Characterization of 15 Earthworm Mitogenomes from Northeast China and Its Phylogenetic Implication (Oligochaeta: Lumbricidae, Moniligastridae)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Preparation and DNA Extraction
2.2. Next Generation Sequencing
2.3. Data Assembly and Mitogenome Annotation
2.4. Statistics of the Earthworm Mitogenomes
2.5. Phylogenetic Analysis
3. Results
3.1. Mitogenome Organization and Nucleotide Composition of the Four Earthworm Species
3.2. Protein-Coding Genes and Codon Usage in the Four Earthworm Species
3.3. RNA Genes of the Four Earthworm Species
3.4. Putative Control Region and Non-Coding Region
3.5. Phylogenetic Analysis
4. Discussion
4.1. Organization of a Partial Mitochondrial Genome
4.2. Genetic Diversity of Lumbricids in Northeast China
4.3. Phylogenetic Inference
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Family | Taxa | Accession Number | Body Color | Habitat | References |
---|---|---|---|---|---|
Lumbricidae | Aporrectodeacaliginosa | CM035405 | - | - | Unpublished |
Aporrectodea tuberculata | OL840316–7, OM687883–6 | Light grey | Forest | This study | |
Aporrectodea trapezoides | OM687882 | Dark brown | Farmland | This study | |
Aporrectodea rosea | MK573632 | - | - | [24] | |
Bimastus parvus | MZ857199 | - | - | [39] | |
Dendrobaena octaedra | MZ857197 | - | - | [39] | |
Eisenia andrei | MZ857198 | - | - | [39] | |
Eisenia balatonica | MK642872 | - | - | [8] | |
Eisenia nana | MK618511 | - | - | [8] | |
Eisenia nordenskioldi | OL840314–5, OM687887–90 | Light reddish | Forest | This study | |
Eisenia nordenskioldi | MK642869 | - | - | [8] | |
Eisenia nordenskioldi | MZ857200 | - | - | [39] | |
Eisenia nordenskioldi nordenskioldi | MK618509 | - | - | [8] | |
Eisenia nordenskioldi nordenskioldi | MK618510 | - | - | [8] | |
Eisenia nordenskioldi nordenskioldi | MK618513 | - | - | [8] | |
Eisenia nordenskioldi nordenskioldi | MK642867 | - | - | [8] | |
Eisenia nordenskioldi nordenskioldi | MK642868 | - | - | [8] | |
Eisenia nordenskioldi pallida | MK618512 | - | - | [8] | |
Eisenia spelaea | MK642870 | - | - | [8] | |
Eisenia tracta | MK642871 | - | - | [8] | |
Lumbricus rubellus | MN102127 | Pink | Forest | [23] | |
Lumbricus terrestris | LTU24570 | - | - | [16] | |
Octolasion tyrtaeum | MZ857201 | - | - | [39] | |
Megascolecidae | Amynthas aspergillus | KJ830749 | - | - | [19] |
Amynthas carnosus | KT429008 | - | - | [21] | |
Amynthas corticis | KM199290 | - | - | [18] | |
Amynthas cucullatus | KT429012 | - | - | [21] | |
Amynthas gracilis | KP688582 | - | - | [18] | |
Amynthas hupeiensis | KT429009 | - | - | [21] | |
Amynthas jiriensis | KT783537 | - | - | [40] | |
Amynthas longisiphonus | KM199289 | - | - | [18] | |
Amynthas moniliatus | KT429020 | - | - | [21] | |
Amynthas morrisi | KT429011 | - | - | [21] | |
Amynthas pectiniferus | KT429018 | - | - | [21] | |
Amynthas robustus | KT429019 | - | - | [21] | |
Amynthas redactus | KT429010 | - | - | [21] | |
Amynthas instabilis | KT429007 | - | - | [21] | |
Amynthas rongshuiensis | KT429014 | - | - | [21] | |
Amynthas spatiosus | KT429013 | - | - | [21] | |
Amynthas triastriatus | KT429016 | - | - | [21] | |
Metaphire schmardae | KT429015 | - | - | [21] | |
Metaphire californica | KP688581 | - | - | [18] | |
Metaphire guillelmi | KT429017 | - | - | [21] | |
Metaphire posthuma | MW222472 | - | - | [41] | |
Metaphire vulgaris | KJ137279 | - | - | [20] | |
Perionyx excavatus | EF494507 | - | - | [42] | |
Tonoscolex birmanicus | KF425518 | - | - | [17] | |
Moniligastridae | Drawida ghilarovi | OL840312–3 | Gray | Forest | This study |
Drawida gisti | MN539609 | - | - | [25] | |
Drawida japonica | KM199288 | - | - | [21] | |
Naididae Outgroup | Tubifex tubifex | MW690579 | - | - | [43] |
Nais communis | MW770354 | - | - | [44] |
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Zhao, H.; Fan, S.; Aspe, N.M.; Feng, L.; Zhang, Y. Characterization of 15 Earthworm Mitogenomes from Northeast China and Its Phylogenetic Implication (Oligochaeta: Lumbricidae, Moniligastridae). Diversity 2022, 14, 714. https://doi.org/10.3390/d14090714
Zhao H, Fan S, Aspe NM, Feng L, Zhang Y. Characterization of 15 Earthworm Mitogenomes from Northeast China and Its Phylogenetic Implication (Oligochaeta: Lumbricidae, Moniligastridae). Diversity. 2022; 14(9):714. https://doi.org/10.3390/d14090714
Chicago/Turabian StyleZhao, Huifeng, Shuanghu Fan, Nonillon M. Aspe, Lichao Feng, and Yufeng Zhang. 2022. "Characterization of 15 Earthworm Mitogenomes from Northeast China and Its Phylogenetic Implication (Oligochaeta: Lumbricidae, Moniligastridae)" Diversity 14, no. 9: 714. https://doi.org/10.3390/d14090714