Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

• Published in: Genes Vol. 10; no. 6; p. 481
• Main Authors: Chen, Haoliang, Lin, Lulu, Xie, Minghui, Zhong, Yongzhi, Zhang, Guangling, Su, Weihua
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 25.06.2019; MDPI
• Subjects: Adults; Animals; Bioinformatics; Bradysia odoriphaga; Cluster analysis; Developmental stages; Gene Ontology; Genes; Genome, Insect - drug effects; Genome, Insect - genetics; Genomes; High-Throughput Nucleotide Sequencing; Insect Proteins - genetics; Insecticide Resistance - genetics; Insecticides - pharmacology; Isoforms; Larva - genetics; Larva - growth & development; Microsatellite Repeats - genetics; Molecular Sequence Annotation; Nematocera - genetics; Nematocera - growth & development; Nucleotide sequence; Ontology; Pesticide resistance; Pesticides; Proteins; Simple sequence repeats; Single Molecule Imaging; single-molecule long-read sequencing; transcriptome; Transcriptome - genetics; Transcriptomes; United States > US; transcriptome; single-molecule long-read sequencing; Bradysia odoriphaga
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes10060481

The damage caused by is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in .