Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species

Liu, Jiabin; Yu, Jiaojiao; Zhou, Ming; Yang, Jiandong

doi:10.1016/j.ijbiomac.2018.12.068

Cited by 23 publications

(26 citation statements)

References 49 publications

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“…The result of ML phylogenetic tree (Figure 1) shows that J. splendida and J. flaviceps formed a monophyletic group in the order ((((Acanthosaura lepidogaster, Acanthosaura armata)), ((J. splendida, J. flaviceps), Pseudocalotes microlepis))), Calotes versicolor) with high bootstrap support values (Figure 1). The phylogenetic relationships in Agamidae here conform to the results of a previous study (Liu et al 2019).…”

supporting

confidence: 89%

“…In addition, the control region was 1482 bp long and is located between the tRNA-Pro and tRNA-Phe genes. The gene arrangement pattern and transcription directions were identical to previous studies on Japalura flaviceps (Liu et al 2019).…”

supporting

confidence: 85%

“…In the last two decades, numerous mitogenomes of vertebrates have been sequenced and improved to obtain a reliable phylogeny (Zhang et al 2003;Zhang et al 2008;Wielstra and Arntzen 2011). Meanwhile, gene duplication, rearrangement, loss, and inversion of the vertebrate mitogenome have been reported (Rest et al 2003;Amer and Kumazawa 2007;Zhuang and Cheng 2010;Liu et al 2019). To further understand the evolution of mitogenome in lizards, we determined the complete mitogenome sequence of J. splendida.…”

mentioning

confidence: 99%

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The complete mitogenome of the splendid japalure Japalura splendida (Squamata, Agamidae)

Huang

Luo

et al. 2019

Mitochondrial DNA Part B

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The complete mitogenome of Japalura splendida (16,673 bp in length) is determined and analyzed in this study. It contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one non-coding regions. All the genes in J. splendida are distributed on the H-strand, except for the ND6 gene and seven tRNA genes which are encoded on the L-strand. The phylogenetic tree suggests that J. splendida and Japalura flaviceps formed a sister group and reveals the order ((((Acanthosaura lepidogaster, Acanthosaura armata), ((J. splendida, J. flaviceps), Pseudocalotes microlepis))), Calotes versicolor) with substantial support for the monophyly.

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supporting

confidence: 89%

supporting

confidence: 85%

mentioning

confidence: 99%

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The complete mitogenome of the splendid japalure Japalura splendida (Squamata, Agamidae)

Huang

Luo

et al. 2019

Mitochondrial DNA Part B

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“…Generally, gene arrangement in vertebrate mitogenomes is relatively conserved and fewer gene arrangement is discovered [6][7][8][9]. In contrast, that in invertebrate mitogenomes is relatively common.…”

Section: Introductionmentioning

confidence: 99%

Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura

Gong

Wang

et al. 2020

Genomics

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Background: Gene arrangement in vertebrate mitochondrial genomes (mitogenomes) is relatively conserved and fewer gene arrangement is discovered. In contrast, that in invertebrate mitogenomes is relatively common. Although a gradually growing number of gene rearrangement in hermit crabs (Paguridae) has been discovered, it is surprising that gene rearrangement in its close relatives, the terrestrial hermit crab (Coenobitidae), was overlooked until 2018. So far, only few studies focused on the phylogenetic studies of Anomura based on molecular evidences. Results: In the present study, the complete mitogenome of a terrestrial hermit crab, Coenobita brevimanus, was sequenced, and largescale gene rearrangements were observed. The genomic features of this terrestrial hermit crab were different from those of any other studied crabs. Five gene clusters (or genes) including eleven tRNAs and two PCGs were found to be rearranged with respect to the pancrustacean ground pattern gene order, which was characterized by multiple translocations and inversions. Two phylogenetic trees (ML and BI tree) arrived at a similar topology based on the nucleotide sequences of the 13 concatenated PCGs. Conclusions: We propose tandem duplication-random loss and recombination model to explain the large-scale gene rearrangements in C. brevimanus mitogenome. The phylogenetic trees showed that all Coenobitidae species clustered into one clade. The polyphyly of Paguroidea was well supported, whereas the non-monophyly of Galatheoidea was not in consistence with previous findings. The phylogenetic relationships of Pylochelidae, Lomidae, and Albuneidae were controversial.

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“…Therefore, mitogenome has been widely used to infer phylogenetic relationships and population genetics in animal [9][10][11]. Furthermore, the gene rearrangements have been reported in various vertebrates [11][12][13][14][15][16], but the organization in most fish mitogenomes is generally considered quite conserved [17,18]. However, we analyzed the complete mitogenome sequence of C. monopus and found a novel gene order in this study.…”

Section: Introductionmentioning

confidence: 80%

Novel Gene Rearrangement and the Complete Mitochondrial Genome of Cynoglossus monopus: Insights into the Envolution of the Family Cynoglossidae (Pleuronectiformes)

Wang

Chen

Tian

et al. 2020

IJMS

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Cynoglossus monopus, a small benthic fish, belongs to the Cynoglossidae, Pleuronectiformes. It was rarely studied due to its low abundance and cryptical lifestyle. In order to understand the mitochondrial genome and the phylogeny in Cynoglossidae, the complete mitogenome of C. monopus has been sequenced and analyzed for the first time. The total length is 16,425 bp, typically containing 37 genes with novel gene rearrangements. The tRNA-Gln gene is inverted from the light to the heavy strand and translocated from the downstream of tRNA-Ile gene to its upstream. The control region (CR) translocated downstream to the 3’-end of ND1 gene adjoining to inverted to tRNA-Gln and left a 24 bp trace fragment in the original position. The phylogenetic trees were reconstructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 32 tonguefish species and two outgroups. The results support the idea that Cynoglossidae is a monophyletic group and indicate that C. monopus has the closest phylogenetic relationship with C. puncticeps. By combining fossil records and mitogenome data, the time-calibrated evolutionary tree of families Cynoglossidae and Soleidae was firstly presented, and it was indicated that Cynoglossidae and Soleidae were differentiated from each other during Paleogene, and the evolutionary process of family Cynoglossidae covered the Quaternary, Neogene and Paleogene periods.

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Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species

Cited by 23 publications

References 49 publications

The complete mitogenome of the splendid japalure Japalura splendida (Squamata, Agamidae)

The complete mitogenome of the splendid japalure Japalura splendida (Squamata, Agamidae)

Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura

Novel Gene Rearrangement and the Complete Mitochondrial Genome of Cynoglossus monopus: Insights into the Envolution of the Family Cynoglossidae (Pleuronectiformes)

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