Characterization of 15 Earthworm Mitogenomes from Northeast China and Its Phylogenetic Implication (Oligochaeta: Lumbricidae, Moniligastridae)

Zhao, Huifeng; Fan, Shuanghu; Aspe, Nonillon M.; Feng, Lichao; Zhang, Yufeng

doi:10.3390/d14090714

Cited by 6 publications

(2 citation statements)

References 60 publications

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“…In Lumbricidae, the length of the control region varies from 400 bp in L. terres tris to 2000 bp in Eisenia fetida. For many species, control regions could not be amplified (Shekhovtsov et al, 2020a) or even recovered using NGS methods (Zhao et al, 2022). Here, we also failed to amplify the lacking part of the control region of D. tellermanica.…”

Section: Organization Of Mitochondrial Genome In Earthwormsmentioning

confidence: 68%

The mitochondrial genome of <i>Dendrobaena tellermanica</i> Perel, 1966 (Annelida: Lumbricidae) and its phylogenetic position

et al. 2023

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Earthworms are an important ecological group that has a significant impact on soil fauna as well as plant communities. Despite their importance, genetic diversity and phylogeny of earthworms are still insufficiently studied. Most studies on earthworm genetic diversity are currently based on a few mitochondrial and nuclear genes. Mitochondrial genomes are becoming a promising target for phylogeny reconstruction in earthworms. However, most studies on earthworm mitochondrial genomes were made on West European and East Asian species, with much less sampling from other regions. In this study, we performed sequencing, assembly, and analysis of the mitochondrial genome of Dendrobaena tellermanica Perel, 1966 from the Northern Caucasus. This species was earlier included into D. schmidti (Michaelsen, 1907), a polytypic species with many subspecies. The genome was assembled as a single contig 15,298 bp long which contained a typical gene set: 13 protein-coding genes (three subunits of cytochrome c oxidase, seven subunits of NADH dehydrogenase, two subunits of ATP synthetase, and cytochrome b), 12S and 16S ribosomal RNA genes, and 22 tRNA genes. All genes were located on one DNA strand. The assembled part of the control region, located between the tRNA-Arg and tRNA-His genes, was 727 bp long. The control region contained multiple hairpins, as well as tandem repeats of the AACGCTT monomer. Phylogenetic analysis based on the complete mitochondrial genomes indicated that the genus Dendrobaena occupied the basal position within Lumbricidae. D. tellermanica was a rather distant relative of the cosmopolitan D. octaedra, suggesting high genetic diversity in this genus. D. schmidti turned out to be paraphyletic with respect to D. tellermanica. Since D. schmidti is known to contain very high genetic diversity, these results may indicate that it may be split into several species.

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Section: Organization Of Mitochondrial Genome In Earthwormsmentioning

confidence: 68%

The mitochondrial genome of <i>Dendrobaena tellermanica</i> Perel, 1966 (Annelida: Lumbricidae) and its phylogenetic position

et al. 2023

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“…Transcriptomes are also used for the phylogenetic analyses of interfamilial relationships of closely related families and intrafamilial relationships of annelids ( Lemer et al, 2015 ; Novo et al, 2016 ; Anderson et al, 2017 ; Stiller et al, 2020 ; Tilic et al, 2020b ; Shekhovtsov et al, 2022 ). Also, there has been an increase in the number of studies that employ genome skimming for phylogenetic analyses based on mitogenomes in recent years ( Richter et al, 2015 ; Bernardino et al, 2017 ; Zhang et al, 2018 ; Zhao et al, 2022 ; Struck et al, 2023 ). Although the publicly available genomic data of annelids are still limited, those of annelids are rapidly accumulating led by large projects, e.g.…”

Section: Introductionmentioning

confidence: 99%

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

Kobayashi

2023

PeerJ

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Background The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA. Methods The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank. Results and Discussion mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22–24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.

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Phylogeny of Lumbricidae based on mitochondrial genomes with emphasis on the genus Dendrobaena

Shekhovtsov,

Rapoport,

Leonov

et al. 2024

Org Divers Evol

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Characterization of 15 Earthworm Mitogenomes from Northeast China and Its Phylogenetic Implication (Oligochaeta: Lumbricidae, Moniligastridae)

Cited by 6 publications

References 60 publications

The mitochondrial genome of <i>Dendrobaena tellermanica</i> Perel, 1966 (Annelida: Lumbricidae) and its phylogenetic position

The mitochondrial genome of <i>Dendrobaena tellermanica</i> Perel, 1966 (Annelida: Lumbricidae) and its phylogenetic position

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

Phylogeny of Lumbricidae based on mitochondrial genomes with emphasis on the genus Dendrobaena

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