The complete mitochondrial genome of Pauropus longiramus (Myriapoda: Pauropoda): Implications on early diversification of the myriapods revealed from comparative analysis

Dong, Yan; Sun, Hongying; Guo, Hua; Pan, Da; Qian, Changyuan; Hao, Sijing; Zhou, Kaiya

doi:10.1016/j.gene.2012.05.049

Cited by 18 publications

(28 citation statements)

References 56 publications

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“…(Table 2). Incomplete stop codons are frequently found in other myriapod mitochondrial protein-encoding genes (Dong et al 2012a) and may be completed by polyadenylation after cleavage of the polycistronic transcript (Ojala et al 1981). Both novel genomes have an overlapping gene region only between atp8 / atp6 .…”

Section: Resultsmentioning

confidence: 99%

“…Most of the tRNAs appear to be truncated and lack one of the arms found in the canonical tRNAs of pauropods and symphylans (Gai et al 2008; Dong et al 2012a). One to two nucleotide mismatches could be found in the acceptor arms of the five tRNAs in Asiomorpha coarctata , and in the four tRNAs in Xystodesmus sp.…”

Section: Discussionmentioning

confidence: 99%

“…All millipedes in which the mt genome has been sequenced, except Sphaerotheriida, have nad6 + cob placements that differ from that of Limulus Polyphemus and the nad6 + cob pattern was supposed to be sound molecular evidence supporting the Helminthomorpha clade. Dong et al (2012a) compared nine known myriapod mt genomes and posited that a translocation of trnT out of the 5' end of nad4L is a common event in derived progoneate lineages. Although taxon sampling is limited, gene synteny has supplied evolutionary evidence relating to Myriapoda phylogenetic and evolutionary history.…”

Section: Introductionmentioning

confidence: 99%

“…Although taxon sampling is limited, gene synteny has supplied evolutionary evidence relating to Myriapoda phylogenetic and evolutionary history. Full mitochondrial genomes of sixteen myriapod species have hitherto been sequenced, however, this number is still far from sufficient considering the high species richness of this group (Sierwald and Bond 2007; Budd and Telford 2009; Dong et al 2012a; Robertson et al 2015). This lack of mitochondrial genome data is hampering phylogenetic and evolutionary studies within the subphylum Myriapoda.…”

Section: Introductionmentioning

confidence: 99%

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Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

Dong¹,

Zhu²,

Bai³

et al. 2016

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A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorpha coarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae) and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae) were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of A. coarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida) and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY) could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

Dong¹,

Zhu²,

Bai³

et al. 2016

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“…Progoneata has found some support from molecular phylogenetics (Gai et al 2008; Regier et al 2010), but it has also been contradicted by a grouping of Chilopoda and Diplopoda (Rehm et al 2014). The most novel hypothesis to emerge from molecular data is an unanticipated union of pauropods and symphylans (Dong et al 2012), a group that has been formalized as Edafopoda (Zwick et al 2012).…”

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confidence: 99%

Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

2016

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Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.

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Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS‐2019 and phylogenetic analysis of the Myriapoda

Zuo

Zhang

Shen

2022

Ecology and Evolution

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The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS‐2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT‐skew (−0.236). Several genes rearrangements were detected and we propose a new rearrangement model: “TD (N\R) L + C” based on the genome‐scale duplication + (non‐random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.

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The complete mitochondrial genome of Pauropus longiramus (Myriapoda: Pauropoda): Implications on early diversification of the myriapods revealed from comparative analysis

Cited by 18 publications

References 56 publications

Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS‐2019 and phylogenetic analysis of the Myriapoda

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