Mitochondrial genome of the pine tip moth<i>Rhyacionia leptotubula</i>(Lepidoptera: Tortricidae)

Zhu, Jia‐Ying; Wei, Shu‐Jun; Li, Qin-Wen; Yang, Song; Yong-he, LI

doi:10.3109/19401736.2012.696632

Cited by 13 publications

(6 citation statements)

References 9 publications

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“…We assembled a molecular dataset for each specimen comprising 1528 bp from the mitochondrial cytochrome oxidase subunit I gene (COI), and 922 bp from the D2 and D3 regions of the 28S rDNA gene (28S). This taxon sampling was augmented with 176 specimens from previous studies (Sperling & Hickey, ; Lee et al ., ; Hulcr et al ., ; Roe & Sperling, ; Lumley & Sperling, , ; Miller et al ., ; Son & Kim, ; Zhao et al ., , 2016; Zhu et al ., ; Dombroskie & Sperling, ; Shi et al ., ; Wu et al ., , ; Timmermans et al ., ; Niu et al ., ; Fagua et al . , b; see Appendix File S2 for GenBank accession numbers and specimens).…”

Section: Methodsmentioning

confidence: 99%

Genus delimitation, biogeography and diversification ofChoristoneuraLederer (Lepidoptera: Tortricidae) based on molecular evidence

Fagua

Condamine

Dombroskie

et al. 2018

Systematic Entomology

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Widely known for pest species that include major modulators of temperate forests, the genus Choristoneura is part of the species-rich tribe Archipini of leafroller moths (Tortricidae). Delimitation of the genus has remained unresolved because no phylogeny has included species endemic to Africa and studies have often omitted the type species of the genus. Further taxonomic confusion has been generated by the transfer of Archips occidentalis (Walsingham) to Choristoneura, creating a homonym with Choristoneura occidentalis Freeman, an important defoliator of North American forests. To define the limits of the genus, we reconstructed a phylogeny using DNA sequences for mitochondrial cytochrome oxidase subunit I and nuclear ribosomal 28S genes. Our ingroup included 23 Choristoneura species-level taxa, complemented by a large sample of outgroups comprising 82 species of Archipini and other Tortricidae. We generated a time-calibrated tree using fossil and secondary calibrations and we inferred biogeographic and diversification processes in Choristoneura. Our analysis recovered the genus as polyphyletic, with Archips occidentalis, Choristoneura simonyi and Choristoneura evanidana excluded from the main clade. Based on the recovered phylogenies and a redefinition, we restrict Choristoneura primarily to species with a northern hemisphere distribution. Our analysis supports A. occidentalis as the sister group of Cacoecimorpha pronubana, C. simonyi as the sister of 'Xenotemna' pallorana, and C. evanidana as the sister of Archips purpurana. A new combination is proposed: Archips evanidana comb.n.; the availability of 'Xenotemna' as a valid name is discussed and A. occidentalis is considered as an orphaned name within the Archipini. We found support for a Holarctic origin of Choristoneura about 23 Ma, followed by early divergence in the Palearctic region. The main divergence occurred at 16 Ma, with one clade in the Nearctic and another in the Palearctic. Subsequent cladogenetic events were synchronous and related to herbivorous specialization, with each clade divided into coniferophagous and polyphagous lineages. Their specialization as conifer feeders temporally matched the expansion of boreal forest during the Miocene. or Zelotherses. Our phylogenetic analysis indicates the closest relationship to Cacoecimorpha; however, we need a larger sample of African and Far East Archipini to corroborate the hypothesis.

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Section: Methodsmentioning

confidence: 99%

Genus delimitation, biogeography and diversification ofChoristoneuraLederer (Lepidoptera: Tortricidae) based on molecular evidence

Fagua

Condamine

Dombroskie

et al. 2018

Systematic Entomology

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“…The pine tip moth, Rhyacionia leptotubula (Lepidoptera: Tortricidae), is an important forestry pest posed a serious threat to Pinus yunnanensis and Pinus armandii , which distributed widely over much of Yunnan province in China [1] . It damages hosts in its larval stage.…”

Section: Introductionmentioning

confidence: 99%

De novo Assembly and Characterization of the Global Transcriptome for Rhyacionia leptotubula Using Illumina Paired-End Sequencing

et al. 2013

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BackgroundThe pine tip moth, Rhyacionia leptotubula (Lepidoptera: Tortricidae) is one of the most destructive forestry pests in Yunnan Province, China. Despite its importance, less is known regarding all aspects of this pest. Understanding the genetic information of it is essential for exploring the specific traits at the molecular level. Thus, we here sequenced the transcriptome of R. leptotubula with high-throughput Illumina sequencing.Methodology/Principal FindingsIn a single run, more than 60 million sequencing reads were generated. De novo assembling was performed to generate a collection of 46,910 unigenes with mean length of 642 bp. Based on Blastx search with an E-value cut-off of 10−5, 22,581 unigenes showed significant similarities to known proteins from National Center for Biotechnology Information (NCBI) non-redundant (Nr) protein database. Of these annotated unigenes, 10,360, 6,937 and 13,894 were assigned to Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. A total of 5,926 unigenes were annotated with domain similarity derived functional information, of which 55 and 39 unigenes respectively encoding the insecticide resistance related enzymes, cytochrome P450 and carboxylesterase. Using the transcriptome data, 47 unigenes belonging to the typical “stress” genes of heat shock protein (Hsp) family were retrieved. Furthermore, 1,450 simple sequence repeats (SSRs) were detected; 3.09% of the unigenes contained SSRs. Large numbers of SSR primer pairs were designed and out of randomly verified primer pairs 80% were successfully yielded amplicons.Conclusions/SignificanceA large of putative R. leptotubula transcript sequences has been obtained from the deep sequencing, which extensively increases the comprehensive and integrated genomic resources of this pest. This large-scale transcriptome dataset will be an important information platform for promoting our investigation of the molecular mechanisms from various aspects in this species.

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“…(2013) Cydia pomonella NC_020003 15,253 Shi et al. (2013) Rhyacionia leptotubula NC_019619 15,877 Zhu et al. (2012) Grapholita molesta NC_014806 15,717 Son and Kim (2011) HQ116416 15,776 Gong et al.…”

Section: Methodsmentioning

confidence: 99%

The Complete Mitochondrial Genome ofBrachmia macroscopa(Lepidoptera: Gelechiidae) and Its Related Phylogenetic Analysis

Dong

Jiang

et al. 2016

J Insect Sci

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The sweet potato leaf folder, Brachmia macroscopa, is an important pest in China. The complete mitogenome, which consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region, was sequenced and found to be 15,394 bp in length (GeneBank no. KT354968). The gene order and orientation of the B. macroscopa mitogenome were similar to those of other sequenced lepidopteran species. All of the PCGs started with ATN as the canonical start codon except for cox1, which started with CGA. In regard to stop codons, most PCGs stopped at TAA except for cox2, which stopped at TA, and nad4, which stopped at a single T. Thirteen PCGs of the available species (33 taxa) were used to demonstrate phylogenetic relationships. The ditrysian cluster was supported as a monophyletic clade at high levels by using maximum likelihood and Bayesian methods. The apoditrysian group, covering the Gelechioidea, formed a monophyletic clade with a bootstrap value of 88% and a posterior probability of 1.00. The superfamily Gelechioidea was supported as a monophyletic lineage by a posterior probability of 1.00.

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Mitochondrial genome of the pine tip mothRhyacionia leptotubula(Lepidoptera: Tortricidae)

Cited by 13 publications

References 9 publications

Genus delimitation, biogeography and diversification ofChoristoneuraLederer (Lepidoptera: Tortricidae) based on molecular evidence

Genus delimitation, biogeography and diversification ofChoristoneuraLederer (Lepidoptera: Tortricidae) based on molecular evidence

De novo Assembly and Characterization of the Global Transcriptome for Rhyacionia leptotubula Using Illumina Paired-End Sequencing

The Complete Mitochondrial Genome ofBrachmia macroscopa(Lepidoptera: Gelechiidae) and Its Related Phylogenetic Analysis

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