A novel gene arrangement among the Stylommatophora by the complete mitochondrial genome of the terrestrial slug Meghimatium bilineatum (Gastropoda, Arionoidea)

Xie, Guanglong; Köhler, Frank; Huang, Xiao‐Chen; Wü, Ray; Zhou, Chunhua; Ouyang, Shan; Wu, Xiaoping

doi:10.1016/j.ympev.2019.03.002

Cited by 24 publications

(25 citation statements)

References 52 publications

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“…Similar to other stylommatophoran mitogenomes, it contains 13 PCGs, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with 1,555 bp. The entire mitogenome of E. planostriata had a high A þ T content of 70.10%, in accordance with other land mollusks (Deng et al 2016;Yang et al 2016;Xie et al 2019). The overall nucleotide composition is as follows: A ¼ 31.7%, C ¼ 13.9%, G ¼ 16.0%, and T ¼ 38.4%.…”

supporting

confidence: 78%

“…Total genomic DNA was extracted using TIANamp Marine Animals DNA Kit (Tiangen Biotech, Beijing, China) according to the manufacturer's instructions, and subsequently sequenced on the Illumina Novaseq 6000 sequencing platform with PE150 strategy. The whole mitochondrial genome sequence was obtained and annotated according to our previous study (Qin et al 2019;Xie et al 2019). We assembled the mitochondrial genome sequences using de novo methods with CLC Genomics Workbench 12.0 (Qiagen).…”

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confidence: 99%

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Complete mitochondrial genome of the land snail Euphaedusa planostriata (Gastropoda: Stylommatophora: Clausiliidae)

Zhang

Huang

Xie

et al. 2021

Mitochondrial DNA Part B

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Clausiliidae snails have been of great interest to conchologists for their unique clausilium structure and rich species diversity. We described the complete mitochondrial genome of Euphaedusa planostriata (Heude, 1882). The mitogenome is 15,041bp in length, with a total of 37 genes, including 13 proteincoding genes, 2 rRNA genes, and 22 tRNA genes. It is consistent with the basic characteristics of the known stylommatophoran mitochondrial genome. Phylogenetic analysis using mitogenomes showed that Euphaedusa planostriata is clustered with Albinaria caerulea, supporting the monophyly of this family. Our study provides valuable information that can be used toward the conservation genetics, taxonomy and evolution of clausiliid snails.

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confidence: 78%

mentioning

confidence: 99%

Complete mitochondrial genome of the land snail Euphaedusa planostriata (Gastropoda: Stylommatophora: Clausiliidae)

Zhang

Huang

Xie

et al. 2021

Mitochondrial DNA Part B

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“…Mitochondrial gene order arrangement involves four gene rearrangement types, namely, transpositions, reverse transpositions, inversions, and TDRL [31,32]. CREx analysis suggested that transposition and TDRL are associated with the evolution of the mitogenomes of deep-sea mussels.…”

Section: Mitochondrial Gene Rearrangementmentioning

confidence: 99%

Phylogenetic Relationships and Adaptation in Deep-Sea Mussels: Insights from Mitochondrial Genomes

Zhang

Sun

et al. 2021

IJMS

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Mitochondrial genomes (mitogenomes) are an excellent source of information for phylogenetic and evolutionary studies, but their application in marine invertebrates is limited. In the present study, we utilized mitogenomes to elucidate the phylogeny and environmental adaptation in deep-sea mussels (Mytilidae: Bathymodiolinae). We sequenced and assembled seven bathymodioline mitogenomes. A phylogenetic analysis integrating the seven newly assembled and six previously reported bathymodioline mitogenomes revealed that these bathymodiolines are divided into three well-supported clades represented by five Gigantidas species, six Bathymodiolus species, and two “Bathymodiolus” species, respectively. A Common interval Rearrangement Explorer (CREx) analysis revealed a gene order rearrangement in bathymodiolines that is distinct from that in other shallow-water mytilids. The CREx analysis also suggested that reversal, transposition, and tandem duplications with subsequent random gene loss (TDRL) may have been responsible for the evolution of mitochondrial gene orders in bathymodiolines. Moreover, a comparison of the mitogenomes of shallow-water and deep-sea mussels revealed that the latter lineage has experienced relaxed purifying selection, but 16 residues of the atp6, nad4, nad2, cob, nad5, and cox2 genes have underwent positive selection. Overall, this study provides new insights into the phylogenetic relationships and mitogenomic adaptations of deep-sea mussels

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“…The sister group relationships between Arionoidea and Urocoptoidea + Enoidea + Helicoidea (Jörger et al, 2010) or Limacoidea + (Succineoidea + Helicoidea) (Dayrat et al, 2011) have also been suggested by previous studies using relatively longer DNA sequences, however in both studies, only five stylommatophoran species were included for phylogenetic analyses. Furthermore, Xie et al (2019b) have proposed sister group relationship between Arionoidea and Succineoidea using only amino acid dataset of mitochondrial PCGs, and stated it might be an artefact of poor taxon sampling.…”

Section: Phylogeny and Divergence Times Of Stylommatophoran Speciesmentioning

confidence: 99%

“…Although there have been some criticisms about the usage of mitogenomes in construction of gastropod phylogeny because of long branch attraction, substitution saturation and strand-specific skew bias (Stöger & Schrödl, 2013), within the recently diversified lineages of gastropods, the use of mitogenomes resulted in highly resolved phylogenies (Williams, Foster & Littlewood, 2014;Osca, Templado & Zardoya, 2014). Besides the use of the mitogenome in sequencebased phylogenies, mitogenome rearrangements can also provide phylogenetic signals (Grande, Templado & Zardoya, 2008;Stöger & Schrödl, 2013;Xie et al, 2019b). Although the mitogenome is widely used in phylogeny of many gastropod groups (Arquez, Colgan & Castro, 2014;Osca, Templado & Zardoya, 2014;Sevigny et al, 2015;Uribe, Zardoya & Puillandre, 2018), there are limited numbers of reported stylommatophoran mitogenomes and phylogenetic studies in Stylommatophora in terms of usage of mitogenome sequence and rearrangement (Romero, Weigand & Pfenninger, 2016;Xie et al, 2019a;Yang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

The complete mitogenome ofArion vulgarisMoquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora

Doğan

Schrödl

Chen

2020

PeerJ

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Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth’s most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes.

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A novel gene arrangement among the Stylommatophora by the complete mitochondrial genome of the terrestrial slug Meghimatium bilineatum (Gastropoda, Arionoidea)

Cited by 24 publications

References 52 publications

Complete mitochondrial genome of the land snail Euphaedusa planostriata (Gastropoda: Stylommatophora: Clausiliidae)

Complete mitochondrial genome of the land snail Euphaedusa planostriata (Gastropoda: Stylommatophora: Clausiliidae)

Phylogenetic Relationships and Adaptation in Deep-Sea Mussels: Insights from Mitochondrial Genomes

The complete mitogenome ofArion vulgarisMoquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora

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