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Secondary structure of tRNA families (trnN-trnP) in earthworm mtDNAs.: The nucleotide substitution pattern for each tRNA family was modeled using as reference the structure determined for A. carnosus.
Source publication
The Pheretima complex within the Megascolecidae family is a major earthworm group. Recently, the systematic status of the Pheretima complex based on morphology was challenged by molecular studies. In this study, we carry out the first comparative mitogenomic study in oligochaetes. The mitogenomes of 15 earthworm species were sequenced and compared...
Contexts in source publication
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... most conserved tRNAs show nucleotide substitutions largely restricted to TΨ C loops and acceptor arms (Figs 3 and 4). Acceptor stems show 0-4 fully compensatory base changes (cbcs) (e.g., G-C vs. A-T in trnM) and/ or hemi-cbc (e.g., A-T vs. G-T in trnM). ...
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... and hemi-cbcs are restricted to individual species or characterized taxa at a higher taxonomic level (family/order), as reported in insects 38 . We also find the similar substitution patterns in our study. An example of the first type is the C-G pair in the trnN acceptor arm of D. japonica is mirrored by T-A in all other earthworms (Fig. 3). In addition, the DHU loop in the trnN of D. japonica is distinct from that of any other species. An exam- ple of a full cbc characterizing a unique family is the T-A pair found in the acceptor stem of trnAs of the family Megascolecidae, while the other two species D. japonica and L. terrestris, not belonging to Megascolecidae, exhibit ...
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... indicat- ing they are closely related species. Figures 3 and 4 depict more examples. ...
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... the inclusion of extra species from other genera within the Pheretima complex is clearly needed to validate this taxonomic revi- sion. Furthermore, as can be seen in Supplementary Fig. S3, branch lengths within the Pheretima complex are generally short, suggesting that pheretimoid worms diversity may have resulted from a relatively recent and rapid radiation. ...
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Citations
... The substitution, deletion and insertion were observed within the genus Aparapotamon, and 100% conservation sites were selected. The comparison of tRNA secondary structures between A. emineoforaminum and other Aparapotamon species was completed manually [66]. ...
Background
Aparapotamon, a freshwater crab genus endemic to China, includes 13 species. The distribution of Aparapotamon spans the first and second tiers of China's terrain ladder, showing great altitudinal differences. To study the molecular mechanisms of adaptive evolution in Aparapotamon, we performed evolutionary analyses, including morphological, geographical, and phylogenetic analyses and divergence time estimation. We sequenced the mitogenomes of Aparapotamon binchuanense and Aparapotamon huizeense for the first time and resequenced three other mitogenomes of Aparapotamon grahami and Aparapotamon gracilipedum. These sequences were combined with NCBI sequences to perform comparative mitogenome analysis of all 13 Aparapotamon species, revealing mitogenome arrangement and the characteristics of protein-coding and tRNA genes.
Results
A new species classification scheme of the genus Aparapotamon has been detected and verified by different aspects, including geographical, morphological, phylogenetics and comparative mitogenome analyses. Imprints from adaptive evolution were discovered in the mitochondrial genomes of group A, including the same codon loss at position 416 of the ND6 gene and the unique arrangement pattern of the tRNA-Ile gene. Multiple tRNA genes conserved or involved in adaptive evolution were detected. Two genes associated with altitudinal adaptation, ATP8 and ND6, which experienced positive selection, were identified for the first time in freshwater crabs.
Conclusions
Geological movements of the Qinghai-Tibet Plateau and Hengduan Mountains likely strongly impacted the speciation and differentiation of the four Aparapotamon groups. After some group A species dispersed from the Hengduan Mountain Range, new evolutionary characteristics emerged in their mitochondrial genomes, facilitating adaptation to the low-altitude environment of China's second terrain tier. Ultimately, group A species spread to high latitudes along the upper reaches of the Yangtze River, showing faster evolutionary rates, higher species diversity and the widest distribution.
... However, barcoding analyses using mitochondrial COI gene sequences have tended to report too many molecular operational taxonomic units (MOTUs) as species and have provided very poor resolution of phylogenetic relationships. Other studies have reported whole mitogenome sequences obtained by Sanger sequencing, and such sequences have been used to study phylogenetic relationships (Zhang et al., 2016). However, available mitogenomic data are few and comprehensive phylogenetic studies dealing with the entire group have not been attempted. ...
... For 197 specimens, we assembled mitogenome and nuclear ribosomal DNA sequences from 5.5 to 60 million Illumina short reads (Table S1). For all samples, we assembled the mitogenome and the gene order was identical to that of pheretimoid species reported in Zhang et al. (2016). Figs. 2 and 3 show ML trees based on mitogenome (aligned length, 13,427 bp) and nuclear 18S-28S (aligned length, 5364 bp) data, respectively. ...
... The species of Metaphire are discriminated from Amynthas by the presence of copulatory pouches (Sims and Easton, 1972). However, separating these genera solely on the basis of the presence/absence of copulatory pouches has been questioned because Amynthas and Metaphire were not recovered as monophyletic groups in molecular phylogenetic trees based on mitochondrial gene sequences (Chang et al., 2008;Jeratthitikul et al., 2017;Zhao et al., 2015;Zhang et al., 2016). Zhao (2015) claimed that Amynthas and Metaphire should be treated as one genus. ...
Megascolecid earthworms of the pheretimoid group are dominant detritivores of soil ecosystems in the Japanese Archipelago and East Asia. However, their diversity and phylogenetic relationships are poorly understood. We assembled whole mitogenome sequences for 197 megascolecid earthworms collected throughout Japan to study the phylogenetic relationships, phylogeography, divergence times, and diversification of important morphological characteristics among pheretimoid earthworms. Using 197 mitogenome sequences and 24 published mitogenome sequences from the East Asian mainland (221 sequences in total), we constructed a maximum likelihood tree and found that the pheretimoid earthworms currently assigned to Amynthas, Metaphire, Duplodicodrilus, and Manus are involved in the most senior genus Amynthas; thus, Amynthas can be treated as the sole genus encompassing all of the above genera. Within the Amynthas group, we identified three major lineages that led to four groups of endemic species in Japan. These lineages originated from different lineages on the East Asian mainland and Taiwan Island, indicating multiple colonization events from the East Asian mainland by different ancestral lineages, possibly after the Miocene. We also assembled nuclear ribosomal DNA sequences encompassing the 18S to 28S rRNA genes. The nuclear gene tree showed major groups consistent with the mitogenome tree except for different (and not well-resolved) relationships among major clades. Our molecular data covered 115-158 native and 7 non-native Amynthas group species in Japan in terms of DNA-based species delimitation. Our findings provide a basis for understanding the evolutionary relationships among diversified megascolecid earthworms in the Amynthas group in Japan and adjacent regions.
... The reported complete mitogenomes of earthworms range from 14,648 to 15,188 base pairs (bp), consisting of 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs) and a putative control region (CR) [16][17][18][19][20][21][22][23][24][25]. Mitochondrial sequences are considered to be ideal genetic markers that are extensively employed for the study of systematics, phylogeography and species delimitation in animals [26][27][28][29][30][31][32]. ...
... Mitogenomes have often proved to be useful in resolving formerly troublesome phylogenies, clarifying the relationships within phylogenetically difficult groups where rapid radiations made other markers ineffective [37,38]. Previously in earthworm mitogenomic studies, more attention was paid to the mitogenomic studies of pheretimoids (Megascolecidae) in the Oriental Realm [18,20,21], while only a few studies were completed on moniligastrids and lumbricids. ...
... The phylogenetic trees of BI and ML reveal that the three families are reciprocal monophyletic with high support (both posterior probabilities (PP) = 1 and bootstrap (BS) = 100, as shown in Figure 6). For Megascolecidae, the species of Amynthas and Metaphire are scattered throughout a multi-clade, which mostly agrees with Zhang et al.'s study [21]. For the details on the trees of Megascolecidae, see Figures S3-S6. ...
Earthworms are an important ecological group, especially in agricultural regions in Northeast China. However, fewer studies focus on this group of organisms compared with other faunal groups. Here, we sequenced 15 new mitogenomes of Aporrectodea tuberculata Eisen, 1874, A. trapezoides Duges, 1828, Eisenia nordenskioldi Eisen, 1878 and Drawida ghilarovi Gates, 1969 in Northeast China using a high-throughput sequencing platform. These incomplete linear and double stranded mitogenomes vary from 14,998 bp to 16,123 bp in size and include 37 genes and a putative control region. Intraspecific genetic divergence was quantified in the lumbricid species, and a control region in D. ghilarovi was reported for the first time by comparison to the mitoge-nomes of the congeners. Phylogenetic analysis based on coding genes and ribosomal DNA da-tasets using BI and ML inferences showed the non-monophyly of Aporrectodea and polyphyly of E. nordenskioldi. Future works should examine the taxonomy, phylogeny and population genetics not only of Lumbricidae but also the other earthworm families on the global scale using mitogenomic and nuclear data.
... To be able to test this hypothesis, we required a comprehensive evolutionary history of ORI events in Annelida. A few previous studies have observed inverted skews in isolated Annelida lineages [5,19,21,22,23], but these studies have not attempted to systematically infer the evolutionary history of ORI events in Annelida, nor study their effects in depth. On this basis, we hypothesized that the list of ORI lineages is incomplete. ...
Background
Several studies have shown that the phylogeny of Annelida is pronouncedly data- and methodology-influenced. Inversions of the origin of replication (ORI) in mitochondrial genomes may interfere with phylogenetic reconstruction, as well as other evolutionary studies in Arthropoda. ORI events and their impacts on evolutionary analyses remain very poorly understood in other metazoan lineages. This also includes the Annelida, in which a handful of studies merely reported inverted base composition skews in isolated lineages.ResultsWe observed that some of the inverted-skew species exhibited long branches and ‘rogue’ behaviour in phylogenetic analyses. This made us hypothesise that ORI events may be a major factor interfering with phylogenetic reconstruction in Annelida. We first inferred the evolutionary history of ORI events in Annelida on a dataset comprising almost all available annelid mitogenomes (174). We identified twelve new ORI species and six ORI events in total. Most ORI events occurred at lower taxonomic levels (species, genus, family), but one was mapped to a common ancestor of sister-families Sabellidae & Serpulidae, and one to the entire suborder Hirudiniformes. In comparison to non-ORI lineages, ORI lineages exhibited a higher: mutational saturation, number of nonsynonymous substitutions, dN/dS ratios, hydropathicity of the translated gene products, and compositional heterogeneity; but a lower codon bias index. They also exhibited relaxed purifying selection pressures. We found several putative examples of ORI events causing artefactual clustering of lineages with homoplastic base composition biases in phylogenetic analyses. We attempted several different strategies aimed at stabilizing the topology, such as the removal of ORI species and third codon sites, but none of these managed to fully stabilize the topology.Conclusions
We inferred the evolutionary history of skews in annelids and explored the underlying mechanisms by which ORI events may cause artefactual clustering. We conclude that ORI events may be one of the causes for the chaotic relationships of Annelida. In the context of currently available strategies for phylogenetic reconstruction, mitogenomes are not suitable for studying the phylum-level and class-level phylogeny of Annelida. Given the strong evidence that ORIs may interfere with evolutionary studies in annelids, researchers should pay close attention to indications of skew inversions.
... Comparison of mitogenomes may reveal important genome-level characteristics, helping us understand genome structure, gene order, phylogenetic relationships, and evolutionary lineages. The earthworm mitogenome is a circular, double-stranded, covalently closed DNA molecule containing 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and one non-coding region (Zhang et al. 2016). Although Lumbricidae is the most important earthworm family in the Northern Hemisphere temperate zone and contains many widespread and invasive cosmopolitan species, only a few complete or nearly complete mitogenomes are available for this family (Boore and Brown 1995;Shekhovtsov and Peltek 2019;Zhang et al. 2019;Shekhovtsov et al. 2020). ...
... including Eisenia nordenskioldi, E. balatonica, E. tracta, E. spelaea, Lumbricus terrestris Linneaus, 1758, andAporrectodea rosea (Savigy, 1826) (Shekhovtsov et al. 2020). Zhang et al. (2016) reported higher AT contents in other earthworm families; for example, Megascolecidae has an AT content of 62.6-67.6%, and the Moniligastridae (Drawida japonica) genome has an AT content as high as 69.7%. However, the mitogenomes of E. fetida (16,560 bp) and E. andrei (15,714 bp) were larger than those of other lumbricid species, such as L. terrestris (14,998 bp), L. rubellus Hoffmeister, 1845 (15,464 bp), and Ap. ...
Composting earthworms of the genus Eisenia play an important role in soil ecosystems. However, taxonomic classification of this genus, especially the sibling species Eisenia fetida and Eisenia andrei , is complicated because of their morphological similarity. In this study, we assessed the utility of the complete mitochondrial genome (mitogenome) for identification and differentiation of the two species. The complete mitogenomes of E. andrei and E. fetida were 15,714 and 16,560 bp, respectively. They contained 37 genes, comprising 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a putative non-coding region, as observed in other earthworms. Sequence comparisons based on the complete nucleotide sequences excluding the non-coding region showed 85.8% similarity, whereas the predicted amino acid sequences of the 13 PCGs were 92.7% similar between the two species. In particular, distinct features were found in the non-coding regions of the mitogenomes. They include a control region associated with putative mitogenome replication and an extended sequence. The extended sequence showed significant differences between the two species and other known earthworm species, suggesting its potential as a feasible molecular marker for species identification. Phylogenetic analysis of the 36 mitogenomes of earthworm species corroborated the monophyly of the genus Eisenia and the taxonomic distinctness of the sibling species pair, E. fetida and E. andrei .
... Many of them concluded that the family Megascolecidae is monophyletic, although several genera such as Amynthas, Metaphire, Pheretima and Polypheretima are non-monophyletic (Aspe and James 2018; Aspe et al. 2021). Thus, taking it a step further Zhao et al. (2015) and Zhang et al. (2016) proposed that genus Amynthas and Metaphire are to be combined as one genus. ...
We discovered the first record of Pheretima vungtauensis from Manipur, North-eastern Region, India, heretofore only known from Vietnam. Because the morphological traits of this species are similar to those of Metaphire houlleti, we undertook an integrated taxonomic approach to evaluate the relationships of these two species. We obtained CO1 (DNA barcode) sequences and analysed them with various bioinformatic tools namely, Assemble Species by Automatic Partitioning (ASAP), Automatic Barcode Gap Discovery (ABGD), Refined Single Linkage (RESL), General Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP) and Multi-rate Poisson Tree Processes (mPTP) and compared the results. The Manipur CO1 sequences of P. vungtauensis form a monophyletic group including the type specimen P. vungtauensis in Bayesian Inference (BI) and Maximum Likelihood (ML) trees. Results of seven different species delimitation approaches were in congruence with P. vungtauensis except the result obtained from GMYC with ultrametric BI tree, which bifurcated P. vungtauensis into two lineages. Comparison of morphological data reveals presence of dense micronephridia on spermathecal ducts, lack of genital markings, spheroidal shape of opening slit of copulatory pouches and presence of 2–3 stalked genital marking glands on or near spermathecal duct as the main diagnostic character of P. vungtauensis from M. houlleti. We conclude that M. houlleti is polyphyletic, or frequently misidentified and/or should be separated into different group of species. It is also clear that P. vungtauensis is a distinct species, distinguishable from M. houlleti by morphological and molecular data.
... This ability helps to characterize the compounds. The earthworm E. eugeniae biomass has been utilized as feeding stock for fish fingerlings [11]. In the present work, the DNA of the worm was extracted from the prostate gland and was subjected to sequencing by the Illumina platform. ...
... So far, 24 mitogenomes are available for earthworms. The size ranges from 14,998 bp to 15,188 bp [11]. The mitochondria genome was obtained by aligning the reads to the mitochondria genome of Lumbricus terrestris with the NCBI accession NC_001673 and size 14,998 bp [3]. ...
... DNA transposons were the major repeats in the Eisenia fetida genome [12]. The number of satellites found in the E. eugeniae genome (58) is more than that in Eisenia fetida [11]. In contrast, the LTRs, LINEs, and SINEs identified were low in the E. eugeniae genome ( Table 2) and were less than that in Eisenia fetida (365,755, 204,621, and 86,934, respectively). ...
Background
Earthworms are annelids. They play a major role in agriculture and soil fertility. Vermicompost is the best organic manure for plant crops. Eudrilus eugeniae is an earthworm well suited for efficient vermicompost production. The worm is also used to study the cell and molecular biology of regeneration, molecular toxicology, developmental biology, etc., because of its abilities like high growth rate, rapid reproduction, tolerability toward wide temperature range, and less cost of maintenance.
Objective
The whole genome has been revealed only for Eisenia andrei and Eisenia fetida.
Methods
In the present work, we sequenced the genome of E. eugeniae using the Illumina platform and generated 160,684,383 paired-end reads
Results
The reads were assembled into a draft genome of size 488 Mb with 743,870 contigs and successfully annotated 24,599 genes. Further, 208 stem cell-specific genes and 3,432 non-coding genes were identified.
... Table 2). The mitogenomes of these five species possessed the typical gene composition that has been hypothesized for most earthworms, including 13 PCGs, 22 tRNA genes, and two rRNA genes (12S and 16S) [25,27]. For these five mitogenomes, there was a 417 to 1093 bp repetitive sequence between tRNA-Arg and tRNA-His, which was suspected to be a putative control region (CR) that also appeared in the mitogenomes of other Lumbricidae species [22][23][24]. ...
Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae.
... They can also be used to elucidate cryptic diversity of invasive taxa, and to assess whether and how populations of invasive species adapt to their new environment. To date, molecular studies of the pheretimoid earthworms have included analysis of mitochondrial and/or nuclear gene sequences (Chang and Chen 2005;Chang et al. 2007Chang et al. , 2008Chang et al. , 2009bMinamiya et al. 2009Minamiya et al. , 2011Novo et al. 2015;Schult et al. 2016; Aspe and James 2018), whole genome (Cunha et al. 2017), mitogenome (Zhang et al. 2016), Random Amplified Polymorphic DNA (RAPD) (Keller et al. 2017;Nguyen et al. 2018), and microsatellites (Cunha et al. 2017). However, only a few of these studies focused on invasive species of Amynthas or Metaphire. ...
The invasion of jumping worms, a small group of pheretimoid earthworm species from Asia, has increasingly become an ecological, environmental and conservation issue in forest ecosystems and urban-suburban landscapes around the world. Their presence is often noticed due to their high abundance, distinctive “jumping” behavior, and prominent granular casts on the soil surface. Although they are known to affect soil carbon dynamics and nutrient availability, no single paper has summarized their profound impacts on soil biodiversity, plant community, and animals of all trophic groups that rely on soil and the leaf litter layer for habitat, food, and shelter. In this study, we summarize the biology, invasion, and ecological impacts of invasive jumping worms across North America. We highlight potential impacts of this second wave of earthworm invasion, contrast them with the preceding European earthworm invasion in temperate forests in North America, and identify annual life cycle, reproductive and cocoon survival strategies, casting behavior and co-invasion dynamics as the key factors that contribute to their successful invasion and distinct ecological impacts. We then suggest potential management and control strategies for practitioners and policy makers, underscore the importance of coordinated community science projects in tracking the spread, and identify knowledge gaps that need to be addressed to understand and control the invasion.
... Generally, earthworms are deemed to be highly polymorphic animals due to their large population size and poor dispersal ability [1][2][3]. These polymorphisms are not only reflected in morphological variations but are also present at the DNA level [4][5][6][7][8]. In recent years, there has been a growing interest in understanding how historical events or contemporary processes gives rise to genetic variation within earthworm species, which shapes the patterns of their current geographic distribution and population genetic structure differentiation [9][10][11][12][13]. ...
