Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

Li, Xuankun; Li, Wenliang; Ding, Shuangmei; Cameron, Stephen L.; Mao, Meng; Shi, Li; Yang, Ding

doi:10.3390/ijms18040773

Cited by 20 publications

(9 citation statements)

References 77 publications

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“…This is comparable to many other insect orders in that deep-level (e.g. families/superfamily) relationships are seemingly robust to analytical decisions such as taxon selection, data inclusion/exclusion or alignment method, while shallow-level relationships show differing degrees of sensitivity 64,[70][71][72][73][74] . The root cause of these sensitivities cannot be determined at this time, as the 'true' phylogeny of thrips is not yet known to compare individual analyses against.…”

Section: Scientific Reports |supporting

confidence: 51%

Rearrangement and evolution of mitochondrial genomes in Thysanoptera (Insecta)

Tyagi

Chakraborty

Cameron

et al. 2020

Sci Rep

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prior to this study, complete mitochondrial genomes from order thysanoptera were restricted to a single family, the thripidae, resulting in a biased view of their evolution. Here we present the sequences for the mitochondrial genomes of four additional thrips species, adding three extra families and an additional subfamily, thus greatly improving taxonomic coverage. thrips mitochondrial genomes are marked by high rates of gene rearrangement, duplications of the control region and tRnA mutations. Derived features of mitochondrial tRnAs in thrips include gene duplications, anticodon mutations, loss of secondary structures and high gene translocation rates. Duplicated control regions are found in the Aeolothripidae and the 'core' thripinae clade but do not appear to promote gene rearrangement as previously proposed. phylogenetic analysis of thrips mitochondrial sequence data supports the monophyly of two suborders, a sister-group relationship between Stenurothripidae and thripidae, and suggests a novel set of relationships between thripid genera. Ancestral state reconstructions indicate that genome rearrangements are common, with just eight gene blocks conserved between any thrips species and the ancestral insect mitochondrial genome. Conversely, 71 derived rearrangements are shared between at least two species, and 24 of these are unambiguous synapomorphies for clades identified by phylogenetic analysis. While the reconstructed sequence of genome rearrangements among the protein-coding and ribosomal RnA genes could be inferred across the phylogeny, direct inference of phylogeny from rearrangement data in MLGo resulted in a highly discordant set of relationships inconsistent with both sequence-based phylogenies and previous morphological analysis. Given the demonstrated rates of genomic evolution within thrips, extensive sampling is needed to fully understand these phenomena across the order.Complete mitochondrial genomes have been shown to be useful for phylogenetic and evolutionary studies at various taxonomic scales, as they provide more phylogenetic information than individual genes alone 1-4 . The mitochondrial genome of metazoans is typically a circular molecule 14-19 kilobases (kb) in length, that contains a conserved set of 37 genes: 13 protein-coding genes (PCGs), ATPase subunits 6 and 8 (atp6 and atp8), Cytochrome oxidase subunits 1 to 3 (cox1-cox3), cytochrome b (cob), NADH dehydrogenase subunits 1-6 and 4 L (nad1-6 and nad4L); the small and large subunit rRNAs (rrnL and rrnS), 22 transfer RNA (tRNA) genes, and a non-coding control region (CR) which contains initiation sites for transcription and replication 1,5 . In addition to sequence variation, metazoan mitochondrial genomes also exhibit variation in a number of features, such as length, tRNA secondary structure, gene order, and the number and internal structure of control regions 6-8 . These features can provide evidence for evolutionary relationships among taxa at high and/or low taxonomic levels beyond that provided by analysis of mitochondrial seq...

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Section: Scientific Reports |supporting

confidence: 51%

Rearrangement and evolution of mitochondrial genomes in Thysanoptera (Insecta)

Tyagi

Chakraborty

Cameron

et al. 2020

Sci Rep

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“…4 ). Atypical numbers and structures of tRNA have been reported in other insects 8 , 38 , 41 – 43 . The factors that may have led to these truncated tRNAs remain unknown, although truncation may be a result of generalized evolutionary pressures for size reduction in mitogenomes 6 , 44 , but such an explanation requires the existence of compensatory mechanisms.…”

Section: Resultsmentioning

confidence: 79%

Comparative analysis of the Liriomyza chinensis mitochondrial genome with other Agromyzids reveals conserved genome features

Chen

Chang

Zheng

et al. 2018

Sci Rep

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Liriomyza chinensis is a serious pest of onions in many countries, especially in East Asia. We sequenced the complete mitochondrial genome of this species and compared it with five other Agromyzidae species. The L. chinensis mitogenome is a double-stranded 16,175 bp circular molecule with an A + T content of 78.3%. It contains 37 genes and a control region as do the sequenced Liriomyza species. The mitogenomes of L. chinensis and other Agromyzidae species showed a clear bias in nucleotide composition with a positive AT-skew. Most PCGs used standard ATN as start codons, and TAN as termination codons. The tRNAs exhibited the typical clover-leaf structure, except for tRNASer(AGN) and the two rRNA genes are conserved with those of other Agromyzids. The L. chinensis mitogenome control region included several conserved regions, including a poly-T, two (TA)n and one poly-A stretch, which are considered important replication and transcription. The 13 PCGs were used to study the phylogeny of L. chinensis and five related Agromyzids. Analysis by maximum likelihood, Bayesian inference and genetic distance suggest congruent phylogenetic relationships in Liriomyza spp. and provide a useful supplement to taxonomic classification by morphology.

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“…The CR regulates the replication and transcription of mitogenome, and many conserved blocks (CBS) were considered to play a key role in the function of CR [ 31 ]. In insect mitogenomes, the CBS are diverse in different lineages [ 31 , 32 ]. In lepidopteran mitogenomes, four conserved elements have been found in nearly all the Ditrysia species, i.e.…”

Section: Resultsmentioning

confidence: 99%

The first mitochondrial genomes for Pyralinae (Pyralidae) and Glaphyriinae (Crambidae), with phylogenetic implications of Pyraloidea

et al. 2018

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In the present study, we report five complete and one nearly complete mitochondrial genomes of the Pyraloidea including the first representatives from the Pyralinae (Pyralidae) and Glaphyriinae (Crambidae). We also conduct a comparative analysis of mitogenomic features of this group. Our results show that Pyraloidea mitogenomes evolved under a common trend found in lepidopteran mitogenomes and share several typical genomic characters. The extra conserved blocks are identified in the Pyraloidea control region, and diverse missing codons formed another unique trait within Pyraloidea mitogenome. Furthermore, we reconstruct the mitogenomic phylogeny of Pyraloidea and confirm the phylogenetic position of Pyralinae and Glaphyriinae within the Pyraloidea using BI and ML method based on multiple mitochondrial datasets.

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Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

Cited by 20 publications

References 77 publications

Rearrangement and evolution of mitochondrial genomes in Thysanoptera (Insecta)

Rearrangement and evolution of mitochondrial genomes in Thysanoptera (Insecta)

Comparative analysis of the Liriomyza chinensis mitochondrial genome with other Agromyzids reveals conserved genome features

The first mitochondrial genomes for Pyralinae (Pyralidae) and Glaphyriinae (Crambidae), with phylogenetic implications of Pyraloidea

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