1. Transcriptome Analysis and Discovery of Genes Relevant to Development in Bradysia odoriphaga at Three Developmental Stages
- Author
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Hao Chen, Xianhong Zhou, Li Rumei, Gao Huanhuan, Zhuang Qianying, Yi Yu, Wenbo Wang, and Yifan Zhai
- Subjects
0106 biological sciences ,0301 basic medicine ,Sequence assembly ,Gene Expression ,lcsh:Medicine ,01 natural sciences ,Genome ,Biochemistry ,Transcriptome ,Larvae ,Sciaridae ,lcsh:Science ,Genetics ,Multidisciplinary ,Insect Metamorphosis ,biology ,Gene Ontologies ,Messenger RNA ,Pupa ,Gene Expression Regulation, Developmental ,High-Throughput Nucleotide Sequencing ,Genomics ,Insects ,Nucleic acids ,Larva ,Insect Proteins ,Transcriptome Analysis ,Research Article ,medicine.medical_specialty ,Arthropoda ,Chive ,03 medical and health sciences ,Molecular genetics ,medicine ,Animals ,Gene Regulation ,KEGG ,Illumina dye sequencing ,Plant Diseases ,Metamorphosis ,Diptera ,Gene Expression Profiling ,lcsh:R ,Organisms ,Biology and Life Sciences ,Computational Biology ,Molecular Sequence Annotation ,Pupae ,biology.organism_classification ,Genome Analysis ,Invertebrates ,Gene expression profiling ,030104 developmental biology ,Gene Ontology ,RNA ,lcsh:Q ,Zoology ,Entomology ,010606 plant biology & botany ,Developmental Biology - Abstract
Bradysia odoriphaga (Diptera: Sciaridae) is the most important pest of Chinese chive (Allium tuberosum) in Asia; however, the molecular genetics are poorly understood. To explore the molecular biological mechanism of development, Illumina sequencing and de novo assembly were performed in the third-instar, fourth-instar, and pupal B. odoriphaga. The study resulted in 16.2 Gb of clean data and 47,578 unigenes (≥125 bp) contained in 7,632,430 contigs, 46.21% of which were annotated from non-redundant protein (NR), Gene Ontology (GO), Clusters of Orthologous Groups (COG), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. It was found that 19.67% of unigenes matched the homologous species mainly, including Aedes aegypti, Culex quinquefasciatus, Ceratitis capitata, and Anopheles gambiae. According to differentially expressed gene (DEG) analysis, 143, 490, and 309 DEGs were annotated as involved in the developmental process in the GO database respectively, in the comparisons of third-instar and fourth-instar larvae, third-instar larvae and pupae, and fourth-instar larvae and pupae. Twenty-five genes were closely related to these processes, including developmental process, reproduction process, and reproductive organs development and programmed cell death (PCD). The information of unigenes assembled in B. odoriphaga through transcriptome and DEG analyses could provide a detailed genetic basis and regulated information for elaborating the developmental mechanism from the larval, pre-pupal to pupal stages of B. odoriphaga.
- Published
- 2016