitogenomes) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. Currently, the phylogenetic location of the genus Varuna (Brachyura: Varunidae) has not been well resolved mainly because of limited representatives (only two extant species). Here, we determined a new mitogenome of this genus (Varuna litterata) and added the published mitogenomes to reconstruct the phylogeny of Varunidae. The 16 368-bp mitogenome contains the entire set of 37 genes and a putative control region. The characteristics of this newly sequenced mitogenome were described and compared with the other 15 Varunidae mitogenomes. All 16 analyzed mitogenomes have identical gene order and similar molecular features. The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity, with comparatively low variability of COI and COII, and high variability of ND6. The nonsynonymous/synonymous substitution rates (dN/dS ratio) analysis shows that all 13 PCGs are under purifying selection and ATP8 gene evolves under the least selective pressure. Twelve tRNA genes, two rRNAs, one PCG, and the putative control region are found to be rearranged with respect to the pancrustacean ground pattern gene order. Tandem duplication/random loss model is adopted to explain the large-scale gene rearrangement events occurring in Varunidae mitogenomes. Phylogenetic analyses show that all Varunidae species are placed into one group, and form a sister clade with Macrophthalmidae. Nevertheless, the phylogenetic relationships within Varunidae are not completely consistent based on the two different datasets used in this study. These findings will contribute to a better understanding of gene rearrangement and molecular evolution in Varunidae mitogenomes, as well as provide insights into the phylogenetic studies of Brachyura.
- varunid crab,
- Varuna litterata,
- mitogenome,
- gene rearrangement,
- tandem duplication/random loss,
- phylogeny

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References(64)

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