Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation

Wang, Xibao; Shang, Yongquan; Wu, Xiaoyang; Wei, Qinguo; Zhou, Shengyang; Sun, Guolei; Mei, Xuesong; Dong, Yuehuan; Sha, Weilai; Zhang, Honghai

doi:10.1007/s13127-022-00574-8

Cited by 8 publications

(6 citation statements)

References 57 publications

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“…Mitochondrial DNA has been one of the most useful tools that are widely used in species identification, phylogenetic studies [22], comparative genomics [23], and management of invasive alien species [24]. Xenostrobus securis, L. fortunei, and Mytilus galloprovincialis and etc., are regarded as notorious invasive species which have caused dramatic and devastating effects on ecosystems [25,26].…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial genomic analyses provide new insights into the “missing” atp8 and adaptive evolution of Mytilidae

et al. 2022

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Background Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments. In addition, some bivalve species are thought to lack the mitochondrial protein-coding gene ATP synthase F0 subunit 8. Increasing studies indicated that the absence of atp8 may be caused by annotation difficulties for atp8 gene is characterized by highly divergent, variable length. Results In this study, the complete mitochondrial genomes of three marine mussels (Xenostrobus securis, Bathymodiolus puteoserpentis, Gigantidas vrijenhoeki) were newly assembled, with the lengths of 14,972 bp, 20,482, and 17,786 bp, respectively. We annotated atp8 in the sequences that we assembled and the sequences lacking atp8. The newly annotated atp8 sequences all have one predicted transmembrane domain, a similar hydropathy profile, as well as the C-terminal region with positively charged amino acids. Furthermore, we reconstructed the phylogenetic trees and performed positive selection analysis. The results showed that the deep-sea bathymodiolines experienced more relaxed evolutionary constraints. And signatures of positive selection were detected in nad4 of Limnoperna fortunei, which may contribute to the survival and/or thriving of this species in freshwater. Conclusions Our analysis supported that atp8 may not be missing in the Mytilidae. And our results provided evidence that the mitochondrial genes may contribute to the adaptation of Mytilidae to different environments.

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Section: Introductionmentioning

confidence: 99%

Mitochondrial genomic analyses provide new insights into the “missing” atp8 and adaptive evolution of Mytilidae

et al. 2022

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“…We analyzed the gut microbiomes of 108 samples representing 16 species belonging to nine families and 14 genera to explore the convergent evolution of the gut microbiome. 16S rRNA gene data of the gut microbiome of the nine species ( Cuon alpinus [Wu et al, 2016 ], Canis lupus [Wu et al, 2017 ], Vulpes Vulpes [Wang, Shang, Wei, et al, 2022 ; Wang, Shang, Wu, et al, 2022 ; Wang, Wu, et al, 2022 ], V. Corsac [Wang, Shang, Wei, et al, 2022 ; Wang, Shang, Wu, et al, 2022 ; Wang, Wu, et al, 2022 ], Cervus elaphus [Wang et al, 2019 ], Ovis musimon [Sun et al, 2019 ], Pantholops hodgsonii [Wang, Shang, Wei, et al, 2022 ; Wang, Shang, Wu, et al, 2022 ; Wang, Wu, et al, 2022 ], Pseudois nayaur [Wang, Shang, Wei, et al, 2022 ; Wang, Shang, Wu, et al, 2022 ; Wang, Wu, et al, 2022 ], and Bos grunniens [Wang, Shang, Wei, et al, 2022 ; Wang, Shang, Wu, et al, 2022 ; Wang, Wu, et al, 2022 ]) were obtained by sequencing in our laboratory. Other 16S rRNA gene data ( C. Nippon [Guan et al, 2017 ], Moschus chrysogaster [Sun et al, 2020 ], Halichoerus grypus [Watkins et al, 2022 ], Nyctereutes procyonoides [Ishida‐Kuroki et al, 2020 ], Enhydra lutris nereis [Dudek et al, 2022 ], Balaenoptera physalus , and Physeter microcephalus [Glaeser et al, 2022 ]) were downloaded from the NCBI SRA database ( www.ncbi.nlm.nih.gov ).…”

Section: Methodsmentioning

confidence: 99%

“…Many studies have focused on the adaptive evolution of marine carnivores using genomics (Noh et al, 2022 ; Yim et al, 2014 ), microbiomics (Dudek et al, 2022 ; Glaeser et al, 2022 ), and transcriptomics (Toren et al, 2020 ). Based on phylogenetic independent contrasts analysis, Wang, Shang, Wu, et al ( 2022 ) found that the evolutionary rate of marine Cetartiodactyla mitochondrial protein‐coding genes was significantly higher than terrestrial Cetartiodactyla. Noh et al ( 2022 ) found that SUMO2 and EP300 (hypoxia genes) were the most significant genes in the Weddell seal ( Leptonychotes weddellii ) compared to other placental mammals.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…The gut microbiome is an important factor for host adaptations to the environment (Wang et al, 2019 ; Wang, Shang, Wei, et al, 2022 ; Wang, Shang, Wu, et al, 2022 ; Wang, Wu, et al, 2022 ). Wang, Shang, Wu, et al ( 2022 ) found that the gut microbiome function of red and corsac foxes can help hosts adapt to different environmental niches. Moreover, to adapt to plateau environments, short‐chain fatty acid (SCFA)‐producing bacteria are significantly enriched in the host gut (Li et al, 2016 ; Zhang et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

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Convergent evolution of the gut microbiome in marine carnivores

Wang

Shang

et al. 2022

Ecology and Evolution

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The gut microbiome can help the host adapt to a variety of environments and is affected by many factors. Marine carnivores have unique habitats in extreme environments. The question of whether marine habitats surpass phylogeny to drive the convergent evolution of the gut microbiome in marine carnivores remains unanswered. In the present study, we compared the gut microbiomes of 16 species from different habitats. Principal component analysis (PCA) and principal coordinate analysis (PCoA) separated three groups according to their gut microbiomes: marine carnivores, terrestrial carnivores, and terrestrial herbivores. The alpha diversity and niche breadth of the gut microbiome of marine carnivores were lower than those of the gut microbiome of terrestrial carnivores and terrestrial herbivores. The gut microbiome of marine carnivores harbored many marine microbiotas, including those belonging to the phyla Planctomycetes, Cyanobacteria, and Proteobacteria, and the genus Peptoclostridium . Collectively, these results revealed that marine habitats drive the convergent evolution of the gut microbiome of marine carnivores. This study provides a new perspective on the adaptive evolution of marine carnivores.

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