Tandem duplication of two tRNA genes in the mitochondrial genome of Tagiades vajuna (Lepidoptera: Hesperiidae)

Liu, Fangfang; Li, Yiping; Jakovlić, Ivan; Yuan, Xiangqun

doi:10.14411/eje.2017.052

Cited by 22 publications

(23 citation statements)

References 48 publications

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“…sculptum [ 21 ], but metastriate ticks belonging to the Rhipicephalus genus appear to exhibit only an identical (7 bp) atp6 / atp8 overlap [ 20 ]. Both overlaps include very small genes ( atp8 = 162 bp, nad4L = 276 bp), which appear to be under lesser evolutionary constraints, as atp8 is often absent from mitogenomes [ 25 ], whereas the nad4 / nad4L overlap is common in mitogenomes of many different groups of animals [ 17 , 18 , 26 – 28 ]. Although annotation of the nad1 gene is usually very difficult in hard ticks, often producing unusually large gene overlaps [ 21 , 29 ], nad1 genes in the studied two mitogenomes are very similar to closely related Rhipicephalus orthologs ( S1 File ), with an overlap of only 4 bp with the neighbouring tRNA-Glu ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…Nucleotide sequences of protein-coding genes (PCGs) were aligned in batches (using codon-alignment mode) with MAFFT [ 54 ] integrated into BioSuite [ 55 ]. As described before [ 17 ], RNAs were aligned by Q-INS-i algorithm, which takes secondary structure information into account, incorporated into MAFFT-with-extensions software [ 56 ]. tRNAs Q, L1, L2, S1 and S2 were removed from the dataset for phylogenetic analysis because their annotation was not consistent in all mitogenomes.…”

Section: Methodsmentioning

confidence: 99%

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Sequencing of complete mitochondrial genomes confirms synonymization of Hyalomma asiaticum asiaticum and kozlovi, and advances phylogenetic hypotheses for the Ixodidae

Liu

Kuermanali

et al. 2018

PLoS ONE

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Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1. sequence the first Hyalomma mitogenome; 2. scrutinise the proposed synonymization using molecular data, i.e. complete mitogenomes of both subspecies: H. a. asiaticum and kozlovi; 3. conduct phylogenomic and comparative analyses of all available Ixodidae mitogenomes. Results corroborate the proposed synonymization: the two mitogenomes are almost identical (99.6%). Genomic features of both mitogenomes are standard for Metastriata; which includes the presence of two control regions and all three "Tick-Box" motifs. Gene order and strand distribution are perfectly conserved for the entire Metastriata group. Suspecting compositional biases, we conducted phylogenetic analyses (29 almost complete mitogenomes) using homogeneous and heterogeneous (CAT) models of substitution. The results were congruent, apart from the deep-level topology of prostriate ticks (Ixodes): the homogeneous model produced a monophyletic Ixodes, but the CAT model produced a paraphyletic Ixodes (and thereby Prostriata), divided into Australasian and non-Australasian clades. This topology implies that all metastriate ticks have evolved from the ancestor of the non-Australian branch of prostriate ticks. Metastriata was divided into three clades: 1. Amblyomminae and Rhipicephalinae (Rhipicephalus, Hyalomma, Dermacentor); 2. Haemaphysalinae and Bothriocrotoninae, plus Amblyomma sphenodonti; 3. Amblyomma elaphense, basal to all Metastriata. We conclude that mitogenomes have the potential to resolve the long-standing debate about the evolutionary history of ticks, but heterogeneous evolutionary models should be used to alleviate the effects of compositional heterogeneity on deep-level relationships.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Sequencing of complete mitochondrial genomes confirms synonymization of Hyalomma asiaticum asiaticum and kozlovi, and advances phylogenetic hypotheses for the Ixodidae

Liu

Kuermanali

et al. 2018

PLoS ONE

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“…Furthermore, because no mitogenomes from the subfamily Trapezitinae were available, we assembled a mitogenome of Rachelia extrusus (C. & R. Felder, 1867) using the same approach. A Bayesian inference tree was constructed by MrBayes (Huelsenbeck and Ronquist 2001) from representative known Hesperiidae mitogenomes (Cao et al 2016;Cong and Grishin 2016;Han et al 2018;Hao et al 2012;Kim et al 2014;Liu et al 2017;Shao et al 2015;Shen et al 2015Shen et al , 2016Wang et al 2014;Wang et al 2015;Wang et al 2016;Zhang et al 2017aZhang et al , 2017b with our four new mitogenomes added, and rooted with the Pterourus glaucus (Papilionidae) mitogenome (Shen et al 2015) (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

The mitogenome of a Malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera)

Zhang

Lees

Shen

et al. 2020

Genome

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Malaza fastuosus is a lavishly patterned skipper butterfly from a genus that has three described species, all endemic to the mainland of Madagascar. To our knowledge, M. fastuosus has not been collected for nearly 50 years. To evaluate the power of our techniques to recover DNA, we used a single foreleg of an at least 140-year-old holotype specimen from the collection of the Natural History Museum London with no destruction of external morphology to extract DNA and assemble a complete mitogenome from next generation sequencing reads. The resulting 15 540 bp mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A+T rich region, similarly to other Lepidoptera mitogenomes. Here we provide the first mitogenome also for Trapezitinae (Rachelia extrusus). Phylogenetic analysis of available skipper mitogenomes places Malaza outside of Trapezitinae and Barcinae + Hesperiinae, with a possible sister relationship to Heteropterinae. Of these, at least Heteropterinae, Trapezitinae, and almost all Hesperiinae have monocot-feeding caterpillars. Malaza appears to be an evolutionarily highly distinct ancient lineage, morphologically with several unusual hesperiid features. The monotypic subfamily Malazinae Lees & Grishin subfam. nov. (type genus Malaza) is proposed to reflect this morphological and molecular evidence.

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“…Conflicting phylogenetic signals among different mitochondrial regions have been reported in a number of metazoan groups, which indicates that different mitochondrial regions can accumulate substitutions in ways that are difficult to model, which can result in biased estimates of phylogeny (Meiklejohn et al, 2014). There is evidence that this compositional heterogeneity may be comparatively highly pronounced in mitogenomes of some arthropod taxa (Cameron, 2014; Hassanin, 2006; Liu, Li, Jakovlić, & Yuan, 2017). We therefore hypothesised that the aforementioned extreme life history diversity of isopods might cause pronounced compositional heterogeneity/heterotachy in their mitogenomes, and interfere with the reconstruction of the Isopoda phylogeny.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial architecture rearrangements produce asymmetrical nonadaptive mutational pressures that subvert the phylogenetic reconstruction in Isopoda

Zhang

Zou

Hua

et al. 2019

Preprint

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The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different datasets often producing starkly incongruent phylogenetic hypotheses. We hypothesised that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different datasets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artefacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artefacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements can produce major compositional biases even on short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

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Tandem duplication of two tRNA genes in the mitochondrial genome of Tagiades vajuna (Lepidoptera: Hesperiidae)

Cited by 22 publications

References 48 publications

Sequencing of complete mitochondrial genomes confirms synonymization of Hyalomma asiaticum asiaticum and kozlovi, and advances phylogenetic hypotheses for the Ixodidae

Sequencing of complete mitochondrial genomes confirms synonymization of Hyalomma asiaticum asiaticum and kozlovi, and advances phylogenetic hypotheses for the Ixodidae

The mitogenome of a Malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera)

Mitochondrial architecture rearrangements produce asymmetrical nonadaptive mutational pressures that subvert the phylogenetic reconstruction in Isopoda

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