The <i>de novo</i> Transcriptome and Its Analysis in the Worldwide Vegetable Pest, <i>Delia antiqua</i> (Diptera: Anthomyiidae)

Zhang, Yujuan; Hao, Youjin; Si, Feng‐Ling; Ren, Shan; Hu, Ganyu; Shen, Li; Chen, Bin

doi:10.1534/g3.113.009779

Cited by 19 publications

(21 citation statements)

References 30 publications

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“…In some instances, unigene sequences greater than 1 kb were considered for screening of SSRs (Zhang et al . ,). The different selection criteria for SSRs may explain the relatively lower abundance of SSRs discovered from other insect transcriptomes (Wei et al .…”

Section: Resultsmentioning

confidence: 99%

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RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862

Hwang

Patnaik

Kang

et al. 2016

Entomological Research

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Grassland butterflies are considered representative indicators of biodiversity and ecosystem health. Their dramatic decline caused by habitat destruction, intensifying agriculture and global warming has prompted concern for conservation. While ecological indices of butterflies have been documented, there is a lack of genomic resources relative to the biological importance of this group. Here, we report, first whole-transcriptomic resource for Fabriciana nerippe, a brush-footed butterfly member that is endangered in Korea. Approximately, 241.3 million clean reads were obtained from paired-end Illumina sequencing of adult whole-body RNA. The de novo assembly resulted in 114 405 unigenes with length ranging from 133 to 33 218 bp. We found 41 868 assembled unigenes homologous to sequences in locally curated PANM-DB (Protostome DB). We assigned gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology terms to 18 085 and 5779 unigenes, respectively. InterProScan predicted 6691 protein domains for the assembled unigene sequences, with the reverse transcriptase and zinc finger domains found to be the most predominant. A total of 315 282 simple sequence repeats (SSRs) were identified from the assembled unigenes, when considering dinucleotide to octanucleotide repeats with a minimum of three repeat units. AT/AT, AAT/ATT, and AAAT/ATTT represented the most prominent SSR repeat types in the transcriptome. The unigene annotation profile and microsatellites generated in the study can serve as a reference resource for closely related species and gene functional analysis studies. Our data can be utilized to study ecological drift and loss of the species, consequently leading to better protection of the population.

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Section: Resultsmentioning

confidence: 99%

“…It has been widely used for the de novo characterization of transcriptome in economically important insects such as Dastarcus helophoroides (Zhang et al . ,) and Ericerus pela (Yang et al . ), endangered endemic insects (Wang et al .…”

Section: Introductionmentioning

confidence: 99%

RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862

Hwang

Patnaik

Kang

et al. 2016

Entomological Research

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“…This transcriptome analysis will likely replace large-scale microarray approaches [20,21], as it’s lower cost, greater sequence yield, and higher sensitivity in detection of low abundant and novel transcripts allows the measurement of transcriptome composition to address the quantitative survey of RNA expression patterns in comparative genomic-levels [19] and develop molecular markers [22]. In the past few years, RNA-seq has been used for a number of genomes investigated, covering bacteria, Archaea and lower eukaryotes to higher eukaryotes.…”

Section: Introductionmentioning

confidence: 99%

De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae)

Chen

Zhang

et al. 2014

Parasites & Vectors

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BackgroundAnopheles sinensis is the major malaria vector in China and Southeast Asia. Vector control is one of the most effective measures to prevent malaria transmission. However, there is little transcriptome information available for the malaria vector. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to build a transcriptome dataset for functional genomics analysis by large-scale RNA sequencing (RNA-seq).MethodsTo provide a more comprehensive and complete transcriptome of An. sinensis, eggs, larvae, pupae, male adults and female adults RNA were pooled together for cDNA preparation, sequenced using the Illumina paired-end sequencing technology and assembled into unigenes. These unigenes were then analyzed in their genome mapping, functional annotation, homology, codon usage bias and simple sequence repeats (SSRs).ResultsApproximately 51.6 million clean reads were obtained, trimmed, and assembled into 38,504 unigenes with an average length of 571 bp, an N50 of 711 bp, and an average GC content 51.26%. Among them, 98.4% of unigenes could be mapped onto the reference genome, and 69% of unigenes could be annotated with known biological functions. Homology analysis identified certain numbers of An. sinensis unigenes that showed homology or being putative 1:1 orthologues with genomes of other Dipteran species. Codon usage bias was analyzed and 1,904 SSRs were detected, which will provide effective molecular markers for the population genetics of this species.ConclusionsOur data and analysis provide the most comprehensive transcriptomic resource and characteristics currently available for An. sinensis, and will facilitate genetic, genomic studies, and further vector control of An. sinensis.

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“…Some species of the family are significant agricultural pests, particularly some from the genus Delia, which include the onion fly (Delia antiqua), the wheat bulb fly (D. coarctata), the turnip root fly (D. floralis), the bean seed fly (D. platura) and the cabbage root fly (D. radicum). D. antiqua is a cosmopolitan pest of crops and the larvae is a major insect pest of onion because onion fly is the optimum pest for the species (Zhang et al 2014). The family also includes inquilines, commensals and parasitic larvae (Huckett 1971, Suwa andDarvas1998).…”

Section: Introductionmentioning

confidence: 99%

Biological traits and susceptibility of Delia antiqua (Meigen, 1826) (Diptera: Anthomyiidae) in onion

Nahar

Sultana

Akter

et al. 2019

Bangladesh J. Zool.

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The pre-oviposition period of mated and unmated female reared on Bangladeshi and Indian onion was 4.5 ± 0.5, 4.37 ± 0.6 days and 4.11 ± 0.09, 4.45 ± 0.32 days, respectively. The oviposition period of mated and unmated female was 5.6 ± 0.6, 6.03 ± 0.6 days and 6.48 ± 0.39, 6.5 ± 0.34 days reared on Bangladeshi and Indian onion, respectively. The life cycle of Delia antiqua consisted of four definite stages: egg, larva, pupa and adult. The incubation period was1.38 ± 0.11 and 1.25 ± 0.05 days; larval period was 5.7 ± 0.7 and 5.4 ± 0.05 days; pupal period was 6.8 ± 0.2 and 6.08 ± 0.2 days, respectively. There were three larval instars in D. antiqua. To complete the total life cycle it required shorter period in Indian than in Bangladeshi onion. The total life cycle of female was 16.73 ± 0.89 and 15.29 ± 0.45 days, respectively on Bangladeshi and Indian onion. The difference between the life cycle of female was significant (p < 0.05) in Bangladeshi and Indian onion. Fecundity was higher in Indian than in Bangladeshi onion. The fecundity of female D. antiqua reared in Bangladeshi and Indian onion was 75.2 ± 4.09 and 89.2 ± 2.39, respectively and it was significantly (p < 0.05) varied. Female lived longer than male D. antiqua. It was more susceptible in Indian than Bangladeshi onion irrespective of the duration of life cycle and fecundity. Bangladesh J. Zool. 47(2): 325-332, 2019

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The de novo Transcriptome and Its Analysis in the Worldwide Vegetable Pest, Delia antiqua (Diptera: Anthomyiidae)

Cited by 19 publications

References 30 publications

RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862

RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862

De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae)

Biological traits and susceptibility of Delia antiqua (Meigen, 1826) (Diptera: Anthomyiidae) in onion

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