Isolation and characterization of microsatellite loci for Rhyacionia leptotubula (Lepidoptera: Tortricidae)

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

doi:10.5897/ajmr11.812

Afr. J. Microbiol. Res.

2011

DOI: 10.5897/ajmr11.812

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Isolation and characterization of microsatellite loci for Rhyacionia leptotubula (Lepidoptera: Tortricidae)

Jia‐Ying Zhu¹,

Song Yang²,

Qin-Wen Li³

et al.

Abstract: Microsatellite as one of the most popular molecular markers provides a useful tool for population genetic structure analysis in insects. But few microsatellite loci have been developed for Lepidoptera. Here we isolated and characterized 9 polymorphic microsatellite loci in Rhyacionia leptotubula (Lepidoptera: Tortricidae). The number of alleles of these loci ranged from 2 to 11. Observed and expected heterozygosities ranged from 0.0000 to 0.5294 and from 0.3905 to 0.8719, respectively. Seven loci show signific… Show more

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

et al. 2013

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

Zhu

Wei

et al. 2012

Mitochondrial DNA

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The complete nucleotide sequence of the mitochondrial genome of the pine tip moth Rhyacionia leptotubula (Lepidoptera, Tortricidae) was determined. The entire genome is 15,877 bp in length, encoding the standard set of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and an A+T-rich control region. The gene order is typical of Lepidoptera and differs from the insect ancestral type in the location of trnM. All protein-coding sequences start with a typical ATN codon, with the exception of COI, which begins with CGA. All tRNA genes could be folded into the typical cloverleaf secondary structure, except trnS2 lacking of dihydrouridine arm. Additionally, the 7-bp long ATACTAA motif is present in the intergenic space sequence located between trnS1 and nad1, and a long T-stretch with conserved ATAGA motif exists in the A+T-rich region, as found in Lepidoptera. The mitogenome given here provides important molecular information to phylogenetic and population genetic researches.

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Isolation and characterization of microsatellite loci for Rhyacionia leptotubula (Lepidoptera: Tortricidae)

Cited by 2 publications

References 2 publications

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

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

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

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